diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c81af3f040c9d1dde9db410fead5417652ed81e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020577 0.022701 0.024082 0.012167 +1 0.020577 0.000001 0.000001 0.017735 0.000001 +2 0.022701 0.000001 0.000001 0.017735 0.000001 +3 0.024082 0.017735 0.017735 0.000001 0.017735 +4 0.012167 0.000001 0.000001 0.017735 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5e2998161de6b54937757f33079fbada6a9ff73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.02161825 Before NNI: tree length is 1.02161825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999995 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d420b17bee75ff5e9638aecaa7b525c01d33e420 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.66957950 Before NNI: tree length is 1.66957950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.98590534 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fdcc1952bfa1c55e74e9c76f6aaeb2c65a2a3433 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21929113 Before NNI: tree length is 0.21980737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.93696507 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000021_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000021_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e57c799e9bb7f1380fdf94a5757e06a62a84ea9a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000021_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017091 0.766834 0.878288 0.308374 +1 0.017091 0.000001 0.763526 0.874980 0.280338 +2 0.766834 0.763526 0.000001 0.764995 0.897421 +3 0.878288 0.874980 0.764995 0.000001 1.008876 +4 0.308374 0.280338 0.897421 1.008876 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000034_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000034_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2801e0dfa29ce1b78b8e3c430059929d765aa492 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000034_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20564167 Before NNI: tree length is 0.20680813 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99803585 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..433d88613036e4e1eb5719c3646c531aed50ab53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010401 0.010712 0.053922 0.010401 +1 0.010401 0.000001 0.002633 0.049158 0.000001 +2 0.010712 0.002633 0.000001 0.049469 0.002633 +3 0.053922 0.049158 0.049469 0.000001 0.049158 +4 0.010401 0.000001 0.002633 0.049158 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed141b15fcf22cbdfa9c31e305ba503afc7e641 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000035_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05821300 Before NNI: tree length is 0.05821300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..13bf6f8b9b6e7af44a67e8768b70c71211136fdb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.02874111 Before NNI: tree length is 2.02874112 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9e427f0ff5a9442eea73724ba940675954b2ec6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061389 0.730255 0.845565 0.025427 +1 0.061389 0.000001 0.668866 0.906954 0.035962 +2 0.730255 0.668866 0.000001 0.812414 0.704828 +3 0.845565 0.906954 0.812414 0.000001 0.870992 +4 0.025427 0.035962 0.704828 0.870992 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000042_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000042_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e05da3cbe4903bd1de124e3a3aa9b2fdd56470d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000042_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.529084 0.337498 0.019621 +1 0.000001 0.000001 0.529084 0.337498 0.019625 +2 0.529084 0.529084 0.000001 0.577818 0.530426 +3 0.337498 0.337498 0.577818 0.000001 0.338840 +4 0.019621 0.019625 0.530426 0.338840 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000043_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000043_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bd7a71c00ce32a09bb608001515c901e4d95316 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000043_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07500425 Before NNI: tree length is 0.07500425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0fdd441c14a90023251dd1a367196f2f8ce1cae7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063546 0.360024 0.290536 0.009057 +1 0.063546 0.000001 0.361437 0.291950 0.057358 +2 0.360024 0.361437 0.000001 0.472199 0.353837 +3 0.290536 0.291950 0.472199 0.000001 0.284349 +4 0.009057 0.057358 0.353837 0.284349 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..139b80ae12f14a7d1ddeb0b1458524eaf708aa86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000047_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59529401 Before NNI: tree length is 0.59529400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..886f1fdac185fbd34d9a6593181a301268705a70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.083332 0.163271 0.010758 +1 0.000001 0.000001 0.083332 0.163271 0.010758 +2 0.083332 0.083332 0.000001 0.155523 0.075753 +3 0.163271 0.163271 0.155523 0.000001 0.155692 +4 0.010758 0.010758 0.075753 0.155692 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000054_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000054_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5960c9520a684fd80398df6ad2d0c773b7155d60 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000054_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05117575 Before NNI: tree length is 0.05117575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000056_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000056_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d10b48c95990e8d801b238bb426d60af35f88967 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000056_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.82095675 Before NNI: tree length is 0.82095675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7da308ed4da9e2375c79d58c25621e6326be667 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40450025 Before NNI: tree length is 0.40450025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbf2b9cda692dcd52a6d6e532c1a06b8a642afb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43172233 Before NNI: tree length is 0.43172225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..62f89cd5372aed6124332dcbc70d3144a2c4735e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003041 0.027582 1.109513 0.006043 +1 0.003041 0.000001 0.026249 1.108180 0.003001 +2 0.027582 0.026249 0.000001 1.097785 0.029250 +3 1.109513 1.108180 1.097785 0.000001 1.111181 +4 0.006043 0.003001 0.029250 1.111181 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..001b911a2db026f2fed6685fd4ccde65f60567e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.74104100 Before NNI: tree length is 0.74104100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000070_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000070_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ecf95e8ecd4d293924dc060df807dfd322a33905 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000070_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.257365 0.384085 0.007097 +1 0.000001 0.000001 0.257365 0.384085 0.007097 +2 0.257365 0.257365 0.000001 0.362880 0.255857 +3 0.384085 0.384085 0.362880 0.000001 0.382578 +4 0.007097 0.007097 0.255857 0.382578 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000071_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000071_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f7ee3e305408716602a26d08d6674df49bd94a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000071_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013206 0.082443 0.284391 0.012703 +1 0.013206 0.000001 0.084004 0.285953 0.003207 +2 0.082443 0.084004 0.000001 0.258806 0.083501 +3 0.284391 0.285953 0.258806 0.000001 0.285449 +4 0.012703 0.003207 0.083501 0.285449 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b664781b1fa6d32dbbef7ee05d43c49bcc498fd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024794 0.218916 0.270454 0.002758 +1 0.024794 0.000001 0.213188 0.264726 0.022036 +2 0.218916 0.213188 0.000001 0.339775 0.216158 +3 0.270454 0.264726 0.339775 0.000001 0.267696 +4 0.002758 0.022036 0.216158 0.267696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..675e5422d18507ba2c47c5d30ba1147cec5093da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42410550 Before NNI: tree length is 0.42410550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..29207174729087c273a05696d9aa570e7b8739f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022705 0.122177 0.256226 0.021533 +1 0.022705 0.000001 0.120358 0.254407 0.009536 +2 0.122177 0.120358 0.000001 0.250200 0.119187 +3 0.256226 0.254407 0.250200 0.000001 0.253236 +4 0.021533 0.009536 0.119187 0.253236 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ee828435321dce60a1450b30160ab4a8cabb7eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32892675 Before NNI: tree length is 0.32892675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf408009b866c69b80b6c8fb0c2fc79f3af01f7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.064693 0.172379 0.267474 0.019912 +1 0.064693 0.000001 0.155393 0.250488 0.065492 +2 0.172379 0.155393 0.000001 0.276170 0.173177 +3 0.267474 0.250488 0.276170 0.000001 0.268273 +4 0.019912 0.065492 0.173177 0.268273 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..73c09fe09a889e633da7ce3d8d4203a4fcc92cb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17914064 Before NNI: tree length is 0.17914063 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..285b8be9ec4f4be0e3c424f89594531103e3aae8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08218450 Before NNI: tree length is 0.08218450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d04613e1e990789337529ff79d7b05027f96383d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17683979 Before NNI: tree length is 0.17683975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1721cbf2929012eff225829bcae67ff94c2bea5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003822 0.042462 0.135912 0.007308 +1 0.003822 0.000001 0.046284 0.139734 0.011130 +2 0.042462 0.046284 0.000001 0.153146 0.043650 +3 0.135912 0.139734 0.153146 0.000001 0.137100 +4 0.007308 0.011130 0.043650 0.137100 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..21cf6e70907ca95a51b405b349ecf8ed734c2435 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003247 0.041120 0.064609 0.000001 +1 0.003247 0.000001 0.043052 0.066541 0.003247 +2 0.041120 0.043052 0.000001 0.062810 0.041120 +3 0.064609 0.066541 0.062810 0.000001 0.064609 +4 0.000001 0.003247 0.041120 0.064609 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..68daacdd25805e6321153998dc0ed4cf49f5ae29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086231 0.539292 0.166867 0.050006 +1 0.086231 0.000001 0.454220 0.253098 0.036225 +2 0.539292 0.454220 0.000001 0.481546 0.490445 +3 0.166867 0.253098 0.481546 0.000001 0.216874 +4 0.050006 0.036225 0.490445 0.216874 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0febfe5161d788c3c00219e1e68743023ac37470 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000085_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.63971343 Before NNI: tree length is 0.64631413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.98025360 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca44b0de3ebe30ec482bb6ae47860140c4e32080 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28138637 Before NNI: tree length is 0.28138637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000091_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000091_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04ef0fe360568b0b27c11116cf3ccd3a59a17a86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000091_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.05333025 Before NNI: tree length is 1.05333025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000094_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000094_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e3df33ce507b7c152d66cf154b6fadb27f3c3c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000094_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017497 0.194118 0.195555 0.221382 +1 0.017497 0.000001 0.185131 0.186569 0.212395 +2 0.194118 0.185131 0.000001 0.007310 0.233608 +3 0.195555 0.186569 0.007310 0.000001 0.235045 +4 0.221382 0.212395 0.233608 0.235045 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000105_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000105_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c0f3858738ca3c99c0ebf7afa975bb5e13dea64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000105_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.92250738 Before NNI: tree length is 1.93756250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.98767579 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..239c559ccdab9917a0f5989a7274a13ae20ba8bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41091764 Before NNI: tree length is 0.41091763 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0069a148aa02fab779048485713dea51408faa40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008368 0.176330 0.299952 0.008368 +1 0.008368 0.000001 0.170912 0.294533 0.000001 +2 0.176330 0.170912 0.000001 0.293128 0.170912 +3 0.299952 0.294533 0.293128 0.000001 0.294533 +4 0.008368 0.000001 0.170912 0.294533 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..590c0ea25bad4fd4258cea1225f02d607165ff59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000108_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38618021 Before NNI: tree length is 0.38618025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000109_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000109_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..38c21da2a80aa37d942f464f24c53aaf7fa8c7bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000109_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.794426 0.813600 0.795927 +1 0.000001 0.000001 0.794426 0.813600 0.795927 +2 0.794426 0.794426 0.000001 0.556217 0.013228 +3 0.813600 0.813600 0.556217 0.000001 0.557718 +4 0.795927 0.795927 0.013228 0.557718 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000111_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000111_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0a7ee3ccd8ae8f98130d5ad0e83b7d67a9ae6c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000111_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27231450 Before NNI: tree length is 0.27231450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..279d0073c3752c3af982d60a91469336f4c09793 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.395663 0.989703 0.072319 +1 0.000001 0.000001 0.395663 0.989703 0.072319 +2 0.395663 0.395663 0.000001 1.338515 0.421131 +3 0.989703 0.989703 1.338515 0.000001 0.917385 +4 0.072319 0.072319 0.421131 0.917385 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000114_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000114_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9c92ea6dbc48711245ee767e8abbb3ee4ebe3e1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000114_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 1.072107 0.028420 0.000001 +1 0.000001 0.000001 1.072107 0.028420 0.000001 +2 1.072107 1.072107 0.000001 1.085138 1.072107 +3 0.028420 0.028420 1.085138 0.000001 0.028420 +4 0.000001 0.000001 1.072107 0.028420 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8b62ea8623bef4483e3189c1b764cf1e079d4d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000162 1.119963 0.011982 0.000324 +1 0.000162 0.000001 1.119801 0.012144 0.000162 +2 1.119963 1.119801 0.000001 1.131945 1.119639 +3 0.011982 0.012144 1.131945 0.000001 0.012306 +4 0.000324 0.000162 1.119639 0.012306 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000117_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000117_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ca33839dabebffb59ed6161db688a4a060fdeb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000117_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019570 0.836891 0.691081 0.013122 +1 0.019570 0.000001 0.848510 0.702701 0.011853 +2 0.836891 0.848510 0.000001 0.789885 0.842062 +3 0.691081 0.702701 0.789885 0.000001 0.696253 +4 0.013122 0.011853 0.842062 0.696253 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9069d8f70c2de889668b3e0715b318f362b79190 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.082384 0.228627 0.000001 +1 0.000001 0.000001 0.082384 0.228627 0.000001 +2 0.082384 0.082384 0.000001 0.219301 0.082384 +3 0.228627 0.228627 0.219301 0.000001 0.228627 +4 0.000001 0.000001 0.082384 0.228627 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4bb7a948e814355a86466c811c72bcc6e3e272a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004751 0.047263 0.131776 0.002296 +1 0.004751 0.000001 0.047150 0.131662 0.004445 +2 0.047263 0.047150 0.000001 0.132556 0.046957 +3 0.131776 0.131662 0.132556 0.000001 0.131470 +4 0.002296 0.004445 0.046957 0.131470 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000121_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/OG0000121_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9915c4906f997659fb4e6469bb0d77a65c52bd7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000121_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 0.17664050 Before NNI: tree length is 0.17664050 + 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/OG0000124_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/OG0000124_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f32b94f36762f4bba4c2bf1bb784ae561e7d4588 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000124_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007905 0.093444 0.129027 0.007905 +1 0.007905 0.000001 0.097431 0.133013 0.000001 +2 0.093444 0.097431 0.000001 0.139525 0.097431 +3 0.129027 0.133013 0.139525 0.000001 0.133013 +4 0.007905 0.000001 0.097431 0.133013 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000126_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/OG0000126_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2581e6bebd02141f85246f91aa37d2e73a15030f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000126_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 0.36179500 Before NNI: tree length is 0.36179500 + 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/OG0000129_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/OG0000129_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ff45691aa866f8b6739ac68bc538b6fee56e16fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000129_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.143117 0.171735 0.269305 0.033577 +1 0.143117 0.000001 0.185226 0.282796 0.134781 +2 0.171735 0.185226 0.000001 0.276281 0.163400 +3 0.269305 0.282796 0.276281 0.000001 0.260970 +4 0.033577 0.134781 0.163400 0.260970 