diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..118b6184a50d6bafd1b2ee81ad8009e96f244ff1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55495933 Before NNI: tree length is 0.55495925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.57127693 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6504d5eddf20676ac8d86255457c0f164a17ebb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004268 0.069228 0.195174 0.004134 +1 0.004268 0.000001 0.064959 0.190905 0.000134 +2 0.069228 0.064959 0.000001 0.138625 0.065093 +3 0.195174 0.190905 0.138625 0.000001 0.191040 +4 0.004134 0.000134 0.065093 0.191040 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..369b243eadbed865bbc67828d0516077a7e003f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010642 0.013044 2.539727 0.106076 +1 0.010642 0.000001 0.004653 2.550368 0.098733 +2 0.013044 0.004653 0.000001 2.552770 0.101135 +3 2.539727 2.550368 2.552770 0.000001 1.311741 +4 0.106076 0.098733 0.101135 1.311741 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c34b6d8693f3bbb212db094e019fe031953cc25b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.98994367 Before NNI: tree length is 1.98844500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.91295205 diff --git a/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 b/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 new file mode 100644 index 0000000000000000000000000000000000000000..764c95e4e3cd99b2ba5a8c5bab86e43aa38f8584 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005709 0.093975 0.025175 0.000001 +1 0.005709 0.000001 0.092151 0.023351 0.005709 +2 0.093975 0.092151 0.000001 0.092443 0.093975 +3 0.025175 0.023351 0.092443 0.000001 0.025175 +4 0.000001 0.005709 0.093975 0.025175 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c91eb555140d54cfc43c557883ef763885e5a236 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08685950 Before NNI: tree length is 0.08685950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..26f745a9e5a65176dbe6a6bffd46174721c02071 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13827776 Before NNI: tree length is 0.13827775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b888694358ba24431395007934870731e53c194c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.004185 0.110104 0.002090 +1 0.000001 0.000001 0.004185 0.110104 0.002090 +2 0.004185 0.004185 0.000001 0.109326 0.004181 +3 0.110104 0.110104 0.109326 0.000001 0.110100 +4 0.002090 0.002090 0.004181 0.110100 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed7871afd5c4b158173512ee01a2db9f8768677d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.067287 0.074289 0.088766 0.029386 +1 0.067287 0.000001 0.090087 0.104565 0.081785 +2 0.074289 0.090087 0.000001 0.105895 0.088787 +3 0.088766 0.104565 0.105895 0.000001 0.103264 +4 0.029386 0.081785 0.088787 0.103264 0.000001 diff --git a/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 b/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 new file mode 100644 index 0000000000000000000000000000000000000000..acfd95bd1746c5441e21978ea76922b7e4302fdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.211222 0.271866 0.000001 +1 0.000001 0.000001 0.211222 0.271866 0.000001 +2 0.211222 0.211222 0.000001 0.227542 0.211222 +3 0.271866 0.271866 0.227542 0.000001 0.271866 +4 0.000001 0.000001 0.211222 0.271866 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2b5cc50613774b4309d6aea144f5d1b173b86f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.36056775 Before NNI: tree length is 2.36056775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000106_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000106_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..782a753411cf804e36436c3e24e23c7b509596c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000106_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013405 0.403182 0.428875 0.027392 +1 0.013405 0.000001 0.397378 0.423070 0.021588 +2 0.403182 0.397378 0.000001 0.346952 0.391531 +3 0.428875 0.423070 0.346952 0.000001 0.417223 +4 0.027392 0.021588 0.391531 0.417223 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c86a26312c608ea21148c4a7f5bea3cb1d41e78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016869 0.122159 0.193046 0.016869 +1 0.016869 0.000001 0.126900 0.197787 0.000001 +2 0.122159 0.126900 0.000001 0.196205 0.126900 +3 0.193046 0.197787 0.196205 0.000001 0.197787 +4 0.016869 0.000001 0.126900 0.197787 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..704aa363971a0a77f8c7f1be9c61661b959ec879 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30862250 Before NNI: tree length is 0.30862250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99110660 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d11b5ac00d5323ca8b51afc51a02127f5b16a280 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014623 0.245706 0.080910 0.012035 +1 0.014623 0.000001 0.243388 0.078591 0.013484 +2 0.245706 0.243388 0.000001 0.206604 0.244567 +3 0.080910 0.078591 0.206604 0.000001 0.079770 +4 0.012035 0.013484 0.244567 0.079770 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..785c933e5c04112d206ddfcd2fc9c5d1a666c393 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18136075 Before NNI: tree length is 0.18136075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..35bcd3d4a00745577966545f5fcab10f28742c7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.21614150 Before NNI: tree length is 1.21614150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..87cf8d7e274289c80f4b06720909e486c4dd96cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.239434 0.457555 0.009568 +1 0.000001 0.000001 0.239434 0.457555 0.009568 +2 0.239434 0.239434 0.000001 0.540534 0.240357 +3 0.457555 0.457555 0.540534 0.000001 0.458477 +4 0.009568 0.009568 0.240357 0.458477 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..388130f07e73636ee192e45b2363e96e9f1eb526 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009375 0.136175 0.017418 0.011771 +1 0.009375 0.000001 0.139352 0.020595 0.014948 +2 0.136175 0.139352 0.000001 0.142776 0.134735 +3 0.017418 0.020595 0.142776 0.000001 0.018371 +4 0.011771 0.014948 0.134735 0.018371 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4035cf303405be820955ebc489c532623f9ba3b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15962575 Before NNI: tree length is 0.15962575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..677fb922999e798c2f105b646d2dc31eb5de5a41 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59769700 Before NNI: tree length is 0.59769700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf06fd46079c7fb65c50e55030b961ff772e5f1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09971900 Before NNI: tree length is 0.09971900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a8158d944ba4715923fa49a3dcd3c77ede6f084 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65198750 Before NNI: tree length is 0.65198750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d9163003f6e45b298865e93128bd38834c7e7853 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.402419 0.327601 0.000001 +1 0.000001 0.000001 0.402419 0.327601 0.000001 +2 0.402419 0.402419 0.000001 0.257667 0.402419 +3 0.327601 0.327601 0.257667 0.000001 0.327601 +4 0.000001 0.000001 0.402419 0.327601 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..55d59d67788aa3688e1dcd9366a8b34049e75b3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51402950 Before NNI: tree length is 0.51402950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d71987499e8bd7e7b7798eb72e91ae6092e10c76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006876 0.282187 2.067150 0.029178 +1 0.006876 0.000001 0.289063 2.074026 0.036053 +2 0.282187 0.289063 0.000001 2.238115 0.304426 +3 2.067150 2.074026 2.238115 0.000001 2.089389 +4 0.029178 0.036053 0.304426 2.089389 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31d44a8c2caeb8ff8f028c20f21c10923d94d146 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13962568 