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000130_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/OG0000130_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b3b1abd4a2a4471c290a13dac381150c780de2b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000130_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 0.40832575 Before NNI: tree length is 0.40832575 + 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/OG0000132_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/OG0000132_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1193e53519143367bbd2487799d9ba924205345 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip_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 1.10005742 Before NNI: tree length is 1.10005738 + 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/OG0000133_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/OG0000133_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9742a04ce5f9e288e9589f29f79abeeb961a6a87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000133_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003616 0.196976 0.260028 0.017032 +1 0.003616 0.000001 0.199081 0.262133 0.019137 +2 0.196976 0.199081 0.000001 0.257283 0.203910 +3 0.260028 0.262133 0.257283 0.000001 0.266962 +4 0.017032 0.019137 0.203910 0.266962 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0092a42357d5540e01082f26707709a4e152b7c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012602 0.043369 0.012027 0.010502 +1 0.012602 0.000001 0.045906 0.008324 0.002766 +2 0.043369 0.045906 0.000001 0.045331 0.043806 +3 0.012027 0.008324 0.045331 0.000001 0.006223 +4 0.010502 0.002766 0.043806 0.006223 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000135_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/OG0000135_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3e0c82f6d7f4f5d1f0a8fab2511dc342ca9755a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000135_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 0.39040308 Before NNI: tree length is 0.39040312 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99752435 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000137_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/OG0000137_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..49e8af76070cd9fd774c33125bf3735651530d5b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000137_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021171 0.023543 0.206304 0.017486 +1 0.021171 0.000001 0.033722 0.909296 0.017795 +2 0.023543 0.033722 0.000001 0.899687 0.030037 +3 0.206304 0.909296 0.899687 0.000001 0.905610 +4 0.017486 0.017795 0.030037 0.905610 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000139_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/OG0000139_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..564f9f1044483de278fc5a99285c776d199e62da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000139_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001955 0.077008 0.043087 0.009895 +1 0.001955 0.000001 0.075567 0.041646 0.008454 +2 0.077008 0.075567 0.000001 0.083829 0.077597 +3 0.043087 0.041646 0.083829 0.000001 0.043675 +4 0.009895 0.008454 0.077597 0.043675 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000139_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/OG0000139_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7acbe78a27ea2c08c5a216ef4b0232e711c751bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000139_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 0.10746072 Before NNI: tree length is 0.10746075 + 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/OG0000141_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/OG0000141_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b099db223d828a69cb7e38c2fe90bdfa8225299 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.085677 0.089136 0.057024 0.042734 +1 0.085677 0.000001 0.034960 0.053617 0.079001 +2 0.089136 0.034960 0.000001 0.057076 0.082460 +3 0.057024 0.053617 0.057076 0.000001 0.050348 +4 0.042734 0.079001 0.082460 0.050348 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000142_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/OG0000142_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fe03cda60aa63b5c5d9c3b70715410a0ea647730 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000142_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013635 0.221096 0.342274 0.012476 +1 0.013635 0.000001 0.212467 0.333644 0.007680 +2 0.221096 0.212467 0.000001 0.344100 0.215142 +3 0.342274 0.333644 0.344100 0.000001 0.336319 +4 0.012476 0.007680 0.215142 0.336319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000142_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/OG0000142_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7e8de3e58d3d0f566c985ecc04de8ef39c4b60bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000142_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 0.45949839 Before NNI: tree length is 0.45949837 + 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/OG0000143_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/OG0000143_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0eeb401ee2588439f5308882111dce0dd0bdbabd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000143_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 0.54066920 Before NNI: tree length is 0.54066925 + 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/OG0000145_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/OG0000145_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0a48930ea1e714ad5e3e1a3b31cf626ecfe2733d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000145_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017661 0.000001 0.585434 0.015873 +1 0.017661 0.000001 1.197980 0.590514 0.031546 +2 0.000001 1.197980 0.000001 1.390936 1.206785 +3 0.585434 0.590514 1.390936 0.000001 0.599319 +4 0.015873 0.031546 1.206785 0.599319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000146_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/OG0000146_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf0450dc30780e9380ec797178a1bb3536c191ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000146_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014813 0.000001 0.343036 0.015940 +1 0.014813 0.000001 0.749031 0.344172 0.009315 +2 0.000001 0.749031 0.000001 0.675913 0.750158 +3 0.343036 0.344172 0.675913 0.000001 0.345299 +4 0.015940 0.009315 0.750158 0.345299 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000146_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/OG0000146_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae6b0bf4d58898a897924ea366f93bde5f3d33fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000146_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 0.65645083 Before NNI: tree length is 0.62300575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.65202391 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000149_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/OG0000149_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8602e703d51066176aef0f33b8cea8edea4b9ce1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.226021 0.224809 0.002202 +1 0.000001 0.000001 0.226021 0.224809 0.002202 +2 0.226021 0.226021 0.000001 0.150345 0.226209 +3 0.224809 0.224809 0.150345 0.000001 0.224997 +4 0.002202 0.002202 0.226209 0.224997 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000149_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/OG0000149_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8347abbd0d8459e07567ee685b303da77cdbb029 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000149_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 0.30178300 Before NNI: tree length is 0.30178300 + 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/OG0000150_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/OG0000150_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0bd6a09b8f589eccaf1fb747dadeb0fcc4730ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000150_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 0.49730611 Before NNI: tree length is 0.49730612 + 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/OG0000151_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/OG0000151_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f7980a351271ee4a2ca48e97386a8e436e6acd72 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000151_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012513 0.115911 0.974754 0.026160 +1 0.012513 0.000001 0.121905 0.980748 0.032154 +2 0.115911 0.121905 0.000001 0.992620 0.116410 +3 0.974754 0.980748 0.992620 0.000001 0.975252 +4 0.026160 0.032154 0.116410 0.975252 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000153_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/OG0000153_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..db65bbf871124b04dd7824e0f3e0e7f84ba6c085 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000153_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.104826 0.210301 0.182308 0.102180 +1 0.104826 0.000001 0.105785 0.556954 0.011371 +2 0.210301 0.105785 0.000001 0.662429 0.116846 +3 0.182308 0.556954 0.662429 0.000001 0.554308 +4 0.102180 0.011371 0.116846 0.554308 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..bb686bd0ac258ce66c36f4edb3ad464bd2eed761 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005436 0.328536 0.021263 0.000001 +1 0.005436 0.000001 0.331607 0.024334 0.005436 +2 0.328536 0.331607 0.000001 0.258938 0.328536 +3 0.021263 0.024334 0.258938 0.000001 0.021263 +4 0.000001 0.005436 0.328536 0.021263 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a43c5ec2027c4e8aa391370235f7fb80fab5a61 --- /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_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 0.27821009 Before NNI: tree length is 0.27821012 + 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/OG0000158_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/OG0000158_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..502b1e5d33ae4a5d192b456c9e7ff896436d7c78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000158_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.201987 0.803098 0.586882 0.458228 +1 0.201987 0.000001 0.628128 0.384895 0.283258 +2 0.803098 0.628128 0.000001 0.841027 0.344869 +3 0.586882 0.384895 0.841027 0.000001 0.496158 +4 0.458228 0.283258 0.344869 0.496158 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000158_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/OG0000158_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4153c7e068332ab643e10448de005261ea40213a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000158_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 1.12225758 Before NNI: tree length is 1.12225750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99973657 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000159_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/OG0000159_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d202e8818a3ff9bc11c8ae8a852d36767d3595c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000159_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.121116 0.417561 0.677750 0.016950 +1 1.121116 0.000001 1.154604 1.273487 1.122996 +2 0.417561 1.154604 0.000001 0.711238 0.419442 +3 0.677750 1.273487 0.711238 0.000001 0.679631 +4 0.016950 1.122996 0.419442 0.679631 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000161_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/OG0000161_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..97fbf27ad5c18aa5c645ebb74f3faf10026cbeb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000161_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 0.08658025 Before NNI: tree length is 0.08658025 + 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/OG0000163_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/OG0000163_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ecfa388768e858797ce66d49d9c455aa8b3ff06 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000163_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 0.30351000 Before NNI: tree length is 0.30351000 + 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/OG0000167_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/OG0000167_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f39cbef9da5bb089b6b3ae5b773c15f3dd96f119 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025593 0.133376 0.301481 0.006065 +1 0.025593 0.000001 0.135212 0.303317 0.027945 +2 0.133376 0.135212 0.000001 0.285101 0.135728 +3 0.301481 0.303317 0.285101 0.000001 0.303832 +4 0.006065 0.027945 0.135728 0.303832 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000169_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/OG0000169_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..daf19d4da363dd53815549598f12f27a04ef05d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000169_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.264590 0.032004 0.142065 0.156399 +1 0.264590 0.000001 0.267296 0.377356 0.391690 +2 0.032004 0.267296 0.000001 0.137214 0.151548 +3 0.142065 0.377356 0.137214 0.000001 0.230646 +4 0.156399 0.391690 0.151548 0.230646 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000171_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/OG0000171_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dacdd141d0438bc4747f110471dd52c620102c39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000171_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 0.61165473 Before NNI: tree length is 0.61165475 + 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/OG0000175_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/OG0000175_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..34ca6af73db6ffe4848d6abd482fd6f322e7d3b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000175_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 0.17009050 Before NNI: tree length is 0.17009050 + 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/OG0000177_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/OG0000177_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..583d5249bdd1dec93ddb10fef81f35527f3ad108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000177_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.247623 0.260773 0.008253 +1 0.000001 0.000001 0.247623 0.260773 0.008253 +2 0.247623 0.247623 0.000001 0.302728 0.246734 +3 0.260773 0.260773 0.302728 0.000001 0.259884 +4 0.008253 0.008253 0.246734 0.259884 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000177_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/OG0000177_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af924e490021aee021bcae79d43ee32dc581077a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000177_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 0.40924450 Before NNI: tree length is 0.40924450 + 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/OG0000179_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/OG0000179_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..10c9e1d917e21a1545fda21f019afbe3bf674fda --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008779 0.079854 0.133963 0.007897 +1 0.008779 0.000001 0.077755 0.131864 0.001460 +2 0.079854 0.077755 0.000001 0.141647 0.076872 +3 0.133963 0.131864 0.141647 0.000001 0.130981 +4 0.007897 0.001460 0.076872 0.130981 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000182_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/OG0000182_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6854c2912417d9627e594b2623182b932dfe0884 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000182_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019144 0.153019 0.362772 0.007095 +1 0.019144 0.000001 0.161757 0.371511 0.015834 +2 0.153019 0.161757 0.000001 0.358506 0.146419 +3 0.362772 0.371511 0.358506 0.000001 0.356173 +4 0.007095 0.015834 0.146419 0.356173 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000183_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/OG0000183_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d4d605eac6be1d77f72d9e34d62f169864d777d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000183_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.066190 0.390411 1.015034 0.006441 +1 0.066190 0.000001 0.415086 1.039709 0.064502 +2 0.390411 0.415086 0.000001 0.904902 0.388723 +3 1.015034 1.039709 0.904902 0.000001 1.013346 +4 0.006441 0.064502 0.388723 1.013346 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000184_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/OG0000184_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a66e69f952416379e42771bda21c28a09e1df729 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000184_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.061023 0.053956 0.000001 +1 0.000001 0.000001 0.061023 0.053956 0.000001 +2 0.061023 0.061023 0.000001 0.047100 0.061023 +3 0.053956 0.053956 0.047100 0.000001 0.053956 +4 0.000001 0.000001 0.061023 0.053956 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000186_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/OG0000186_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c5b6117d8b9376b05761a14a55df34f513e298c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000186_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013038 0.148921 0.322991 0.011577 +1 0.013038 0.000001 0.143116 0.317185 0.005772 +2 0.148921 0.143116 0.000001 0.331095 0.137344 +3 0.322991 0.317185 0.331095 0.000001 0.311414 +4 0.011577 0.005772 0.137344 0.311414 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000187_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/OG0000187_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d16239a55a65ef888071aa9849566d5fe5e96346 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000187_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007032 0.094366 0.155008 0.011863 +1 0.007032 0.000001 0.090941 0.151582 0.009548 +2 0.094366 0.090941 0.000001 0.160519 0.096882 +3 0.155008 0.151582 0.160519 0.000001 0.157523 +4 0.011863 0.009548 0.096882 0.157523 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000189_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/OG0000189_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..280350ee273e5bb19b0907542291ddc0fe6a773d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042538 0.159444 0.416813 0.049357 +1 0.042538 0.000001 0.163616 0.420985 0.030128 +2 0.159444 0.163616 0.000001 0.418289 0.170435 +3 0.416813 0.420985 0.418289 0.000001 0.427804 +4 0.049357 0.030128 0.170435 0.427804 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000189_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/OG0000189_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d54cd4d69a063b6aa68be728b8e372eb8edbd398 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000189_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 0.53910150 Before NNI: tree length is 0.53910150 + 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/OG0000190_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/OG0000190_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f5c4db3ff805245748c110dba6d6aeae0036c3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000190_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000179 0.029552 0.360649 0.017480 +1 0.000179 0.000001 0.029374 0.360470 0.017301 +2 0.029552 0.029374 0.000001 0.369112 0.031010 +3 0.360649 0.360470 0.369112 0.000001 0.362106 +4 0.017480 0.017301 0.031010 0.362106 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000190_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/OG0000190_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d428ed624a51ab63842a0897c5db75d3ed1557c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000190_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 0.38912533 Before NNI: tree length is 0.38912537 + 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/OG0000192_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/OG0000192_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2144dacc1dba93931d6bdaa5e06ea0199fa99da3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip_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 0.51730137 Before NNI: tree length is 0.51730137 + 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/OG0000200_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/OG0000200_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d486d2e8719cfbf25b2314047169105f1fcaaedd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000200_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013628 0.084090 0.157818 0.015035 +1 0.013628 0.000001 0.081133 0.154861 0.001407 +2 0.084090 0.081133 0.000001 0.137007 0.082540 +3 0.157818 0.154861 0.137007 0.000001 0.156268 +4 0.015035 0.001407 0.082540 0.156268 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000200_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/OG0000200_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..55dc430255d842bdd6fb851f5e93da5c481575ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000200_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 0.19620000 Before NNI: tree length is 0.19620000 + 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/OG0000203_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/OG0000203_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..33242c2ef6955925b1549c884b925455bb916cd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000203_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 0.56261950 Before NNI: tree length is 0.56261950 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..77dd6eacd8c4025f346a52c42dc05c90a42d3abc --- /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_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 0.62400728 Before NNI: tree length is 0.62400725 + 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/OG0000206_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/OG0000206_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..de6145ca59d8ed9b9d9878babb1294ca2fd6e279 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000206_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 2.39801217 Before NNI: tree length is 2.39801225 + 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/OG0000208_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/OG0000208_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..97164d1b90ad289b6f6a3aef43aafa34d9dfb4f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000208_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 0.17032125 Before NNI: tree length is 0.17032125 + 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/OG0000209_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/OG0000209_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a8e892a4026074bf400e5014d1c6e717dc8d5ada --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000209_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003823 0.312732 0.374248 0.000439 +1 0.003823 0.000001 0.316555 0.378071 0.004262 +2 0.312732 0.316555 0.000001 0.420753 0.312292 +3 0.374248 0.378071 0.420753 0.000001 0.373808 +4 0.000439 0.004262 0.312292 0.373808 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000212_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/OG0000212_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..906a2da26dbbf7ae6e2be27b43d4a8b010bce125 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000212_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031195 0.249735 0.423085 0.007770 +1 0.031195 0.000001 0.255049 0.428399 0.030930 +2 0.249735 0.255049 0.000001 0.368834 0.249470 +3 0.423085 0.428399 0.368834 0.000001 0.422820 +4 0.007770 0.030930 0.249470 0.422820 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000212_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/OG0000212_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b292203c9881d32a17a6e6f6584643045801c1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000212_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 0.54283400 Before NNI: tree length is 0.54283400 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..748b633a358be33aa7183dffabead7b346589b1f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009091 0.034462 0.073033 0.000001 +1 0.009091 0.000001 0.042198 0.080769 0.009091 +2 0.034462 0.042198 0.000001 0.075115 0.034462 +3 0.073033 0.080769 0.075115 0.000001 0.073033 +4 0.000001 0.009091 0.034462 0.073033 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000214_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/OG0000214_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5f589ae827881b99631e955775a1529c97036c4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000214_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016323 0.451032 0.349815 0.012750 +1 0.016323 0.000001 0.459369 0.358152 0.011599 +2 0.451032 0.459369 0.000001 0.290362 0.455796 +3 0.349815 0.358152 0.290362 0.000001 0.354579 +4 0.012750 0.011599 0.455796 0.354579 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..40f3882e734175c3541283ab21d267b276c56a62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip_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 0.22727550 Before NNI: tree length is 0.22727550 + 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/OG0000216_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/OG0000216_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cfacc827d52294652c310aa43e1c4444b6314f12 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000216_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 0.27402863 Before NNI: tree length is 0.27402862 + 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/OG0000217_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/OG0000217_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..172e26ef86eb8bca3f7968533f5ab60671ed9969 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000217_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 0.35180150 Before NNI: tree length is 0.35180150 + 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/OG0000218_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/OG0000218_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e72606f25f57d358cabf1f4efdf0a22b9f6d967a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000218_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 0.92139587 Before NNI: tree length is 0.92139587 + 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/OG0000220_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/OG0000220_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc75571937cd863610f391e7ca014ffb45e0fb10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.070415 0.644789 0.512029 0.040764 +1 0.070415 0.000001 0.630152 0.497393 0.073795 +2 0.644789 0.630152 0.000001 0.638618 0.648169 +3 0.512029 0.497393 0.638618 0.000001 0.515409 +4 0.040764 0.073795 0.648169 0.515409 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000220_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/OG0000220_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac4e7a83054503b11aa86a144fc73c43590a659e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000220_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 0.94767927 Before NNI: tree length is 0.94767925 + 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/OG0000221_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/OG0000221_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..541784175363929a0d49f5b6c781eac3f14b9500 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000221_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 0.09076150 Before NNI: tree length is 0.09076150 + 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/OG0000223_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/OG0000223_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..689348bf49016d49e3c20919bce3c3f5122ccff2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000223_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.123898 0.163446 0.004902 +1 0.000001 0.000001 0.123898 0.163446 0.004902 +2 0.123898 0.123898 0.000001 0.210392 0.123831 +3 0.163446 0.163446 0.210392 0.000001 0.163379 +4 0.004902 0.004902 0.123831 0.163379 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000224_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/OG0000224_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..071c469c4a8c3c3ae07990779414dfebc28dbfb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000224_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018748 0.051643 0.237014 0.018072 +1 0.018748 0.000001 0.063328 0.248698 0.020493 +2 0.051643 0.063328 0.000001 0.245145 0.062651 +3 0.237014 0.248698 0.245145 0.000001 0.248022 +4 0.018072 0.020493 0.062651 0.248022 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000224_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/OG0000224_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8d9297e42e1dd0a3b9e8376eb0dae2ac7dc5bec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000224_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 0.29202559 Before NNI: tree length is 0.29202562 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..683190e54a6b18e419f083a4236a07d8245f531a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037239 0.248069 0.478582 0.037239 +1 0.037239 0.000001 0.243675 0.474188 0.000001 +2 0.248069 0.243675 0.000001 0.544478 0.243675 +3 0.478582 0.474188 0.544478 0.000001 0.474188 +4 0.037239 0.000001 0.243675 0.474188 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000226_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/OG0000226_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..212af95b32411eaafe23761702bc9f59512e27bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000226_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052599 0.198233 0.571201 0.052599 +1 0.052599 0.000001 0.217689 0.590657 0.000001 +2 0.198233 0.217689 0.000001 0.547855 0.217689 +3 0.571201 0.590657 0.547855 0.000001 0.590657 +4 0.052599 0.000001 0.217689 0.590657 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000227_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/OG0000227_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d3631392f12fad30e2aae7b6582b5e23a6cabe84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000227_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006051 0.118215 0.378879 0.006051 +1 0.006051 0.000001 0.123831 0.384496 0.000001 +2 0.118215 0.123831 0.000001 0.353688 0.123831 +3 0.378879 0.384496 0.353688 0.000001 0.384496 +4 0.006051 0.000001 0.123831 0.384496 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000228_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/OG0000228_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1c95b35db6ac901c953482f8b84286d3f124002 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000228_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 0.85073625 Before NNI: tree length is 0.85073625 + 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/OG0000229_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/OG0000229_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..226b3940614d1037edffd43e7a0e5603d790ea01 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000229_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 0.32581400 Before NNI: tree length is 0.32581400 + 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/OG0000230_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/OG0000230_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a0f871d074df1d75e7346d5d3a58eccde8b60552 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000230_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033560 0.186718 0.552957 0.033560 +1 0.033560 0.000001 0.193753 0.559992 0.000001 +2 0.186718 0.193753 0.000001 0.607140 0.193753 +3 0.552957 0.559992 0.607140 0.000001 0.559992 +4 0.033560 0.000001 0.193753 0.559992 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000230_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/OG0000230_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f77b20cec3e37da321a7d4129acee6757fb19de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000230_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 0.69370550 Before NNI: tree length is 0.69370550 + 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/OG0000231_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/OG0000231_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e5d6155f8f5096a381fec01ded06a77e14b8065 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip_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 0.57564162 Before NNI: tree length is 0.57564162 + 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/OG0000233_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/OG0000233_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8741177f6a7790b598777618d59f4e5eb8e74583 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000233_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030665 0.226211 0.429634 0.030665 +1 0.030665 0.000001 0.245136 0.448560 0.000001 +2 0.226211 0.245136 0.000001 0.446390 0.245136 +3 0.429634 0.448560 0.446390 0.000001 0.448560 +4 0.030665 0.000001 0.245136 0.448560 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000233_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/OG0000233_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f837de247b6ef8cfe1f8e11495cba8b99da4820e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000233_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 0.57591329 Before NNI: tree length is 0.57591325 + 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/OG0000235_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/OG0000235_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..371e63a5d77abab33dcf204ced0aa8b263b9bd1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.301826 0.161670 0.000001 +1 0.000001 0.000001 0.301826 0.161670 0.000001 +2 0.301826 0.301826 0.000001 0.268739 0.301826 +3 0.161670 0.161670 0.268739 0.000001 0.161670 +4 0.000001 0.000001 0.301826 0.161670 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000236_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/OG0000236_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d776f576546e057b545888529fbec2fa68ae23cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000236_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010018 0.042943 0.044487 0.000001 +1 0.010018 0.000001 0.042363 0.043907 0.010018 +2 0.042943 0.042363 0.000001 0.016883 0.042943 +3 0.044487 0.043907 0.016883 0.000001 0.044487 +4 0.000001 0.010018 0.042943 0.044487 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000236_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/OG0000236_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa663938bf767adc05577d4c13abd0152d7ad2bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000236_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 0.05687600 Before NNI: tree length is 0.05687600 + 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/OG0000240_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/OG0000240_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e04f24afdb2c2b4c4c83b9cb0c4b2780d74a62d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000240_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013219 0.305310 0.250685 0.021652 +1 0.013219 0.000001 0.295612 0.240986 0.011954 +2 0.305310 0.295612 0.000001 0.288494 0.297590 +3 0.250685 0.240986 0.288494 0.000001 0.242965 +4 0.021652 0.011954 0.297590 0.242965 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000242_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/OG0000242_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..401175552a666091fbfbdd834d75ba85d483653c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000242_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006849 0.047543 0.107173 0.004590 +1 0.006849 0.000001 0.048146 0.107776 0.009476 +2 0.047543 0.048146 0.000001 0.121503 0.050169 +3 0.107173 0.107776 0.121503 0.000001 0.109799 +4 0.004590 0.009476 0.050169 0.109799 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c535d66c6aeeb1f267057dc615c451a9fc5b477 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_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 0.27575050 Before NNI: tree length is 0.27575050 + 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/OG0000248_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/OG0000248_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c998c43439a11894232380654001bdcf03c3caf9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000248_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.056795 0.386497 0.807134 0.067757 +1 0.056795 0.000001 0.380755 0.801392 0.047574 +2 0.386497 0.380755 0.000001 0.931921 0.391717 +3 0.807134 0.801392 0.931921 0.000001 0.812354 +4 0.067757 0.047574 0.391717 0.812354 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000249_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/OG0000249_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dac24211f87c93738a0a68e9c0949f7f6b986a13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000249_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 0.36296239 Before NNI: tree length is 0.36296238 + 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/OG0000253_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/OG0000253_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..002d38449ec22e40faf0fdc0fb787179a5573457 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000253_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.050619 0.061105 0.004861 +1 0.000001 0.000001 0.050619 0.061105 0.004861 +2 0.050619 0.050619 0.000001 0.029501 0.053054 +3 0.061105 0.061105 0.029501 0.000001 0.063540 +4 0.004861 0.004861 0.053054 0.063540 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000253_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/OG0000253_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f9acaacc3be8e78ac1bb90cd1d505702e63ad626 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000253_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 0.07426100 Before NNI: tree length is 0.07426100 + 