Before NNI: tree length is 0.13962575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0355eebf5f56f4583221439ac230560f497ac5c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25842335 Before NNI: tree length is 0.25842338 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d8afa7e9aa656e36638e9e3c4f335fcd1056f91d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.071855 0.142096 0.006804 +1 0.000001 0.000001 0.071855 0.142096 0.006804 +2 0.071855 0.071855 0.000001 0.148036 0.072537 +3 0.142096 0.142096 0.148036 0.000001 0.142778 +4 0.006804 0.006804 0.072537 0.142778 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd85f9d4dcff86d7f7f534ce97a992b05a9ea77b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23007767 Before NNI: tree length is 0.23007775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a256a84349e6b28e311cce975d0ba2744cdf630f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027084 0.269187 0.534981 0.027084 +1 0.027084 0.000001 0.267273 0.533068 0.000001 +2 0.269187 0.267273 0.000001 0.570233 0.267273 +3 0.534981 0.533068 0.570233 0.000001 0.533068 +4 0.027084 0.000001 0.267273 0.533068 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..646024a2e9580d0525ce80f917592b63c598411a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007537 0.333001 0.362870 0.011839 +1 0.007537 0.000001 0.330415 0.360284 0.004303 +2 0.333001 0.330415 0.000001 0.349400 0.334718 +3 0.362870 0.360284 0.349400 0.000001 0.364586 +4 0.011839 0.004303 0.334718 0.364586 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3032e88a3d05cbf9b8326f9df2f0f550b4d1718 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028955 0.322487 0.824793 0.057707 +1 0.028955 0.000001 0.329503 0.831809 0.064723 +2 0.322487 0.329503 0.000001 0.849917 0.319178 +3 0.824793 0.831809 0.849917 0.000001 0.821483 +4 0.057707 0.064723 0.319178 0.821483 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..80a822157cbc271d34ffc0723679491267fce10c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022543 0.267340 0.520745 0.035252 +1 0.022543 0.000001 0.254125 0.507530 0.022037 +2 0.267340 0.254125 0.000001 0.453665 0.248408 +3 0.520745 0.507530 0.453665 0.000001 0.501812 +4 0.035252 0.022037 0.248408 0.501812 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb0aeb5b20ee412d136fc8921bb8b17b59eafb4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017333 0.612600 0.305529 0.013237 +1 0.017333 0.000001 0.595267 0.322863 0.030570 +2 0.612600 0.595267 0.000001 0.918130 0.625837 +3 0.305529 0.322863 0.918130 0.000001 0.292293 +4 0.013237 0.030570 0.625837 0.292293 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5c3ac4c166ceebff5574ae963d0a4a8881269973 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12337682 Before NNI: tree length is 0.12337675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eae99d6a1c467a07f2a62a5806693ff3a09b48dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08547200 Before NNI: tree length is 0.08547200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9d26edf22f43f882a77bdcf086938215fedd7ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021163 0.290076 0.507062 0.020758 +1 0.021163 0.000001 0.292064 0.509050 0.022745 +2 0.290076 0.292064 0.000001 0.560130 0.284077 +3 0.507062 0.509050 0.560130 0.000001 0.501063 +4 0.020758 0.022745 0.284077 0.501063 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a5d8a39fea2dbc00c63334e766b3fbc783ea702 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.308846 0.735846 0.007463 +1 0.000001 0.000001 0.308846 0.735846 0.007463 +2 0.308846 0.308846 0.000001 0.808325 0.304803 +3 0.735846 0.735846 0.808325 0.000001 0.731804 +4 0.007463 0.007463 0.304803 0.731804 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..70350e94bf8f9c64762181f2f81bf1687d039151 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26858500 Before NNI: tree length is 0.26858500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b95477711307bbbc90591c020c9474d53f159d57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013648 0.087406 0.031959 0.005819 +1 0.013648 0.000001 0.098479 0.043032 0.012268 +2 0.087406 0.098479 0.000001 0.098612 0.090651 +3 0.031959 0.043032 0.098612 0.000001 0.035204 +4 0.005819 0.012268 0.090651 0.035204 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e41e24b56642eed6742bc8e753e58d63f755fae6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003711 0.044836 0.090492 0.003711 +1 0.003711 0.000001 0.042395 0.088050 0.000001 +2 0.044836 0.042395 0.000001 0.076779 0.042395 +3 0.090492 0.088050 0.076779 0.000001 0.088050 +4 0.003711 0.000001 0.042395 0.088050 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..02a5937c878f1327539c135154fb8f9fca7d253f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037232 0.353168 0.300381 0.005409 +1 0.037232 0.000001 0.328592 0.275805 0.037214 +2 0.353168 0.328592 0.000001 0.396226 0.353151 +3 0.300381 0.275805 0.396226 0.000001 0.300364 +4 0.005409 0.037214 0.353151 0.300364 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9d71120d7f02a8065f303a90e614db8daf1f472 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.95771300 Before NNI: tree length is 0.95771300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0d670bcc87acebff723355d85dacabcdd37fa03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44135400 Before NNI: tree length is 0.44135400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b1a4f0d914b2f947870aa444d02fef342d8ad45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023223 0.193715 0.500968 0.048316 +1 0.023223 0.000001 0.184607 0.491860 0.039209 +2 0.193715 0.184607 0.000001 0.432785 0.183549 +3 0.500968 0.491860 0.432785 0.000001 0.490802 +4 0.048316 0.039209 0.183549 0.490802 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f47fa88104c81469fcf79a6eedcff98d86e94c23 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58986675 Before NNI: tree length is 0.58986675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e29fdfe793d53b9a930f89f252114c8c0d42a62d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015378 0.155302 0.284130 0.015378 +1 0.015378 0.000001 0.148989 0.277818 0.000001 +2 0.155302 0.148989 0.000001 0.295509 0.148989 +3 0.284130 0.277818 0.295509 0.000001 0.277818 +4 0.015378 0.000001 0.148989 0.277818 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..65ce7c96543f3c417c9383b123a652fb1902e5de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039667 0.382933 0.573781 0.046601 +1 0.039667 0.000001 0.400678 0.591526 0.028141 +2 0.382933 0.400678 0.000001 0.615306 0.407612 +3 0.573781 0.591526 0.615306 0.000001 0.598460 +4 0.046601 0.028141 0.407612 0.598460 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0431c51075d33f04900a2bd2d2064e72024960a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029853 0.105905 0.302121 0.000001 +1 0.029853 0.000001 0.099651 0.295867 0.029853 +2 0.105905 0.099651 0.000001 0.287236 0.105905 +3 0.302121 0.295867 0.287236 0.000001 0.302121 +4 0.000001 0.029853 0.105905 0.302121 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..15b15c356d19264da51e03f799b315fd8632efa2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000549_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 0.31635050 Before NNI: tree length is 0.31635050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1992cc5e6593dd27d6bcaa69dcd64ea4d7702096 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007843 0.149031 0.134183 0.000001 +1 0.007843 0.000001 0.152061 0.137214 0.007843 +2 0.149031 0.152061 0.000001 0.221137 0.149031 +3 0.134183 0.137214 0.221137 0.000001 0.134183 +4 0.000001 0.007843 0.149031 0.134183 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..229884686f82b85965fa26912c3f03afd98a2bae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007893 0.075617 0.171424 0.016246 +1 0.007893 0.000001 0.070903 0.166709 0.011532 +2 0.075617 0.070903 0.000001 0.158589 0.072712 +3 0.171424 0.166709 0.158589 0.000001 0.168518 +4 0.016246 0.011532 0.072712 0.168518 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c6ef6f578343f77579f556b532db2472520cc535 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016298 0.095114 0.133849 0.048337 +1 0.016298 0.000001 0.083009 0.121743 0.036232 +2 0.095114 0.083009 0.000001 0.121083 0.096977 +3 0.133849 0.121743 0.121083 0.000001 0.135712 +4 0.048337 0.036232 0.096977 0.135712 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4aa0fd11b1d61f6170a3f3a41de2f6c28f87f2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000557_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 0.20221936 Before NNI: tree length is 0.20221937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39ea61c5509ea08ded4c4a88ce053b19dae3fbac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028270 1.011351 0.954121 0.050537 +1 0.028270 0.000001 1.005769 0.948540 0.044955 +2 1.011351 1.005769 0.000001 0.394935 1.003009 +3 0.954121 0.948540 0.394935 0.000001 0.945780 +4 0.050537 0.044955 1.003009 0.945780 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000568_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000568_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e7d6680ceae637248081d68983eccfeee05ab70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000568_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 0.26781175 Before NNI: tree length is 0.26781175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000570_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000570_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb7d6f82625730a10688dcb778f9bb39edfe279b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000570_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 0.40105025 Before NNI: tree length is 0.40105025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..66a4b4a99e71a1af8f6f542bac1660146cd3d7db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_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 0.31781800 Before NNI: tree length is 0.31781800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000601_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000601_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ed463773479672a7189e8f9c685f9528224180c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000601_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 0.70129450 Before NNI: tree length is 0.70129450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a4f9f9b1a324836b315b45e40ce8553f9d38b43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000611_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 0.33866771 Before NNI: tree length is 0.33866775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5714058bd312efaa6e352e2841c884bffd8a7666 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_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 0.61369650 Before NNI: tree length is 0.61369650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd8fb903064015379d82916705a22986151c3867 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000615_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 0.09374704 Before NNI: tree length is 0.09374700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbf86c7145c1e06f0b2a3ebbb1de5bd48c73a924 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_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 0.85937150 Before NNI: tree length is 0.85937150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000627_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000627_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aaa323574a45384baab18b397074e58c3b9ae013 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000627_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 0.86423225 Before NNI: tree length is 0.86423225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000628_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000628_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9145ef024f61b252e32bd64402b373feeffcef5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000628_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 0.14004573 Before NNI: tree length is 0.14004575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000630_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000630_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ffe386c8f30ddddd2add8459e0562ceb0f6d704d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000630_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 0.20012250 Before NNI: tree length is 0.20012250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000640_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000640_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9170ed1505fbf0461af0ddec5a20708f742f4e47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000640_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 0.15163450 Before NNI: tree length is 0.15163450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..98966b273cf448dff18777a877305ebcd9da43d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015193 0.054322 0.118995 0.010964 +1 0.015193 0.000001 0.059177 0.123850 0.008306 +2 0.054322 0.059177 0.000001 0.120288 0.054948 +3 0.118995 0.123850 0.120288 0.000001 0.119621 +4 0.010964 0.008306 0.054948 0.119621 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5c8036db93b2343da773873890d7a3b33ab50136 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023712 0.292916 0.528069 0.026959 +1 0.023712 0.000001 0.302149 0.537302 0.036192 +2 0.292916 0.302149 0.000001 0.535663 0.302985 +3 0.528069 0.537302 0.535663 0.000001 0.538137 +4 0.026959 0.036192 0.302985 0.538137 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f6833eb1b7ef1a83215bf86ccaa6daa104deb70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_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 0.58331939 Before NNI: tree length is 0.58331938 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..12325454ff1591963be86c9c533ed5e4b431472c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012048 0.284331 0.294118 0.010125 +1 0.012048 0.000001 0.285130 0.294917 0.004773 +2 0.284331 0.285130 0.000001 0.278644 0.283207 +3 0.294118 0.294917 0.278644 0.000001 0.292994 +4 0.010125 0.004773 0.283207 0.292994 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000692_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000692_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ad9c6743b25aedece72e33cae85182c325d35fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000692_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 0.10790100 Before NNI: tree length is 0.10790100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4f8d6856b306919d93bd466ec4bd3ddbfee05c78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004506 0.022968 0.044406 0.003959 +1 0.004506 0.000001 0.025446 0.046884 0.005293 +2 0.022968 0.025446 0.000001 0.055598 0.024899 +3 0.044406 0.046884 0.055598 0.000001 0.046337 +4 0.003959 0.005293 0.024899 0.046337 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ea2205324a5f056443ae6044dc5155cf16d116a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_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 0.31189650 Before NNI: tree length is 0.31189650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7c97c8c1da6387ddde6eb1b0c0f9376afe1f4d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_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 0.47338678 Before NNI: tree length is 0.47338675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f397f6a887f4b6ceb07a277b3db803e886130c54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006771 0.068213 0.108956 0.009556 +1 0.006771 0.000001 0.064344 0.105088 0.005688 +2 0.068213 0.064344 0.000001 0.127337 0.064761 +3 0.108956 0.105088 0.127337 0.000001 0.105505 +4 0.009556 0.005688 0.064761 0.105505 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d5c76e8aea8cca85d9638ab9f864bcd00e0b664b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_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 