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/OG0000254_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/OG0000254_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea5db4c8da859ff8ac69848fe6654f39d2e03daf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000254_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 0.78872991 Before NNI: tree length is 0.78872987 + 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/OG0000256_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/OG0000256_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed4ac13a82e304399c63a5c42dd64581809c754 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000256_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 0.26722500 Before NNI: tree length is 0.26722500 + 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/OG0000257_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/OG0000257_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a22102764b20924668faa81f4a57cee34ac8808c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000257_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 0.30733973 Before NNI: tree length is 0.30733975 + 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/OG0000258_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/OG0000258_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c831d0b53d0cc24cfa75fe5dbf05a9ab858d9042 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000258_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049243 0.249003 0.512278 0.035882 +1 0.049243 0.000001 0.234839 0.498114 0.049168 +2 0.249003 0.234839 0.000001 0.506162 0.248928 +3 0.512278 0.498114 0.506162 0.000001 0.512203 +4 0.035882 0.049168 0.248928 0.512203 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000258_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/OG0000258_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5ca549511b1844c39ef85f855ad86391b7602e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000258_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 0.66916450 Before NNI: tree length is 0.66916450 + 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/OG0000259_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/OG0000259_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..76024377c557947216d9d4a6842f82fbe3a1592a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000259_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002448 0.102943 0.225357 0.002448 +1 0.002448 0.000001 0.103708 0.226123 0.000001 +2 0.102943 0.103708 0.000001 0.228180 0.103708 +3 0.225357 0.226123 0.228180 0.000001 0.226123 +4 0.002448 0.000001 0.103708 0.226123 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000259_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/OG0000259_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3cbe2790b514b154d134a7de3131748ebd9c9696 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000259_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 0.27984729 Before NNI: tree length is 0.27984725 + 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/OG0000273_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/OG0000273_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea9f403c908ba5c08d9ff3d5ee451f2d5e612182 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000273_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 0.15794000 Before NNI: tree length is 0.15794000 + 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/OG0000276_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/OG0000276_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d6ab893bd6e8559410a676de2b8e58f3d46116e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000276_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 0.39890300 Before NNI: tree length is 0.39890300 + 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/OG0000277_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/OG0000277_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88d53f11a19642ffd78cf95422548dac63e5c0fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007988 0.069988 0.227331 0.010288 +1 0.007988 0.000001 0.074360 0.231703 0.005792 +2 0.069988 0.074360 0.000001 0.208938 0.076659 +3 0.227331 0.231703 0.208938 0.000001 0.234002 +4 0.010288 0.005792 0.076659 0.234002 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000278_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/OG0000278_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8833099a61d81c94d6327e0e156e7c0e5731f9a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000278_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 0.10664700 Before NNI: tree length is 0.10664700 + 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/OG0000279_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/OG0000279_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..64ac92d2f60e1db601b6078dc02fdc2a1ac0c622 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000279_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032901 0.112748 0.533527 0.032901 +1 0.032901 0.000001 0.080329 0.501109 0.000001 +2 0.112748 0.080329 0.000001 0.532216 0.080329 +3 0.533527 0.501109 0.532216 0.000001 0.501109 +4 0.032901 0.000001 0.080329 0.501109 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000280_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/OG0000280_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0805830cbf5a7bbb07518f39c8996a06169aa14d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000280_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 0.12988850 Before NNI: tree length is 0.12988850 + 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/OG0000281_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/OG0000281_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..21a24b059da564b813d45bbcff077989eb5b799a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004423 0.155488 0.397645 0.003731 +1 0.004423 0.000001 0.157520 0.399677 0.001273 +2 0.155488 0.157520 0.000001 0.423593 0.156828 +3 0.397645 0.399677 0.423593 0.000001 0.398985 +4 0.003731 0.001273 0.156828 0.398985 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000283_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/OG0000283_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a816b47535432822e99c2a0f837f3017a9f18850 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000283_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 0.14722422 Before NNI: tree length is 0.14722425 + 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/OG0000284_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/OG0000284_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b31132426f32d68e784c31246f6072d43a997956 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000284_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.055632 0.140319 0.000001 +1 0.000001 0.000001 0.055632 0.140319 0.000001 +2 0.055632 0.055632 0.000001 0.142659 0.055632 +3 0.140319 0.140319 0.142659 0.000001 0.140319 +4 0.000001 0.000001 0.055632 0.140319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000284_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/OG0000284_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8dcfb5785ed464db661e3a1148b63b493f930c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000284_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 0.16930600 Before NNI: tree length is 0.16930600 + 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/OG0000285_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/OG0000285_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d461be4e7a675776951c83b6b2862110866cca5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000285_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 0.49035525 Before NNI: tree length is 0.49035525 + 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/OG0000286_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/OG0000286_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..553abb0b4e20a10a025602ca313951da0856c9b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000286_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 1.55599617 Before NNI: tree length is 1.55599613 + 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/OG0000287_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/OG0000287_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3dcbddac0945c107a73bcf1d7efcae111442b13b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000287_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028404 0.119881 1.286544 0.141489 +1 0.028404 0.000001 0.135748 1.260529 0.157355 +2 0.119881 0.135748 0.000001 1.393889 0.167461 +3 1.286544 1.260529 1.393889 0.000001 1.415496 +4 0.141489 0.157355 0.167461 1.415496 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000287_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/OG0000287_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8cc8d40fbef19b1b250b7158e7779b955a5f544 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000287_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 1.49588549 Before NNI: tree length is 1.49588550 + 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/OG0000288_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/OG0000288_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f61655129db26b1e4b7459a0d5c85178cfbd2362 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003507 0.021084 0.023496 0.003485 +1 0.003507 0.000001 0.024591 0.027003 0.006992 +2 0.021084 0.024591 0.000001 0.030571 0.022222 +3 0.023496 0.027003 0.030571 0.000001 0.024634 +4 0.003485 0.006992 0.022222 0.024634 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000289_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/OG0000289_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..08cb21a042a586deb3b0255bd18f7e79238c0035 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000289_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 0.15088345 Before NNI: tree length is 0.15088350 + 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/OG0000294_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/OG0000294_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fb0862ba03ac92ee6b10fb532c0bb7add07218aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000294_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031210 0.036438 0.124456 0.029218 +1 0.031210 0.000001 0.044024 0.132041 0.017941 +2 0.036438 0.044024 0.000001 0.127660 0.042032 +3 0.124456 0.132041 0.127660 0.000001 0.130049 +4 0.029218 0.017941 0.042032 0.130049 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000296_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/OG0000296_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f13c9767f87534c0f8ac6c39c4c2acc0c437357 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000296_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001999 0.009119 0.018619 0.000001 +1 0.001999 0.000001 0.009362 0.018862 0.001999 +2 0.009119 0.009362 0.000001 0.024292 0.009119 +3 0.018619 0.018862 0.024292 0.000001 0.018619 +4 0.000001 0.001999 0.009119 0.018619 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000297_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/OG0000297_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..24552fcd93d10de68edf9b50b9f80f7292cdeb6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000297_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016690 0.051047 0.124571 0.013021 +1 0.016690 0.000001 0.035732 0.126327 0.005248 +2 0.051047 0.035732 0.000001 0.160684 0.039606 +3 0.124571 0.126327 0.160684 0.000001 0.122658 +4 0.013021 0.005248 0.039606 0.122658 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000298_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/OG0000298_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..834bc65b65a01558022aedf958781e033cbe3735 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000298_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 0.03214600 Before NNI: tree length is 0.03214600 + 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/OG0000299_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/OG0000299_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7851b35f0dd8155b0436921c60dc4b60a853a338 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000299_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 0.09960100 Before NNI: tree length is 0.09960100 + 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/OG0000301_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/OG0000301_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dfc3e5194ba33ab8b1142f7f90224ddad652f584 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000301_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061753 0.188793 0.061623 0.061753 +1 0.061753 0.000001 0.196648 0.069478 0.000001 +2 0.188793 0.196648 0.000001 0.172905 0.196648 +3 0.061623 0.069478 0.172905 0.000001 0.069478 +4 0.061753 0.000001 0.196648 0.069478 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000303_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/OG0000303_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bd3ab1ba9a915ed0f65dbb009e35618ff9f5bd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000303_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 0.29438016 Before NNI: tree length is 0.29438012 + 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/OG0000304_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/OG0000304_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1422722a33f958a1632ce0a2642a8c8d1a3be800 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000304_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 0.29731550 Before NNI: tree length is 0.29731550 + 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/OG0000310_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/OG0000310_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..948896fa22f75d733ba000182de07459e70ab7ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000310_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 0.15072550 Before NNI: tree length is 0.15072550 + 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/OG0000311_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/OG0000311_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f2cc042a37d38179fcf6d6f6a42dd7d3ff3a24c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000311_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 0.13248900 Before NNI: tree length is 0.13248900 + 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/OG0000312_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/OG0000312_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..20a1cffa98e5fd01b1667e0e67f18336be2c8f73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000312_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061024 0.552960 0.535203 0.057302 +1 0.061024 0.000001 0.562142 0.544385 0.055375 +2 0.552960 0.562142 0.000001 0.505989 0.558420 +3 0.535203 0.544385 0.505989 0.000001 0.540663 +4 0.057302 0.055375 0.558420 0.540663 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000314_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/OG0000314_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8b3ee5b21498602874eb6e646594eb537c8c0523 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000314_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030795 0.603819 1.412559 0.030795 +1 0.030795 0.000001 0.608888 1.417627 0.000001 +2 0.603819 0.608888 0.000001 1.336222 0.608888 +3 1.412559 1.417627 1.336222 0.000001 1.417627 +4 0.030795 0.000001 0.608888 1.417627 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a4f1e3d88c2d07c9b1eec0f6bf318c2bbe02d020 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.031958 0.130195 0.003093 +1 0.000001 0.000001 0.031958 0.130195 0.003093 +2 0.031958 0.031958 0.000001 0.116539 0.029423 +3 0.130195 0.130195 0.116539 0.000001 0.127661 +4 0.003093 0.003093 0.029423 0.127661 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000317_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/OG0000317_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..032880335c868744ee2ec1cff3e52d5191916686 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000317_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039267 0.357446 0.706067 0.063540 +1 0.039267 0.000001 0.374479 0.723100 0.040928 +2 0.357446 0.374479 0.000001 0.662171 0.398752 +3 0.706067 0.723100 0.662171 0.000001 0.747373 +4 0.063540 0.040928 0.398752 0.747373 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000317_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/OG0000317_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d96e8801b4fb7e1c4c48ba5f779c976798882c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000317_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 0.92359250 Before NNI: tree length is 0.92359250 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..2cf09d83a875b05f3456b16ae267fd01bf8e3935 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034112 0.192344 0.072654 0.039562 +1 0.034112 0.000001 0.175253 0.055563 0.023459 +2 0.192344 0.175253 0.000001 0.205919 0.181690 +3 0.072654 0.055563 0.205919 0.000001 0.062001 +4 0.039562 0.023459 0.181690 0.062001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000325_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/OG0000325_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fc3b6841d7952de128ec485521d85f9183388d52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000325_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084082 0.493277 1.300351 0.046819 +1 0.084082 0.000001 0.457275 1.264348 0.052516 +2 0.493277 0.457275 0.000001 1.271304 0.461712 +3 1.300351 1.264348 1.271304 0.000001 1.268785 +4 0.046819 0.052516 0.461712 1.268785 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000326_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/OG0000326_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..15b32f362e8fe89090d4bf8d90ae2008b00c5a16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000326_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030651 0.146334 0.278589 0.035464 +1 0.030651 0.000001 0.156155 0.288410 0.008451 +2 0.146334 0.156155 0.000001 0.260380 0.160968 +3 0.278589 0.288410 0.260380 0.000001 0.293222 +4 0.035464 0.008451 0.160968 0.293222 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000326_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/OG0000326_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2faeb0058a318be64a5baa48e57b316e94620a19 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000326_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 0.36951935 Before NNI: tree length is 0.36951937 + 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/OG0000327_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/OG0000327_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f9576cac56bbb905e25774af7f566f771cca6ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000327_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027319 0.154104 0.875204 0.029977 +1 0.027319 0.000001 0.147838 0.868938 0.023711 +2 0.154104 0.147838 0.000001 0.862025 0.142340 +3 0.875204 0.868938 0.862025 0.000001 0.863440 +4 0.029977 0.023711 0.142340 0.863440 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000327_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/OG0000327_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..67668f84d450b4d752cde4ce10f307758be712bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000327_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 0.96529950 Before NNI: tree length is 0.96529950 + 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/OG0000329_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/OG0000329_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b82f6ba92e67180235e3fedc0d1d3ccfb2ed348b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000329_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008071 0.111732 0.543618 0.008071 +1 0.008071 0.000001 0.109020 0.540905 0.000001 +2 0.111732 0.109020 0.000001 0.532661 0.109020 +3 0.543618 0.540905 0.532661 0.000001 0.540905 +4 0.008071 0.000001 0.109020 0.540905 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000329_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/OG0000329_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fffd6854c9055cfe38e642fe9dd6335f793e14f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000329_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 0.59668518 Before NNI: tree length is 0.59668525 + 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/OG0000330_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/OG0000330_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ce53cb9bddc68dee6ddfdd55e4ada07422212c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000330_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.085450 0.449851 0.798593 0.065237 +1 0.085450 0.000001 0.458666 0.807408 0.030550 +2 0.449851 0.458666 0.000001 0.808879 0.438453 +3 0.798593 0.807408 0.808879 0.000001 0.787195 +4 0.065237 0.030550 0.438453 0.787195 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000333_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/OG0000333_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8aeacb1dd3a15b2cb678f2c7a7d86c23583bfa8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000333_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 0.78005875 Before NNI: tree length is 0.78005875 + 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/OG0000334_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/OG0000334_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7bf11f1179d2cdf975c522bc6a6a8b578c27f4a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016645 0.085180 0.140238 0.014061 +1 0.016645 0.000001 0.071193 0.126251 0.003212 +2 0.085180 0.071193 0.000001 0.147529 0.071748 +3 0.140238 0.126251 0.147529 0.000001 0.126805 +4 0.014061 0.003212 0.071748 0.126805 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000337_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/OG0000337_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..14b678395342028f53483085275a4b5a72fd99e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000337_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 0.17573875 Before NNI: tree length is 0.17573875 + 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/OG0000339_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/OG0000339_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..164aeef7c7483a6e16b3f7d53da74e3e34284e43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000339_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 0.65592791 Before NNI: tree length is 0.65592788 + 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/OG0000340_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/OG0000340_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7b083b14316bc51debf34fe7ac12ba15fb74678 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000340_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003454 0.253785 0.242727 0.000001 +1 0.003454 0.000001 0.255997 0.244939 0.003454 +2 0.253785 0.255997 0.000001 0.350854 0.253785 +3 0.242727 0.244939 0.350854 0.000001 0.242727 +4 0.000001 0.003454 0.253785 0.242727 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000342_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/OG0000342_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f2d2d350f894bca67b4bd78ab2c550919eb606e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000342_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 0.28340386 Before NNI: tree length is 0.28340388 + 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/OG0000345_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/OG0000345_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8599b0e1fea3f498cb5d0b86fdb8f762e8bc8ed2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000345_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030927 0.136976 0.176652 0.026255 +1 0.030927 0.000001 0.117091 0.156767 0.016736 +2 0.136976 0.117091 0.000001 0.127504 0.122786 +3 0.176652 0.156767 0.127504 0.000001 0.162462 +4 0.026255 0.016736 0.122786 0.162462 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000345_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/OG0000345_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5dd538929d72016236df750ab6c3c428c730064 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000345_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 0.23211925 Before NNI: tree length is 0.23211925 + 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/OG0000346_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/OG0000346_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..35e7ce3598d2152dd9896d3c44d0cd4eea7569e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000346_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.113224 0.373074 0.000001 +1 0.000001 0.000001 0.113224 0.373074 0.000001 +2 0.113224 0.113224 0.000001 0.401442 0.113224 +3 0.373074 0.373074 0.401442 0.000001 0.373074 +4 0.000001 0.000001 0.113224 0.373074 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000350_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/OG0000350_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..79a85dc24fd31907c293537fe8b9b48591dfaa88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000350_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 0.79490425 Before NNI: tree length is 0.79490425 + 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/OG0000351_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/OG0000351_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..aaf3a21d9e5063d07e63160407939641fbb2c6e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000351_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007061 0.089870 0.167277 0.009856 +1 0.007061 0.000001 0.084850 0.162258 0.004836 +2 0.089870 0.084850 0.000001 0.165613 0.081188 +3 0.167277 0.162258 0.165613 0.000001 0.158595 +4 0.009856 0.004836 0.081188 0.158595 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000354_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/OG0000354_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0d35a6aa2872fce8d6b130a29228433f52c32db9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000354_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042982 0.765999 1.047620 0.064207 +1 0.042982 0.000001 0.751385 1.033006 0.049592 +2 0.765999 0.751385 0.000001 1.090782 0.745364 +3 1.047620 1.033006 1.090782 0.000001 1.026986 +4 0.064207 0.049592 0.745364 1.026986 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a73dc4b80b329b01c1f07a7b1fdceb10e7a8c36 --- /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_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 0.69978629 Before NNI: tree length is 0.69978625 + 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/OG0000359_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/OG0000359_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32a2c6963066824b5b250d6de6d7849c7a7bacad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000359_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 0.22464509 Before NNI: tree length is 0.22464513 + 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/OG0000360_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/OG0000360_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c86cf56280dffd6fdd3f12d85090d7363cf2e45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000360_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004695 0.072789 0.126164 0.004695 +1 0.004695 0.000001 0.072789 0.126164 0.000001 +2 0.072789 0.072789 0.000001 0.097767 0.072789 +3 0.126164 0.126164 0.097767 0.000001 0.126164 +4 0.004695 0.000001 0.072789 0.126164 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000360_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/OG0000360_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7d11b5ffd7b5dc82934a077d416686dc853fc33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000360_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 0.15070800 Before NNI: tree length is 0.15070800 + 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/OG0000361_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/OG0000361_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6fadf1061b18d5a627db054591604fac4e81a8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000361_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.039700 0.124166 0.000001 +1 0.000001 0.000001 0.039700 0.124166 0.000001 +2 0.039700 0.039700 0.000001 0.136673 0.039700 +3 0.124166 0.124166 0.136673 0.000001 0.124166 +4 0.000001 0.000001 0.039700 0.124166 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000362_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/OG0000362_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bbf0ef96b2c447fb608b3e8ac1660df9b50f3290 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000362_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008174 0.037744 0.212356 0.013012 +1 0.008174 0.000001 0.045918 0.220530 0.005563 +2 0.037744 0.045918 0.000001 0.215407 0.050756 +3 0.212356 0.220530 0.215407 0.000001 0.225368 +4 0.013012 0.005563 0.050756 0.225368 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000366_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/OG0000366_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..832b0ba632fdbee7edde13deba97352ee6160bfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000366_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 0.23149515 Before NNI: tree length is 0.23149512 + 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/OG0000367_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/OG0000367_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d34857c005650bd8f1db0e4e2ea40de56a04082 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000367_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 0.56233114 Before NNI: tree length is 0.56233113 + 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/OG0000368_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/OG0000368_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad5432f8ef61e7f3fd49e8577c1a1d12d9601e62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000368_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 1.10340000 Before NNI: tree length is 1.10340000 + 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/OG0000369_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/OG0000369_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d278d2916a2bdbdddf9ebe81af905dbe5bd4cfe3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000369_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035374 0.166193 0.295652 0.035374 +1 0.035374 0.000001 0.131305 0.260764 0.000001 +2 0.166193 0.131305 0.000001 0.244564 0.131305 +3 0.295652 0.260764 0.244564 0.000001 0.260764 +4 0.035374 0.000001 0.131305 0.260764 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000369_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/OG0000369_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8656721eebe060b05070e9e025e653b145c511aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000369_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 0.35344800 Before NNI: tree length is 0.35344800 + 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/OG0000373_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/OG0000373_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1cd22688a540b6129b6f3835d368bedee7f75e37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000373_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 0.47135025 Before NNI: tree length is 0.47135025 + 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/OG0000375_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/OG0000375_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7838f51507df3bcad0e691d37a651c10320f1989 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000375_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019130 0.080228 0.184998 0.019130 +1 0.019130 0.000001 0.074251 0.179021 0.000001 +2 0.080228 0.074251 0.000001 0.188847 0.074251 +3 0.184998 0.179021 0.188847 0.000001 0.179021 +4 0.019130 0.000001 0.074251 0.179021 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000376_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/OG0000376_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd851887e4a64c67af655a4d602faf169655d43a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000376_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 0.50246725 Before NNI: tree length is 0.50246725 + 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/OG0000378_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/OG0000378_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..73f86032f25f7e08b7a2fb9d365aa605209bcdd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000378_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 0.39526006 Before NNI: tree length is 0.39526000 + 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/OG0000382_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/OG0000382_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..659d0f91086e1c2f3553b7a757ac4fb93b094c5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000382_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.214783 0.688455 0.000001 +1 0.000001 0.000001 0.214783 0.688455 0.000001 +2 0.214783 0.214783 0.000001 0.726493 0.214783 +3 0.688455 0.688455 0.726493 0.000001 0.688455 +4 0.000001 0.000001 0.214783 0.688455 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000382_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/OG0000382_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..95d37166b468d9a5f0afee80ea7d38ab96b5f1d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000382_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 0.81486650 Before NNI: tree length is 0.81486650 + 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/OG0000384_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/OG0000384_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf3b56019a490d508f22e620cc5f88708cbf940a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000384_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020357 0.214478 0.374703 0.031762 +1 0.020357 0.000001 0.218363 0.378588 0.035647 +2 0.214478 0.218363 0.000001 0.409895 0.224031 +3 0.374703 0.378588 0.409895 0.000001 0.384256 +4 0.031762 0.035647 0.224031 0.384256 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000385_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/OG0000385_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f83c25655afe8dd0c1f9bc00246edc2367c2c6cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000385_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 0.18369125 Before NNI: tree length is 0.18369125 + 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/OG0000386_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/OG0000386_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fe0f90179e824381ce06cec48a8ab8b951cd8ee5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000386_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000080 0.079418 0.118358 0.003281 +1 0.000080 0.000001 0.079498 0.118438 0.003201 +2 0.079418 0.079498 0.000001 0.129761 0.082699 +3 0.118358 0.118438 0.129761 0.000001 0.121639 +4 0.003281 0.003201 0.082699 0.121639 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000390_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/OG0000390_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b240953cf2f6804d8404a4c891186d03b8e4e7b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000390_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 0.61863800 Before NNI: tree length is 0.61863800 + 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/OG0000391_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/OG0000391_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5ccabcd655b678eb01d21c1d9a009233ce042ccb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000391_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032825 0.195338 0.340170 0.012678 +1 0.032825 0.000001 0.178587 0.323419 0.031825 +2 0.195338 0.178587 0.000001 0.336010 0.194338 +3 0.340170 0.323419 0.336010 0.000001 0.339170 +4 0.012678 0.031825 0.194338 0.339170 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000392_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/OG0000392_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ae4a940117495451e023fef1ef1914aca1f3c8b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000392_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.077866 0.359738 0.741399 0.068431 +1 0.077866 0.000001 0.410768 0.792430 0.027322 +2 0.359738 0.410768 0.000001 0.761228 0.401332 +3 0.741399 0.792430 0.761228 0.000001 0.782994 +4 0.068431 0.027322 0.401332 0.782994 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75deba2c4d716db2408759294bc181d684458ced --- /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_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 1.04378280 Before NNI: tree length is 1.04378275 + 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/OG0000394_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/OG0000394_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..68e1307ce72b3ef9cfe982d7374c57c384a522a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000394_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011692 0.117592 0.146295 0.010031 +1 0.011692 0.000001 0.117669 0.146372 0.021722 +2 0.117592 0.117669 0.000001 0.143025 0.127623 +3 0.146295 0.146372 0.143025 0.000001 0.156326 +4 0.010031 0.021722 0.127623 0.156326 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000397_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/OG0000397_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..015980e5b11f2c09753fcce9ee81cdd180ebe66a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000397_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 0.45333550 Before NNI: tree length is 0.45333550 + 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/OG0000398_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/OG0000398_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5d782849c68002caf97019043e73a02c55136a62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000398_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005669 