0.20951700 Before NNI: tree length is 0.20951700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..63bb77a7ff2e5b2bee4b6515837bfd26525da685 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004377 0.404193 0.493209 0.017948 +1 0.004377 0.000001 0.402830 0.491845 0.020503 +2 0.404193 0.402830 0.000001 0.466245 0.420320 +3 0.493209 0.491845 0.466245 0.000001 0.509336 +4 0.017948 0.020503 0.420320 0.509336 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa158af6be7a6b34fbb604ad2f684c488f36adaf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000726_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 0.47741050 Before NNI: tree length is 0.47741050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2810fd9c60a0a9fecf83573c99e4077506307e8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.080037 0.006329 +1 0.000001 0.000001 0.000001 0.080037 0.006329 +2 0.000001 0.000001 0.000001 0.080037 0.006329 +3 0.080037 0.080037 0.080037 0.000001 0.085144 +4 0.006329 0.006329 0.006329 0.085144 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..df416379850d066790e6bbe672bd312072a7c049 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_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 0.18859077 Before NNI: tree length is 0.18859075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000758_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000758_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2e90cdd8ea7250c320c2bd3bd118f250e9241dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000758_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 0.99048285 Before NNI: tree length is 0.99048288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7740d40668b733bd59fa9bee4bc8d6931bd50640 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010224 0.117597 0.241938 0.012545 +1 0.010224 0.000001 0.119371 0.243711 0.017347 +2 0.117597 0.119371 0.000001 0.239598 0.124721 +3 0.241938 0.243711 0.239598 0.000001 0.249062 +4 0.012545 0.017347 0.124721 0.249062 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b93635a0370de7030675b76554e78943ed8f49ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_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 0.52647789 Before NNI: tree length is 0.52647787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1fe7e5bd0017f133cfd87a70f71c5fdb8e7498a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.299207 0.281996 0.179881 0.300177 +1 0.299207 0.000001 0.111228 0.269579 0.129409 +2 0.281996 0.111228 0.000001 0.252368 0.098683 +3 0.179881 0.269579 0.252368 0.000001 0.270550 +4 0.300177 0.129409 0.098683 0.270550 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000792_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000792_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42e33504c09021169d1f354c7dbc276512a1df5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000792_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 0.17407940 Before NNI: tree length is 0.17407937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..340a385fe18c727afe2365f342b0acdbc25bffad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005985 0.040758 0.131063 0.008171 +1 0.005985 0.000001 0.043548 0.133852 0.010961 +2 0.040758 0.043548 0.000001 0.127517 0.043296 +3 0.131063 0.133852 0.127517 0.000001 0.133600 +4 0.008171 0.010961 0.043296 0.133600 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..722b5fd3a01a5c9b3c02b3fd8019175e578680e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000813_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 0.92847926 Before NNI: tree length is 0.92847925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4828a1bcf7fb84e736b6019bc761495dcb9791ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_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 0.14942925 Before NNI: tree length is 0.14942925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..49eb178de9530cd58c10dca5d30c6c9b6a3d0863 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000819_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 0.67958461 Before NNI: tree length is 0.67958462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000830_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000830_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..beac252ce7cc8e41dec94fced58aaf77bdd251cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000830_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 0.09888975 Before NNI: tree length is 0.09888975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..50a7f72d189ab189e89d5081a4ffcc3cafc6727b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012651 0.014656 0.011442 0.017351 +1 0.012651 0.000001 0.012002 0.014717 0.014697 +2 0.014656 0.012002 0.000001 0.016722 0.013337 +3 0.011442 0.014717 0.016722 0.000001 0.019417 +4 0.017351 0.014697 0.013337 0.019417 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000845_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000845_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18f496dc05fc5893dc7c7a70ac44d60d317a6e58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000845_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 0.41831089 Before NNI: tree length is 0.41831088 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f83048960e1f619cd6e90b1be2340f3ce102fba1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000847_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 0.46279450 Before NNI: tree length is 0.46279450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b893ff846c012233af977cf265dd974a535f881c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009465 0.086923 0.152181 0.010849 +1 0.009465 0.000001 0.086392 0.151650 0.015910 +2 0.086923 0.086392 0.000001 0.200794 0.093369 +3 0.152181 0.151650 0.200794 0.000001 0.158627 +4 0.010849 0.015910 0.093369 0.158627 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e03b23b5dd363b217d06162c12c1dfa649d272d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_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 0.53053800 Before NNI: tree length is 0.53053800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000866_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000866_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af883304a8724bc83c4fe79352770ad25c0a9d67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000866_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 0.09237392 Before NNI: tree length is 0.09237387 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b92ae2d0ca224214b0a020319089a63fcf61ce78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004889 0.025506 0.036687 0.009884 +1 0.004889 0.000001 0.029533 0.040713 0.013910 +2 0.025506 0.029533 0.000001 0.038268 0.018031 +3 0.036687 0.040713 0.038268 0.000001 0.029212 +4 0.009884 0.013910 0.018031 0.029212 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f330baf7e16c8259f9c528b3671472fdd3c6eb76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004469 0.200154 0.394172 0.021926 +1 0.004469 0.000001 0.198046 0.392063 0.019818 +2 0.200154 0.198046 0.000001 0.409997 0.192556 +3 0.394172 0.392063 0.409997 0.000001 0.386573 +4 0.021926 0.019818 0.192556 0.386573 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3df6a3ad6dfc5ff10af12e4c291a747ebd5bc551 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032224 0.156096 0.307945 0.034303 +1 0.032224 0.000001 0.148375 0.300225 0.012138 +2 0.156096 0.148375 0.000001 0.275921 0.150455 +3 0.307945 0.300225 0.275921 0.000001 0.302304 +4 0.034303 0.012138 0.150455 0.302304 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000883_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000883_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..46377fd240a2281ed6d6d813ece4c1f0c433f2b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000883_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 0.26977971 Before NNI: tree length is 0.26977975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000888_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000888_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b672d008aa25ab57022728637d306106d3c3aff4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000888_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 0.65903429 Before NNI: tree length is 0.65903425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..458d0752be1ccdc9fbbf0f9594c953a4ce6f218a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_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 0.28370311 Before NNI: tree length is 0.28370312 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbe279627b2cec77bad8ef3475c5865656d99a4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000895_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 0.14131000 Before NNI: tree length is 0.14131000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..77030d3a83b2fbeb507dc71ab551fafad90c4575 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011236 0.692173 0.616183 0.011236 +1 0.011236 0.000001 0.699687 0.623696 0.000001 +2 0.692173 0.699687 0.000001 0.826665 0.699687 +3 0.616183 0.623696 0.826665 0.000001 0.623696 +4 0.011236 0.000001 0.699687 0.623696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cd717653eec7328a92fae8c4667f7ed8b087a2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000942_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 0.18776686 Before NNI: tree length is 0.18776688 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e30e0ec4e965a6c51a8030ce4b6106f38c784740 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_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 0.41141450 Before NNI: tree length is 0.41141450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..269578f0d91672957a1b7467153190e9735bb884 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000961_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 0.50985200 Before NNI: tree length is 0.50985200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000966_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000966_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ecf516e56f95737f2e16d0a72e8202158884c893 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000966_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 0.42625365 Before NNI: tree length is 0.42625363 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ba821ab79448ac425a81c1743c47e55e29d89cd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004535 0.037534 0.193204 0.002012 +1 0.004535 0.000001 0.038962 0.194633 0.002907 +2 0.037534 0.038962 0.000001 0.200955 0.036439 +3 0.193204 0.194633 0.200955 0.000001 0.192110 +4 0.002012 0.002907 0.036439 0.192110 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc2f4c912a4741bb1aeb6779a283198a36fb6aa9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.024910 0.306677 0.046487 +1 0.000001 0.000001 0.024910 0.306677 0.046487 +2 0.024910 0.024910 0.000001 0.281766 0.028964 +3 0.306677 0.306677 0.281766 0.000001 0.310731 +4 0.046487 0.046487 0.028964 0.310731 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d4099974056e0b35a2b62041c82a0481271d2ff4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013907 0.137976 0.455776 0.000001 +1 0.013907 0.000001 0.133320 0.451120 0.013907 +2 0.137976 0.133320 0.000001 0.464231 0.137976 +3 0.455776 0.451120 0.464231 0.000001 0.455776 +4 0.000001 0.013907 0.137976 0.455776 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42516378acc42dec64dc87833e469ddfbab5326a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007175 0.030953 0.190575 0.000001 +1 0.007175 0.000001 0.027780 0.193039 0.007175 +2 0.030953 0.027780 0.000001 0.216816 0.030953 +3 0.190575 0.193039 0.216816 0.000001 0.190575 +4 0.000001 0.007175 0.030953 0.190575 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3707b1dd67e5bd1794fd14e3e3b8a6b2967f5a54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006987 0.050018 0.104620 0.000877 +1 0.006987 0.000001 0.048388 0.102990 0.006197 +2 0.050018 0.048388 0.000001 0.091444 0.049228 +3 0.104620 0.102990 0.091444 0.000001 0.103829 +4 0.000877 0.006197 0.049228 0.103829 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de76812de99a3ce347073826ae7494a0afe2c6f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045276 0.452304 0.630912 0.017327 +1 0.045276 0.000001 0.451507 0.630116 0.041730 +2 0.452304 0.451507 0.000001 0.597616 0.448757 +3 0.630912 0.630116 0.597616 0.000001 0.627366 +4 0.017327 0.041730 0.448757 0.627366 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fe326723fa315222aa7573855f1f22f0d4cb612c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003337 0.078280 0.220604 0.002857 +1 0.003337 0.000001 0.074943 0.217268 0.000479 +2 0.078280 0.074943 0.000001 0.204742 0.075422 +3 0.220604 0.217268 0.204742 0.000001 0.217747 +4 0.002857 0.000479 0.075422 0.217747 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ec45e35fd097eb4e7d1a692ce0f3cdb6af74327 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001042_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 0.56570950 Before NNI: tree length is 0.56570950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..21c9168e30a913483d1addd0f6c785c3d3b60bdd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009828 0.252000 0.766055 0.009828 +1 0.009828 0.000001 0.255587 0.769642 0.000001 +2 0.252000 0.255587 0.000001 0.667569 0.255587 +3 0.766055 0.769642 0.667569 0.000001 0.769642 +4 0.009828 0.000001 0.255587 0.769642 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ef64c0d8e5105eecad661ae150c988a153ae0d19 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001049_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 0.11703272 Before NNI: tree length is 0.11703275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12e9fe858448c0155f7badaf86d158ca7f40378b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_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 0.43856429 Before NNI: tree length is 0.43856425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81340b8baad61fb00a00df64e42b36f2f7a8a9de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001087_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 0.34901050 Before NNI: tree length is 0.34901050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..80da685e915e4cb2a2d8dbc7c4aefef5d1124fb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001104_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 0.12312150 Before NNI: tree length is 0.12312150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6cfb8bbf9cf7a8f2cedafeac50e49a83f8947b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001108_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 0.39654300 Before NNI: tree length is 0.39654300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8d21acdf2b57984a9f0c4961e2d1d5f52c90251 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_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 0.35502000 Before NNI: tree length is 0.35502000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c5eb12fb168d8dce483e6e5fa64dd97deb59b3cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017541 0.044924 0.120339 0.008848 +1 0.017541 0.000001 0.030639 0.106054 0.015334 +2 0.044924 0.030639 0.000001 0.105361 0.042717 +3 0.120339 0.106054 0.105361 0.000001 0.118132 +4 0.008848 0.015334 0.042717 0.118132 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04de9ddba08d013ab3014dc528383d97c4e79df3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_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 1.16391050 Before NNI: tree length is 1.16391050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba4622c186b0226ba75bb2944c060e7573a3f06d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001139_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 0.50388065 Before NNI: tree length is 0.50388063 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbcab4b1c06ee13250a522414079d065cc2c55c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009573 