0.097397 0.162796 0.008250 +1 0.005669 0.000001 0.097290 0.162690 0.002581 +2 0.097397 0.097290 0.000001 0.196857 0.099871 +3 0.162796 0.162690 0.196857 0.000001 0.165271 +4 0.008250 0.002581 0.099871 0.165271 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000405_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/OG0000405_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..638fb306be49afe7607e0055017de8d0c93f7507 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000405_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 0.54863200 Before NNI: tree length is 0.54863200 + 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/OG0000406_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/OG0000406_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ff96c8b1f12d89c0669ac584bd3e4f4f18d506e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000406_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.072390 0.138645 0.000001 +1 0.000001 0.000001 0.072390 0.138645 0.000001 +2 0.072390 0.072390 0.000001 0.177457 0.072390 +3 0.138645 0.138645 0.177457 0.000001 0.138645 +4 0.000001 0.000001 0.072390 0.138645 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000408_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/OG0000408_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb2f78e7fa5e90e63469f2b545afa0333ae219ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000408_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 1.19869200 Before NNI: tree length is 1.19869200 + 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/OG0000410_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/OG0000410_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e9a4f2230d1021bcefc7f1018efd8388ec495433 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000410_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.085343 0.410759 0.514240 0.112547 +1 0.085343 0.000001 0.369103 0.472583 0.070890 +2 0.410759 0.369103 0.000001 0.488467 0.365795 +3 0.514240 0.472583 0.488467 0.000001 0.469276 +4 0.112547 0.070890 0.365795 0.469276 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000410_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/OG0000410_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a674b2277de337ef461196267d2156bd78c2ae4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000410_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 0.76236761 Before NNI: tree length is 0.76236762 + 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/OG0000412_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/OG0000412_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..741819782a17d10987323c116c010afe9273d5ff --- /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_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 0.91812975 Before NNI: tree length is 0.91812975 + 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/OG0000413_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/OG0000413_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf09b6b5751632c44bf57506fc13957d39bb407f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000413_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.022368 0.149000 0.000001 +1 0.000001 0.000001 0.022368 0.149000 0.000001 +2 0.022368 0.022368 0.000001 0.166539 0.022368 +3 0.149000 0.149000 0.166539 0.000001 0.149000 +4 0.000001 0.000001 0.022368 0.149000 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000415_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/OG0000415_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a097d55a2dc4c95d585e0794b7fa60c9d9a4117c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000415_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010369 0.086473 0.168568 0.009182 +1 0.010369 0.000001 0.085680 0.167776 0.005484 +2 0.086473 0.085680 0.000001 0.175414 0.084494 +3 0.168568 0.167776 0.175414 0.000001 0.166589 +4 0.009182 0.005484 0.084494 0.166589 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000415_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/OG0000415_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebbae4ab267f8e986c2e75d8d74e1bb72ad3f93c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000415_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 0.22216439 Before NNI: tree length is 0.22216437 + 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/OG0000416_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/OG0000416_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb3bff6cf29af44ed2d7332b4b5f96c457d34339 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012312 0.030684 0.090494 0.014462 +1 0.012312 0.000001 0.029213 0.089022 0.012990 +2 0.030684 0.029213 0.000001 0.088057 0.026602 +3 0.090494 0.089022 0.088057 0.000001 0.086411 +4 0.014462 0.012990 0.026602 0.086411 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..f9e26f8189dd4335044780396436b5308822e9f9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015352 0.107878 0.028424 0.007429 +1 0.015352 0.000001 0.105383 0.025930 0.009475 +2 0.107878 0.105383 0.000001 0.096042 0.102001 +3 0.028424 0.025930 0.096042 0.000001 0.022547 +4 0.007429 0.009475 0.102001 0.022547 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000424_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/OG0000424_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c898f0fbdc13e0222066d8a5c66e466776df445 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000424_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 0.07269109 Before NNI: tree length is 0.07269112 + 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/OG0000426_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/OG0000426_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..92df4e5287c0ca06f350f8a54826a99e14694cb8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000426_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005120 0.029232 0.415919 0.000001 +1 0.005120 0.000001 0.024112 0.410798 0.005120 +2 0.029232 0.024112 0.000001 0.416938 0.029232 +3 0.415919 0.410798 0.416938 0.000001 0.415919 +4 0.000001 0.005120 0.029232 0.415919 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000426_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/OG0000426_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..07995ea39932fa0cc4bc435bf60e15509bcafe1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000426_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 0.43104483 Before NNI: tree length is 0.43104475 + 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/OG0000428_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/OG0000428_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f24bd35d33155814fd0a976ae3fa1432210fd7eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000428_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 0.39672700 Before NNI: tree length is 0.39672700 + 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/OG0000429_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/OG0000429_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9241d1da26cbbf4ea83439d771357481f8edfef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000429_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006966 0.174631 0.604754 0.018276 +1 0.006966 0.000001 0.174956 0.605079 0.018601 +2 0.174631 0.174956 0.000001 0.592609 0.176341 +3 0.604754 0.605079 0.592609 0.000001 0.606465 +4 0.018276 0.018601 0.176341 0.606465 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000431_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/OG0000431_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..25318f310239f80739272a212b6a05fdb9b83a92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000431_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 0.27685350 Before NNI: tree length is 0.27685350 + 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/OG0000438_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/OG0000438_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6eb1406f1773812a10197bac114bab5186f783a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000438_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 0.27291900 Before NNI: tree length is 0.27291900 + 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/OG0000439_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/OG0000439_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a8949d63056c7def7a05c6bd4cff00204938b49f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036716 0.053586 0.122337 0.039840 +1 0.036716 0.000001 0.044411 0.113161 0.004734 +2 0.053586 0.044411 0.000001 0.115191 0.047535 +3 0.122337 0.113161 0.115191 0.000001 0.116285 +4 0.039840 0.004734 0.047535 0.116285 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000441_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/OG0000441_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..40d4243e6e1e57ad7d0f08923797c8de91e73d1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.064599 0.108963 0.374053 0.053525 +1 0.064599 0.000001 0.072362 0.337452 0.024390 +2 0.108963 0.072362 0.000001 0.334053 0.068753 +3 0.374053 0.337452 0.334053 0.000001 0.333844 +4 0.053525 0.024390 0.068753 0.333844 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000441_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/OG0000441_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18ee42a936ff13cff3df74ad2f46ca614ccd88d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000441_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 0.42919141 Before NNI: tree length is 0.42919137 + 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/OG0000442_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/OG0000442_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7163185d9cf7bad8c240d0cc18a08999fdfca9d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000442_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015940 0.027702 0.384645 0.017884 +1 0.015940 0.000001 0.031414 0.388358 0.015946 +2 0.027702 0.031414 0.000001 0.375859 0.033357 +3 0.384645 0.388358 0.375859 0.000001 0.390301 +4 0.017884 0.015946 0.033357 0.390301 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000442_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/OG0000442_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4504a217f3792c3f1e78c7d817b013cac81122f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000442_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 0.41287408 Before NNI: tree length is 0.41287400 + 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/OG0000443_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/OG0000443_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..972322a9e4cb749a95442cdb94712e79b0249e90 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007620 0.017152 0.420293 0.008097 +1 0.007620 0.000001 0.016460 0.419602 0.010690 +2 0.017152 0.016460 0.000001 0.417212 0.020223 +3 0.420293 0.419602 0.417212 0.000001 0.423364 +4 0.008097 0.010690 0.020223 0.423364 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000446_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/OG0000446_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0d7a37918b00ccb2c4732d51682990e054015399 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000446_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000834 0.013771 0.146648 0.000834 +1 0.000834 0.000001 0.014605 0.147482 0.000001 +2 0.013771 0.014605 0.000001 0.146353 0.014605 +3 0.146648 0.147482 0.146353 0.000001 0.147482 +4 0.000834 0.000001 0.014605 0.147482 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000451_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/OG0000451_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a33bd38d397a02275c69d23c2e7b12ae1305087 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000451_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 0.03965200 Before NNI: tree length is 0.03965200 + 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/OG0000452_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/OG0000452_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b65e2656805ebd9f4b403ae286e9eb4149d35f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000452_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 0.11597624 Before NNI: tree length is 0.11597625 + 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/OG0000453_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/OG0000453_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6d31498d0002547237ddccb49d996baca054aa6 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006226 0.095304 0.202482 0.027978 +1 0.006226 0.000001 0.090757 0.197935 0.023431 +2 0.095304 0.090757 0.000001 0.201193 0.103838 +3 0.202482 0.197935 0.201193 0.000001 0.211016 +4 0.027978 0.023431 0.103838 0.211016 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000454_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/OG0000454_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2581b29eb3e746cede56f8d7b2b76da5c762f86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000454_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 0.47010555 Before NNI: tree length is 0.47010550 + 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/OG0000455_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/OG0000455_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0edb2de8e86e656ec6d1503714d414b4fa53edc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000455_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.202742 0.409370 0.047020 +1 0.000001 0.000001 0.202742 0.409370 0.047020 +2 0.202742 0.202742 0.000001 0.422634 0.228231 +3 0.409370 0.409370 0.422634 0.000001 0.434859 +4 0.047020 0.047020 0.228231 0.434859 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000455_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/OG0000455_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c19a742414e4d5ebf82d721163c828df8f8fa66b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000455_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 0.55362800 Before NNI: tree length is 0.55362800 + 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/OG0000460_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/OG0000460_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9ae9d9b704c121e5c1f2973d5c75df8c4a6d3b51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000460_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041617 0.891524 0.868246 0.133678 +1 0.041617 0.000001 0.892722 0.869444 0.134876 +2 0.891524 0.892722 0.000001 1.051402 0.937997 +3 0.868246 0.869444 1.051402 0.000001 0.914718 +4 0.133678 0.134876 0.937997 0.914718 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000463_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/OG0000463_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3d9fa889a99f543a2ea47b248960d5ea07624dd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000463_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004682 0.018059 0.030038 0.000001 +1 0.004682 0.000001 0.020038 0.032017 0.004682 +2 0.018059 0.020038 0.000001 0.032305 0.018059 +3 0.030038 0.032017 0.032305 0.000001 0.030038 +4 0.000001 0.004682 0.018059 0.030038 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000466_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/OG0000466_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4987adcb5b13d2fd455fe21f6c89397ba5c70547 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000466_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007510 0.066434 0.184325 0.014221 +1 0.007510 0.000001 0.063958 0.181849 0.011745 +2 0.066434 0.063958 0.000001 0.187914 0.060069 +3 0.184325 0.181849 0.187914 0.000001 0.177960 +4 0.014221 0.011745 0.060069 0.177960 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000466_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/OG0000466_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c53cd2e3ba256ebdd445e24a11d79aa76a2219d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000466_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 0.22578150 Before NNI: tree length is 0.22578150 + 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/OG0000468_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/OG0000468_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..05d628349d55cc606d10f330cc0d00e45e306772 --- /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_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 0.53391125 Before NNI: tree length is 0.53391125 + 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/OG0000471_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/OG0000471_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88743d0d7d7df7f72be4d5214e010e7e38b561bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000471_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009242 0.404119 0.228025 0.007683 +1 0.009242 0.000001 0.404837 0.228742 0.006889 +2 0.404119 0.404837 0.000001 0.409721 0.403278 +3 0.228025 0.228742 0.409721 0.000001 0.227184 +4 0.007683 0.006889 0.403278 0.227184 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000471_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/OG0000471_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b338edda397006397e8e1fa8f25fb1c29fe7b4d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000471_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 0.52857739 Before NNI: tree length is 0.52857738 + 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/OG0000472_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/OG0000472_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be0937461b958846773f7b4d851139bd44156242 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000472_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008700 0.170952 0.437132 0.011673 +1 0.008700 0.000001 0.173698 0.439878 0.014419 +2 0.170952 0.173698 0.000001 0.460574 0.160719 +3 0.437132 0.439878 0.460574 0.000001 0.426900 +4 0.011673 0.014419 0.160719 0.426900 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000473_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/OG0000473_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b20c502ba491641b5d586d3adec52c3f1524df59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000473_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 0.23811430 Before NNI: tree length is 0.23811425 + 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/OG0000475_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/OG0000475_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a04d96b834656c98e16782faed58ea2d21d0eb80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000475_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 0.20979690 Before NNI: tree length is 0.20979687 + 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/OG0000476_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/OG0000476_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4219cb547210bfbaf9c3e64a57e14ad50bf7169b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000476_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 