0.145268 0.391089 0.001080 +1 0.009573 0.000001 0.141475 0.387296 0.010653 +2 0.145268 0.141475 0.000001 0.415846 0.146348 +3 0.391089 0.387296 0.415846 0.000001 0.392169 +4 0.001080 0.010653 0.146348 0.392169 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7dbc1fa35358033e4814e54a9da1495e0e82f94c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_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 0.13458100 Before NNI: tree length is 0.13458100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b00027037b207b71c99e34c671504f5bc0e4438 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001178_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 0.23134675 Before NNI: tree length is 0.23134675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b94ff85b38270adda7801ba6d9b81b0159902fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009868 0.060634 0.120362 0.004235 +1 0.009868 0.000001 0.057710 0.117438 0.008201 +2 0.060634 0.057710 0.000001 0.121642 0.058967 +3 0.120362 0.117438 0.121642 0.000001 0.118695 +4 0.004235 0.008201 0.058967 0.118695 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55dfa1444428e7236b737362a57c757de1539764 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.813047 1.752828 0.089914 +1 0.000001 0.000001 0.813047 1.752828 0.089914 +2 0.813047 0.813047 0.000001 1.640820 0.738824 +3 1.752828 1.752828 1.640820 0.000001 1.678606 +4 0.089914 0.089914 0.738824 1.678606 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a17a336bab896049967877aa81bce7ce370190a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001192_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 0.41554510 Before NNI: tree length is 0.41554513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b09669df42f7a7786481dd2a14a34236fe3e462e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_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 0.43975175 Before NNI: tree length is 0.43975175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc23e4a671cc9cab6aba36625102f35e8e1938d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001234_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 1.43544165 Before NNI: tree length is 1.43544163 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..696c389750110e90a7b7a72b83af9a4dd12a0c5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037423 0.202257 0.492277 0.033015 +1 0.037423 0.000001 0.202139 0.492160 0.020858 +2 0.202257 0.202139 0.000001 0.574661 0.197730 +3 0.492277 0.492160 0.574661 0.000001 0.487751 +4 0.033015 0.020858 0.197730 0.487751 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5228d8e9c4fd4ae99c2b686bb4efa6cf38ba5066 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.097285 0.560128 0.036259 +1 0.000001 0.000001 0.097285 0.560128 0.036259 +2 0.097285 0.097285 0.000001 0.544738 0.104265 +3 0.560128 0.560128 0.544738 0.000001 0.567108 +4 0.036259 0.036259 0.104265 0.567108 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..48db8a2d6a611b37b164c8f3df18420282e60fc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.096126 0.182322 0.000001 +1 0.000001 0.000001 0.096126 0.182322 0.000001 +2 0.096126 0.096126 0.000001 0.195030 0.096126 +3 0.182322 0.182322 0.195030 0.000001 0.182322 +4 0.000001 0.000001 0.096126 0.182322 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1ac0018d70ec6c06b16d869d768e420ca2eb840d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034608 0.215094 0.489268 0.024356 +1 0.034608 0.000001 0.219129 0.493304 0.019407 +2 0.215094 0.219129 0.000001 0.452564 0.208877 +3 0.489268 0.493304 0.452564 0.000001 0.483051 +4 0.024356 0.019407 0.208877 0.483051 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..133f9cdb6a9021e54aa053af888b5563eeb4bfd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001260_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 0.74713546 Before NNI: tree length is 0.74713550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..781b81aaf3fe7042cbf0e85a38a245a360706e1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000656 0.014597 0.055871 0.000656 +1 0.000656 0.000001 0.013941 0.056527 0.001312 +2 0.014597 0.013941 0.000001 0.070469 0.015253 +3 0.055871 0.056527 0.070469 0.000001 0.055215 +4 0.000656 0.001312 0.015253 0.055215 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..21e0e2ae1822d1bb97ac019636336c6ef5b3fe79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012851 0.103429 0.187858 0.015000 +1 0.012851 0.000001 0.103223 0.187651 0.014793 +2 0.103429 0.103223 0.000001 0.163019 0.099603 +3 0.187858 0.187651 0.163019 0.000001 0.184031 +4 0.015000 0.014793 0.099603 0.184031 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1b7b21b3db6eeb1c76825a26ce831bfa7b09d40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001273_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 0.23906190 Before NNI: tree length is 0.23906187 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2cefa56ab53036202474563603959d919d5f35ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003003 0.291694 0.356236 0.009553 +1 0.003003 0.000001 0.292157 0.356699 0.010016 +2 0.291694 0.292157 0.000001 0.380064 0.295685 +3 0.356236 0.356699 0.380064 0.000001 0.360227 +4 0.009553 0.010016 0.295685 0.360227 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d0aa1f1a90377277973dcfa1d6400c13c9f8015 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008641 0.221424 0.311130 0.005668 +1 0.008641 0.000001 0.225316 0.315021 0.002972 +2 0.221424 0.225316 0.000001 0.260164 0.222344 +3 0.311130 0.315021 0.260164 0.000001 0.312049 +4 0.005668 0.002972 0.222344 0.312049 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001307_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001307_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f163ad7b762e1e1b29b2c8520bc240381a92971 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001307_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 0.16469938 Before NNI: tree length is 0.16469937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc61e57c45cbbeb4baca797efadbab5a58e8302c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_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 2.16564417 Before NNI: tree length is 2.16564412 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5799da419e713614c8657fbd4f14cc3c4c604f16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003436 0.122470 0.279007 0.000431 +1 0.003436 0.000001 0.125906 0.282443 0.003867 +2 0.122470 0.125906 0.000001 0.249941 0.122039 +3 0.279007 0.282443 0.249941 0.000001 0.278576 +4 0.000431 0.003867 0.122039 0.278576 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001363_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001363_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2979542af483d31f1b1817687845aaa08f10cb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001363_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 0.06290100 Before NNI: tree length is 0.06290100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9c520580f36f8c3db44924087b1cf8facfa4f003 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018121 0.049930 0.082947 0.018121 +1 0.018121 0.000001 0.036568 0.069584 0.000001 +2 0.049930 0.036568 0.000001 0.055827 0.036568 +3 0.082947 0.069584 0.055827 0.000001 0.069584 +4 0.018121 0.000001 0.036568 0.069584 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cf4fa1efd91266c60163d683340ec7c14d412be4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.012716 0.000001 +1 0.000001 0.000001 0.000001 0.012716 0.000001 +2 0.000001 0.000001 0.000001 0.012716 0.000001 +3 0.012716 0.012716 0.012716 0.000001 0.012716 +4 0.000001 0.000001 0.000001 0.012716 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d28c2f2d4b1143fdedc9469ba40f8562954794e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001399_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 0.01873550 Before NNI: tree length is 0.01873550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999999 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4cb01d97eaa5bde7d0e5ec5d95dfc9b579c2481f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001988 0.024369 0.050709 0.000001 +1 0.001988 0.000001 0.024678 0.051017 0.001988 +2 0.024369 0.024678 0.000001 0.054111 0.024369 +3 0.050709 0.051017 0.054111 0.000001 0.050709 +4 0.000001 0.001988 0.024369 0.050709 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e89ef55b22c3dfe343672ec7a8b0106b81b6110 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001404_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 0.11389325 Before NNI: tree length is 0.11389325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5234929e4d26229a44941aaff6ebe63b2590cfed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_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 0.50957127 Before NNI: tree length is 0.50957125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4379f63fcc030f3fd37cffb5256115217f1165b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.123959 0.150860 0.020896 +1 0.000001 0.000001 0.123959 0.150860 0.020896 +2 0.123959 0.123959 0.000001 0.143650 0.110601 +3 0.150860 0.150860 0.143650 0.000001 0.137502 +4 0.020896 0.020896 0.110601 0.137502 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e49b3237560efd700751ec70d69ebd2d0df16a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001426_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 0.39367700 Before NNI: tree length is 0.39367700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e52c81ab205b053a3985886a25b8e4c0cb6645b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.082139 0.106344 0.006851 +1 0.000001 0.000001 0.082139 0.106344 0.006851 +2 0.082139 0.082139 0.000001 0.104945 0.078316 +3 0.106344 0.106344 0.104945 0.000001 0.102522 +4 0.006851 0.006851 0.078316 0.102522 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001434_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001434_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ba33850da1991cc4956f4557eedc345d0865792 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001434_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 0.48548285 Before NNI: tree length is 0.48548288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001480_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001480_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c186a3dec62921acf6ba4d68b39a25cf62dc7e30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001480_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 0.14256460 Before NNI: tree length is 0.14256462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf782b7cd379bf6788ce9f6d41f74510f6a2d3f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030222 0.290396 0.684140 0.081933 +1 0.030222 0.000001 0.270370 0.664114 0.061907 +2 0.290396 0.270370 0.000001 0.692414 0.290485 +3 0.684140 0.664114 0.692414 0.000001 0.684229 +4 0.081933 0.061907 0.290485 0.684229 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9121865b118c15c945b283a354c4d99cc67f71a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_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 0.07200950 Before NNI: tree length is 0.07200950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d2cdde972b233847774e84061d1e79fec1024d60 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025712 0.137783 0.443378 0.025829 +1 0.025712 0.000001 0.128928 0.434523 0.039478 +2 0.137783 0.128928 0.000001 0.396758 0.151549 +3 0.443378 0.434523 0.396758 0.000001 0.457144 +4 0.025829 0.039478 0.151549 0.457144 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8b435bfaca3bdf24e37ea4f493922e402ffb631c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.099173 0.195023 0.440667 0.000001 +1 0.099173 0.000001 0.117380 0.363024 0.099173 +2 0.195023 0.117380 0.000001 0.356039 0.195023 +3 0.440667 0.363024 0.356039 0.000001 0.440667 +4 0.000001 0.099173 0.195023 0.440667 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b1d1acb5182ca9df4851990c3b24a07306cd859 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_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 0.38773885 Before NNI: tree length is 0.38773888 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..72be35429ceaa1093d52d1e781bb68b85db5529e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.127090 0.979689 0.613213 0.021711 +1 0.127090 0.000001 1.006853 0.664187 0.115291 +2 0.979689 1.006853 0.000001 1.516786 0.967890 +3 0.613213 0.664187 1.516786 0.000001 0.601414 +4 0.021711 0.115291 0.967890 0.601414 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c9c85f6e36c4914edb97dc35bf0fd5bf2aa91aa3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.013363 0.013363 0.000001 +1 0.000001 0.000001 0.013363 0.013363 0.000001 +2 0.013363 0.013363 0.000001 0.000001 0.013363 +3 0.013363 0.013363 0.000001 0.000001 0.013363 +4 0.000001 0.000001 0.013363 0.013363 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001548_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001548_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5894575a72d8ae1b702f897b24d487ea570059de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001548_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 0.46815920 Before NNI: tree length is 0.46815925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..65d4b37eb3cdf332d21c1dea44735edcf07b3cc0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001550_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 0.29465250 Before NNI: tree length is 0.29465250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b067f3b1eba8a00c3ce1f8185a78ea6e52bc31c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012827 0.331735 0.323832 0.000001 +1 0.012827 0.000001 0.332165 0.324263 0.012827 +2 0.331735 0.332165 0.000001 0.395217 0.331735 +3 0.323832 0.324263 0.395217 0.000001 0.323832 +4 0.000001 0.012827 0.331735 0.323832 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a461085215d353350833b54235eb8cefe5291a8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_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 0.06419850 Before NNI: tree length is 0.06419850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..76cb2b8f0b2312e4c8778d7a32af37a19a4f3ffe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011153 0.033870 0.137989 0.011814 +1 0.011153 0.000001 0.032548 0.136666 0.010492 +2 0.033870 0.032548 0.000001 0.131557 0.027726 +3 0.137989 0.136666 0.131557 0.000001 0.131844 +4 0.011814 0.010492 0.027726 0.131844 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b9807df0a3ab7b26f75c8f0c1fe8f9fe0ebbcfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001587_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 1.52919050 Before NNI: tree length is 1.52919050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..35ca027df68c80297af7ee06ad844bc482aebb8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024381 0.729097 0.569705 0.031698 +1 0.024381 0.000001 0.722932 0.563540 0.028667 +2 0.729097 0.722932 0.000001 1.040100 0.733384 +3 0.569705 0.563540 1.040100 0.000001 0.573992 +4 0.031698 0.028667 0.733384 0.573992 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69c5648687f40dcc736d10fccf32e0b13ecc0ad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013848 0.197347 0.575999 0.014148 +1 0.013848 0.000001 0.202966 0.581617 0.007500 +2 0.197347 0.202966 0.000001 0.563248 0.203266 +3 0.575999 0.581617 0.563248 0.000001 0.581917 +4 0.014148 0.007500 0.203266 0.581917 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74fba1aca4a7f992aa12286a2f17ad1d2ec137e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004093 0.045373 0.039230 0.011850 +1 0.004093 0.000001 0.041280 0.035137 0.007757 +2 0.045373 0.041280 0.000001 0.045786 0.046224 +3 0.039230 0.035137 0.045786 0.000001 0.040080 +4 0.011850 0.007757 0.046224 0.040080 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..217920e3954d8de37ec58e77bd92476dfb135e3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001603_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 