0.62852975 Before NNI: tree length is 0.62852975 + 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/OG0000477_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/OG0000477_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9e331f42b5b891e666d929362209dc1eb616abfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000477_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.198697 0.509941 0.825609 0.175350 +1 0.198697 0.000001 0.569475 0.885143 0.056030 +2 0.509941 0.569475 0.000001 0.602662 0.546128 +3 0.825609 0.885143 0.602662 0.000001 0.861796 +4 0.175350 0.056030 0.546128 0.861796 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000477_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/OG0000477_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ff0d9169651f38dab7585c653e2e866744475ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000477_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 1.11456300 Before NNI: tree length is 1.11456300 + 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/OG0000478_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/OG0000478_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0924e0a3a5e33acf7f8bcd929b477b452e50395c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000478_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 0.31782143 Before NNI: tree length is 0.31782150 + 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/OG0000480_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/OG0000480_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb6c1321e6d0aadd9bc569e522fc07ba2440a8f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000480_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040094 0.044524 0.271153 0.040094 +1 0.040094 0.000001 0.006472 0.292027 0.000001 +2 0.044524 0.006472 0.000001 0.296457 0.006472 +3 0.271153 0.292027 0.296457 0.000001 0.292027 +4 0.040094 0.000001 0.006472 0.292027 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000480_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/OG0000480_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..300c77b41092fc5ab378bb43101a9bb014e2152c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000480_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 0.30708850 Before NNI: tree length is 0.30708850 + 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/OG0000481_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/OG0000481_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2adf76f9e30cc8a9c8ab559786de96ec3bfba3cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000481_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012332 0.168219 0.363676 0.014169 +1 0.012332 0.000001 0.180490 0.375947 0.005280 +2 0.168219 0.180490 0.000001 0.324144 0.182328 +3 0.363676 0.375947 0.324144 0.000001 0.377785 +4 0.014169 0.005280 0.182328 0.377785 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000482_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/OG0000482_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef9e22a21364668afeff920e6b156bd00148bb8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000482_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014112 0.198685 0.614653 0.025956 +1 0.014112 0.000001 0.195338 0.611306 0.022609 +2 0.198685 0.195338 0.000001 0.629002 0.196394 +3 0.614653 0.611306 0.629002 0.000001 0.612362 +4 0.025956 0.022609 0.196394 0.612362 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000483_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/OG0000483_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c4570e909859e8c093620b95acca3e4ef2fbe61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010645 0.153677 0.275752 0.003038 +1 0.010645 0.000001 0.153078 0.275153 0.007653 +2 0.153677 0.153078 0.000001 0.270196 0.150686 +3 0.275752 0.275153 0.270196 0.000001 0.272761 +4 0.003038 0.007653 0.150686 0.272761 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000483_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/OG0000483_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c447c40f3ce706535a495d636d82bc197428f16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000483_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 0.35485875 Before NNI: tree length is 0.35485875 + 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/OG0000484_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/OG0000484_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..33270e2b8b44c42a221d0cacac1ad024b8f6074b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000484_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039592 0.247271 0.629365 0.029055 +1 0.039592 0.000001 0.260382 0.642476 0.022131 +2 0.247271 0.260382 0.000001 0.626788 0.249845 +3 0.629365 0.642476 0.626788 0.000001 0.631939 +4 0.029055 0.022131 0.249845 0.631939 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000484_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/OG0000484_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a731fb82cf3323cab50347db8386288cbeb40215 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000484_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 0.78386050 Before NNI: tree length is 0.78386050 + 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/OG0000488_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/OG0000488_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8877e987e597fe4b0b4944a9bde3b483b17cadb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000488_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 0.31778640 Before NNI: tree length is 0.31778638 + 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/OG0000493_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/OG0000493_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..549211574b05f70f99cfb683366cfaab8b600955 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000493_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 0.09185000 Before NNI: tree length is 0.09185000 + 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/OG0000498_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/OG0000498_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..024d2fbbe8ec6c44e7742cdb9afa0bd498831273 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000498_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012381 0.189542 0.437904 0.000001 +1 0.012381 0.000001 0.190594 0.438957 0.012381 +2 0.189542 0.190594 0.000001 0.453079 0.189542 +3 0.437904 0.438957 0.453079 0.000001 0.437904 +4 0.000001 0.012381 0.189542 0.437904 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000498_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/OG0000498_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f14bee1e77c6dbf7371355e51db0528300bbcb05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000498_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 0.54697970 Before NNI: tree length is 0.54697975 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..5027c134fbd95fcbf4947ca43a3f45103e26534f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008197 0.281643 0.214741 0.000001 +1 0.008197 0.000001 0.283961 0.217059 0.008197 +2 0.281643 0.283961 0.000001 0.375808 0.281643 +3 0.214741 0.217059 0.375808 0.000001 0.214741 +4 0.000001 0.008197 0.281643 0.214741 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000501_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/OG0000501_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca2daccc9daf231395e08da8cace1e7b9440d0d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000501_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 0.78975800 Before NNI: tree length is 0.78975800 + 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/OG0000503_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/OG0000503_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..da74ceaf862564672adddac4ad164bc15bd41b74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000503_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 0.68473975 Before NNI: tree length is 0.68473975 + 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/OG0000506_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/OG0000506_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1eab09631966350bc2a41159251575135671f186 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000506_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.077134 0.210503 0.633735 0.026122 +1 0.077134 0.000001 0.210618 0.633849 0.072736 +2 0.210503 0.210618 0.000001 0.638089 0.206106 +3 0.633735 0.633849 0.638089 0.000001 0.629338 +4 0.026122 0.072736 0.206106 0.629338 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000506_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/OG0000506_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6ab9422c37421acc0b2ce93a21fda52f6c4869d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000506_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 0.79065006 Before NNI: tree length is 0.79065000 + 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/OG0000509_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/OG0000509_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6b45bcbdc0bac68bf175fb25b9b7b6e32752498 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000509_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 0.36106310 Before NNI: tree length is 0.36106313 + 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/OG0000510_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/OG0000510_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39237a3603cd05c8bf0daa7ae4ffc8d17da5bc48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000510_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018366 0.019717 0.187465 0.013263 +1 0.018366 0.000001 0.030575 0.198323 0.024122 +2 0.019717 0.030575 0.000001 0.193060 0.007231 +3 0.187465 0.198323 0.193060 0.000001 0.186606 +4 0.013263 0.024122 0.007231 0.186606 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000512_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/OG0000512_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5260a5311b5bb8321cb69336880c1863a41e62a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000512_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018329 0.239574 0.162045 0.012769 +1 0.018329 0.000001 0.245671 0.168143 0.005560 +2 0.239574 0.245671 0.000001 0.277054 0.240112 +3 0.162045 0.168143 0.277054 0.000001 0.162583 +4 0.012769 0.005560 0.240112 0.162583 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000514_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/OG0000514_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..25a66a77556b207a4ee5b89fe0d742e35db20645 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000514_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 0.21429500 Before NNI: tree length is 0.21429500 + 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/OG0000517_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/OG0000517_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e4970f16cef1ff215b38dca9d614894eb33f20d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000517_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007929 0.164885 0.434925 0.024229 +1 0.007929 0.000001 0.166946 0.436986 0.026290 +2 0.164885 0.166946 0.000001 0.403928 0.166001 +3 0.434925 0.436986 0.403928 0.000001 0.436041 +4 0.024229 0.026290 0.166001 0.436041 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000520_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/OG0000520_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3705646a128d0d4c47811b70dc1929ef571af42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000520_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013141 0.144063 0.170710 0.012739 +1 0.013141 0.000001 0.144921 0.171568 0.022322 +2 0.144063 0.144921 0.000001 0.171894 0.153244 +3 0.170710 0.171568 0.171894 0.000001 0.179890 +4 0.012739 0.022322 0.153244 0.179890 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000520_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/OG0000520_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58d40b98eedda5a4cb936fc538204fce7b2031ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000520_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 0.26129287 Before NNI: tree length is 0.26129287 + 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/OG0000521_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/OG0000521_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2112451c69f188f4a2323633d327d236e3a23dfc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048356 0.420544 0.458384 0.038120 +1 0.048356 0.000001 0.442494 0.480334 0.030389 +2 0.420544 0.442494 0.000001 0.431283 0.432258 +3 0.458384 0.480334 0.431283 0.000001 0.470098 +4 0.038120 0.030389 0.432258 0.470098 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000521_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/OG0000521_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b4224545f38da7c96fcdf91d26b5c9822620353 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000521_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 0.70033500 Before NNI: tree length is 0.70033500 + 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/OG0000522_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/OG0000522_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbb792bbf16415ab2c3900e2eb125ce19710d7cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000522_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039545 0.203770 0.228281 0.034113 +1 0.039545 0.000001 0.198627 0.223138 0.020498 +2 0.203770 0.198627 0.000001 0.163862 0.193196 +3 0.228281 0.223138 0.163862 0.000001 0.217707 +4 0.034113 0.020498 0.193196 0.217707 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000523_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/OG0000523_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fdb6d9aafd4a458325cd1442c2b259c90846c4ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000523_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017955 0.083242 0.110182 0.012456 +1 0.017955 0.000001 0.082819 0.109759 0.015118 +2 0.083242 0.082819 0.000001 0.104057 0.080405 +3 0.110182 0.109759 0.104057 0.000001 0.107344 +4 0.012456 0.015118 0.080405 0.107344 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000524_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/OG0000524_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..aaea3a31d83373b0b44cd28bba092ee72032ca7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000524_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.076634 0.042005 0.615401 0.077664 +1 0.076634 0.000001 0.087852 0.622218 0.070108 +2 0.042005 0.087852 0.000001 0.626619 0.088882 +3 0.615401 0.622218 0.626619 0.000001 0.623248 +4 0.077664 0.070108 0.088882 0.623248 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000524_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/OG0000524_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4a74a437118977e5695d743b725bf615cceffa4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000524_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 0.71930700 Before NNI: tree length is 0.71930700 + 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/OG0000527_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/OG0000527_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..677b9e17246dc06d8345d6445f974beaf4a3023b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000527_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.093743 0.116476 0.110472 0.113831 +1 0.093743 0.000001 0.077405 0.086100 0.080341 +2 0.116476 0.077405 0.000001 0.108833 0.103073 +3 0.110472 0.086100 0.108833 0.000001 0.106189 +4 0.113831 0.080341 0.103073 0.106189 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000529_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/OG0000529_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5157111a20f0e6d0254a5d91126b08bd642fdc27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000529_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041689 0.137996 0.196768 0.060643 +1 0.041689 0.000001 0.133169 0.191941 0.030364 +2 0.137996 0.133169 0.000001 0.234109 0.152123 +3 0.196768 0.191941 0.234109 0.000001 0.210895 +4 0.060643 0.030364 0.152123 0.210895 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000533_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/OG0000533_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..352162dfaa99cf7fd76672f0cad37eda69230d66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000533_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009907 0.037824 0.164122 0.009084 +1 0.009907 0.000001 0.039510 0.165808 0.010770 +2 0.037824 0.039510 0.000001 0.151653 0.034564 +3 0.164122 0.165808 0.151653 0.000001 0.160861 +4 0.009084 0.010770 0.034564 0.160861 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000533_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/OG0000533_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dec7164fe9f950ce4d86af9c7bca93e0e48bff0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000533_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 0.18550782 Before NNI: tree length is 0.18550775 + 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/OG0000534_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/OG0000534_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..72d894ffaf10f01338ee70450fe358d86d348510 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000534_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.250394 0.658313 1.020571 0.073815 +1 0.250394 0.000001 0.908707 1.270965 0.324209 +2 0.658313 0.908707 0.000001 0.907513 0.584498 +3 1.020571 1.270965 0.907513 0.000001 0.946756 +4 0.073815 0.324209 0.584498 0.946756 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf5471c95d5e1195ca92fc3ca3cfcc6e35e5bab0 --- /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_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 0.35943100 Before NNI: tree length is 0.35943100 + 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/OG0000541_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/OG0000541_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..828464c27052607a3e9324d225f9fb3786517710 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000541_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010450 0.152001 0.212211 0.004317 +1 0.010450 0.000001 0.151120 0.211330 0.014767 +2 0.152001 0.151120 0.000001 0.204802 0.156319 +3 0.212211 0.211330 0.204802 0.000001 0.216528 +4 0.004317 0.014767 0.156319 0.216528 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000541_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/OG0000541_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a66b5015124924df04e67af495003fafbd9dcb24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000541_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 0.29360861 Before NNI: tree length is 0.29360863 + 