0.22002800 Before NNI: tree length is 0.22002800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001605_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001605_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8af1fc481de8c3271e293eb2fd9e79f73d39576 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001605_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 0.17720750 Before NNI: tree length is 0.17720750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..67e8912a39a620e8e8b29f1d38e519cd93896fe6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_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 0.07115550 Before NNI: tree length is 0.07115550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..789e216ca2d7ce09c396c2e5633f3b11409c5292 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006987 0.267109 0.265563 0.172886 +1 0.006987 0.000001 0.260123 0.258576 0.165900 +2 0.267109 0.260123 0.000001 0.193792 0.424151 +3 0.265563 0.258576 0.193792 0.000001 0.422604 +4 0.172886 0.165900 0.424151 0.422604 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d12fa128e5dbbe4542f549972233f8f327c47fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037572 0.337573 0.037294 0.037101 +1 0.037572 0.000001 0.327513 0.036873 0.012281 +2 0.337573 0.327513 0.000001 0.336874 0.327042 +3 0.037294 0.036873 0.336874 0.000001 0.036403 +4 0.037101 0.012281 0.327042 0.036403 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9096c94a45cb2261bafb911082ca980199f06f10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.020308 0.018693 0.004538 +1 0.000001 0.000001 0.020308 0.018693 0.004538 +2 0.020308 0.020308 0.000001 0.037714 0.018634 +3 0.018693 0.018693 0.037714 0.000001 0.021945 +4 0.004538 0.004538 0.018634 0.021945 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..621281ee991023b7141946cdacd76691cc51c32d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.500547 1.037844 0.006739 +1 0.000001 0.000001 0.500547 1.037844 0.006739 +2 0.500547 0.500547 0.000001 0.902746 0.499170 +3 1.037844 1.037844 0.902746 0.000001 1.036467 +4 0.006739 0.006739 0.499170 1.036467 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..97ceecc764f19b031993183de5947cd9811a7a18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.062187 0.036595 0.046847 0.061169 +1 0.062187 0.000001 0.060751 0.063369 0.007420 +2 0.036595 0.060751 0.000001 0.045411 0.059733 +3 0.046847 0.063369 0.045411 0.000001 0.062352 +4 0.061169 0.007420 0.059733 0.062352 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bccd7198f82f56e0a1fe2f14a8dcc0d836386c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001676_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 0.44315965 Before NNI: tree length is 0.44315962 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a8aec451430a517faa4d372636bcce2693f350c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_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 0.15949100 Before NNI: tree length is 0.15949100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..00e16b768b9a0ecb6710da4cecde0ce75b7fd3fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009974 0.159819 0.356440 0.013019 +1 0.009974 0.000001 0.158300 0.354921 0.011500 +2 0.159819 0.158300 0.000001 0.340094 0.156186 +3 0.356440 0.354921 0.340094 0.000001 0.352807 +4 0.013019 0.011500 0.156186 0.352807 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f25327babcc7b555f0069c4dd4e018df1e144b71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048947 0.467100 0.390594 0.033038 +1 0.048947 0.000001 0.454990 0.378484 0.048478 +2 0.467100 0.454990 0.000001 0.424818 0.466632 +3 0.390594 0.378484 0.424818 0.000001 0.390125 +4 0.033038 0.048478 0.466632 0.390125 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c87b0bd40ffbc9799ef839a86d4461d713c21ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.111106 0.384263 0.002010 +1 0.000001 0.000001 0.111106 0.384263 0.002010 +2 0.111106 0.111106 0.000001 0.333242 0.109096 +3 0.384263 0.384263 0.333242 0.000001 0.382253 +4 0.002010 0.002010 0.109096 0.382253 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ca7a7fe8891694f01763f833f178d92a02233585 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.145423 0.724965 0.000001 +1 0.000001 0.000001 0.145423 0.724965 0.000001 +2 0.145423 0.145423 0.000001 0.732793 0.145423 +3 0.724965 0.724965 0.732793 0.000001 0.724965 +4 0.000001 0.000001 0.145423 0.724965 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a36b23b4908f13cd35d8d94319679f05c228d42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_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 0.10467550 Before NNI: tree length is 0.10467550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ff2220ffbd2c4512152a10471ee14e9a78489c4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012672 0.070427 0.158158 0.002094 +1 0.012672 0.000001 0.072733 0.160463 0.011579 +2 0.070427 0.072733 0.000001 0.150319 0.069334 +3 0.158158 0.160463 0.150319 0.000001 0.157065 +4 0.002094 0.011579 0.069334 0.157065 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bd20ed0c3c5d35b53492c854ee5ad280b8f7d97e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016701 0.276482 0.404105 0.013986 +1 0.016701 0.000001 0.271741 0.399364 0.020273 +2 0.276482 0.271741 0.000001 0.439758 0.280054 +3 0.404105 0.399364 0.439758 0.000001 0.407676 +4 0.013986 0.020273 0.280054 0.407676 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000002_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000002_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..bc9ef2eb3a7c19cb4f207e647d336ffc45e29d64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000002_tree_id.txt.tre @@ -0,0 +1,2 @@ +(2:0.00147650,(3:-0.00222550,(1:-0.00208583,0:0.00209883):0.00431233):0.00787300,4:0.00040650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..78ea948e0ad84b7d383d8a2565d35670bc612f68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre @@ -0,0 +1,2 @@ +((1:-0.00070825,0:0.00070925):0.00513800,(3:0.01361975,2:0.03753125):0.00595050,4:0.00284250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000018_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000018_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..f55b8d195647593248e8d752744339413ebab09a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000018_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00002511,((3:0.53626000,2:0.22298900):0.79196275,0:0.00387625):0.00620475,4:0.00621589); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000020_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000020_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..44075a3a0804f64a0ead4fd50c075263c8c9c682 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000020_tree_id.txt.tre @@ -0,0 +1,2 @@ +(0:0.01047050,((3:0.43264883,2:0.10833517):0.21008914,1:-0.13754807):0.15411757,4:0.00070550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000025_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000025_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..5f7d7890d0710486381bcaff8ddc53311c0f4200 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000025_tree_id.txt.tre @@ -0,0 +1,2 @@ +((1:0.00000025,(2:0.02610200,0:0.00000000):0.00066175):0.52819425,3:0.52819475,4:-0.52819375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000031_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000031_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..e40b89f94ec0ca3b44c6fe51c9872063a5e8a61a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000031_tree_id.txt.tre @@ -0,0 +1,2 @@ +(0:0.00413412,((3:0.13228563,2:0.00633938):0.05861987,1:-0.00000037):0.00013437,4:-0.00000012); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..eab6a68ff8eac6cbc140a790f741363446fd7c3d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre @@ -0,0 +1,2 @@ +((1:0.00155300,(3:0.35796714,0:0.00111586):0.00141414):0.01153948,2:0.01158767,4:0.01456533); 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