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/OG0000543_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/OG0000543_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d838adee1704526cab511fe9cdf8d24c9def17ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000543_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 0.76699000 Before NNI: tree length is 0.76699000 + 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/OG0000545_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/OG0000545_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a9a146ad571769c3c4f644dcf770fe6a8b1d8ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000545_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 1.16955620 Before NNI: tree length is 1.16955625 + 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/OG0000546_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/OG0000546_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02ced2bad8c6ac06c24f210e503b6070af950baf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000546_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 0.09282200 Before NNI: tree length is 0.09282200 + 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/OG0000550_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/OG0000550_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad426b94599dd0976ea4346a0b0335b15df3925e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000550_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.140729 0.199079 0.001688 +1 0.000001 0.000001 0.140729 0.199079 0.001688 +2 0.140729 0.140729 0.000001 0.184090 0.140106 +3 0.199079 0.199079 0.184090 0.000001 0.198456 +4 0.001688 0.001688 0.140106 0.198456 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000550_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/OG0000550_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d7a41b0f69b22603038467ec0e7ea178d0bbae8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000550_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 0.26248200 Before NNI: tree length is 0.26248200 + 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/OG0000551_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/OG0000551_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a243f229994bb34fd44cb111ed14d2058eae3050 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000551_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.647144 0.655800 0.027558 +1 0.000001 0.000001 0.647144 0.655800 0.027558 +2 0.647144 0.647144 0.000001 0.290953 0.659736 +3 0.655800 0.655800 0.290953 0.000001 0.668393 +4 0.027558 0.027558 0.659736 0.668393 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2e03461dcbae63aba89195d120f33c96b2face8 --- /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_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 0.21107465 Before NNI: tree length is 0.21107462 + 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/OG0000559_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/OG0000559_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..52ac2ab31db16d30bc5c9376f9ddc25f389b1445 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000559_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 0.45213660 Before NNI: tree length is 0.45213663 + 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/OG0000560_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/OG0000560_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c2e41f7efe4941caefd765a726228f4ac4cce47e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000560_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022845 0.233352 0.355644 0.014218 +1 0.022845 0.000001 0.229935 0.352226 0.014889 +2 0.233352 0.229935 0.000001 0.358126 0.225397 +3 0.355644 0.352226 0.358126 0.000001 0.347688 +4 0.014218 0.014889 0.225397 0.347688 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000561_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/OG0000561_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f26f813e90cd1a24234a52058bbfeef958660c2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000561_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 0.51747125 Before NNI: tree length is 0.51747125 + 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/OG0000563_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/OG0000563_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cdee2ec07d173f5f8a1d5cf11eaf2bc456d8b232 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000563_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016630 0.052754 0.104678 0.006353 +1 0.016630 0.000001 0.048306 0.100230 0.013656 +2 0.052754 0.048306 0.000001 0.088454 0.049779 +3 0.104678 0.100230 0.088454 0.000001 0.101703 +4 0.006353 0.013656 0.049779 0.101703 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000563_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/OG0000563_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..96697dd07dbc10649d9dc95bba7648faf6d28e45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000563_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 0.13072325 Before NNI: tree length is 0.13072325 + 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/OG0000564_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/OG0000564_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..617dce0f76b75b03ab62624cef951f37bc723955 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000564_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.518078 0.480666 0.295500 0.521476 +1 0.518078 0.000001 0.143794 0.476664 0.025789 +2 0.480666 0.143794 0.000001 0.439252 0.147192 +3 0.295500 0.476664 0.439252 0.000001 0.480062 +4 0.521476 0.025789 0.147192 0.480062 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1092af3a42e3ba20f00fadbc639783476130ae1 --- /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_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 1.21264538 Before NNI: tree length is 1.21264538 + 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/OG0000567_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/OG0000567_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4f90e39c70b0b66304e8520bed0df7a0048cd2e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000567_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023984 0.112673 0.104520 0.025165 +1 0.023984 0.000001 0.107242 0.099088 0.015511 +2 0.112673 0.107242 0.000001 0.128720 0.108422 +3 0.104520 0.099088 0.128720 0.000001 0.100269 +4 0.025165 0.015511 0.108422 0.100269 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000571_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/OG0000571_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..060435e88eabce047a3395ae33e7003323465e2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000571_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007260 0.069308 0.153810 0.012607 +1 0.007260 0.000001 0.069780 0.154282 0.009191 +2 0.069308 0.069780 0.000001 0.148920 0.075127 +3 0.153810 0.154282 0.148920 0.000001 0.159629 +4 0.012607 0.009191 0.075127 0.159629 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000571_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/OG0000571_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a800d3c68270335345bd3394a2fc4b447e67df16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000571_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 0.19715400 Before NNI: tree length is 0.19715400 + 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/OG0000580_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/OG0000580_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cf0f10f6c884555f8055a6197ab4398f30c67b31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000580_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015759 0.270728 0.138428 0.025199 +1 0.015759 0.000001 0.274251 0.141952 0.028722 +2 0.270728 0.274251 0.000001 0.278005 0.272381 +3 0.138428 0.141952 0.278005 0.000001 0.140082 +4 0.025199 0.028722 0.272381 0.140082 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000581_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/OG0000581_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..08b9a93e7f889fe5e218b08eebbaa559bd279ca4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000581_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 0.35090700 Before NNI: tree length is 0.35090700 + 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/OG0000582_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/OG0000582_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aac5ad7c23db88a0ea378465baa41e3a59bf1d82 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000582_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 0.29501525 Before NNI: tree length is 0.29501525 + 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/OG0000584_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/OG0000584_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..188bea4cd1a52dacdac85032a420a3081fbc9a5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000584_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.109719 0.602193 0.800870 0.099307 +1 0.109719 0.000001 0.618871 0.817548 0.030391 +2 0.602193 0.618871 0.000001 0.848451 0.608458 +3 0.800870 0.817548 0.848451 0.000001 0.807135 +4 0.099307 0.030391 0.608458 0.807135 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000587_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/OG0000587_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..206fb51188acec7633ac5ae2293d09026a1b69f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.031653 0.146590 0.000001 +1 0.000001 0.000001 0.031653 0.146590 0.000001 +2 0.031653 0.031653 0.000001 0.155858 0.031653 +3 0.146590 0.146590 0.155858 0.000001 0.146590 +4 0.000001 0.000001 0.031653 0.146590 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000587_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/OG0000587_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..243d0fbd39dbd016e8b7c6df79576c5b618092a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000587_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 0.16705150 Before NNI: tree length is 0.16705150 + 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/OG0000589_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/OG0000589_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74f93f06980eb21997eab68e62fad914fe3a390f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000589_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.138106 0.519726 0.018997 +1 0.000001 0.000001 0.138106 0.519726 0.018997 +2 0.138106 0.138106 0.000001 0.538441 0.130934 +3 0.519726 0.519726 0.538441 0.000001 0.512555 +4 0.018997 0.018997 0.130934 0.512555 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000590_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/OG0000590_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b90318785c720f7ff8de450856c9e7ed142b828 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000590_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 0.44651542 Before NNI: tree length is 0.44651537 + 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/OG0000591_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/OG0000591_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7c035336527452fd3de303112bfa54fdbf3eb07d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000591_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006553 0.035192 0.163600 0.003832 +1 0.006553 0.000001 0.034813 0.163221 0.003454 +2 0.035192 0.034813 0.000001 0.155094 0.031649 +3 0.163600 0.163221 0.155094 0.000001 0.160057 +4 0.003832 0.003454 0.031649 0.160057 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000593_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/OG0000593_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b363802d4f0d631b72b1799cb5626556efeebe7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000593_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063613 0.164779 0.276393 0.058038 +1 0.063613 0.000001 0.114212 0.225826 0.007472 +2 0.164779 0.114212 0.000001 0.282490 0.106740 +3 0.276393 0.225826 0.282490 0.000001 0.218354 +4 0.058038 0.007472 0.106740 0.218354 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000594_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/OG0000594_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..baa287b2325f83e21ebb5997624f08bcd14d9383 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000594_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 0.68388186 Before NNI: tree length is 0.68388187 + 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/OG0000596_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/OG0000596_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..338a45f4cc0fa903071c6c8ebbd786d00c7b5ad4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000596_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010882 0.101982 0.272186 0.024382 +1 0.010882 0.000001 0.097027 0.267231 0.019427 +2 0.101982 0.097027 0.000001 0.234472 0.084466 +3 0.272186 0.267231 0.234472 0.000001 0.254671 +4 0.024382 0.019427 0.084466 0.254671 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000597_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/OG0000597_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b36f8e60fcab951d41437ff9307fff38e41eb156 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000597_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 0.12935800 Before NNI: tree length is 0.12935800 + 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/OG0000600_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/OG0000600_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a7bc1f87b29180b7b2767818199dc310034c2c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000600_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 0.08410504 Before NNI: tree length is 0.08410500 + 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/OG0000604_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/OG0000604_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ef794099ba8b99b7ede85d8e8a44a64faaf9c42a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000604_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 0.65793030 Before NNI: tree length is 0.65793025 + 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/OG0000606_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/OG0000606_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f457ef1164e99eb1e999a77180de5f0e2be0d112 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000606_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011701 0.133052 0.185397 0.009797 +1 0.011701 0.000001 0.128755 0.181100 0.003148 +2 0.133052 0.128755 0.000001 0.174789 0.126850 +3 0.185397 0.181100 0.174789 0.000001 0.179196 +4 0.009797 0.003148 0.126850 0.179196 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000606_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/OG0000606_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..926f27db76b21882752d10c9c5f325b4f4ed3da0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000606_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 0.25094289 Before NNI: tree length is 0.25094287 + 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/OG0000608_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/OG0000608_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64ae447862d4bef6202fae613359c5275fbeadce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000608_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 0.29426356 Before NNI: tree length is 0.29426350 + 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/OG0000609_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/OG0000609_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..52fefd2aa1988fb811d970e8fd16a6e993d2e12f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000609_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 0.20128700 Before NNI: tree length is 0.20128700 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..307a5dd24753d86894de675fe358ef98216cbaa5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.154150 0.274273 0.006267 +1 0.000001 0.000001 0.154150 0.274273 0.006267 +2 0.154150 0.154150 0.000001 0.244206 0.152588 +3 0.274273 0.274273 0.244206 0.000001 0.272712 +4 0.006267 0.006267 0.152588 0.272712 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000612_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/OG0000612_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a6ef23e4d10f0a46428c0789113afee454ed25b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000612_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 0.56454000 Before NNI: tree length is 0.56454000 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..93cfeb657c1ae1b98221a6425766b98765978713 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001357 0.037433 0.069949 0.000151 +1 0.001357 0.000001 0.038790 0.071307 0.001207 +2 0.037433 0.038790 0.000001 0.077397 0.037583 +3 0.069949 0.071307 0.077397 0.000001 0.070100 +4 0.000151 0.001207 0.037583 0.070100 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000617_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/OG0000617_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a3552de482ace9e4ad95f8675072a0e4c67d231 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000617_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.152014 0.238857 0.000001 +1 0.000001 0.000001 0.152014 0.238857 0.000001 +2 0.152014 0.152014 0.000001 0.217404 0.152014 +3 0.238857 0.238857 0.217404 0.000001 0.238857 +4 0.000001 0.000001 0.152014 0.238857 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000619_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/OG0000619_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8046a444218ccb0dee4ecf95de98cb8655dec932 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000619_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009069 0.057042 0.190583 0.011348 +1 0.009069 0.000001 0.059393 0.192934 0.008811 +2 0.057042 0.059393 0.000001 0.204463 0.061672 +3 0.190583 0.192934 0.204463 0.000001 0.195213 +4 0.011348 0.008811 0.061672 0.195213 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000624_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/OG0000624_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bff66d190e90be021f3d741965d9aee527bc6642 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000624_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 0.39942250 Before NNI: tree length is 0.39942250 + 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/OG0000625_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/OG0000625_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3d546c2a662db82f6a2ad34ec69403874b07fa38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.070455 0.222258 0.000001 +1 0.000001 0.000001 0.070455 0.222258 0.000001 +2 0.070455 0.070455 0.000001 0.241988 0.070455 +3 0.222258 0.222258 0.241988 0.000001 0.222258 +4 0.000001 0.000001 0.070455 0.222258 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000625_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/OG0000625_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..29689be703764cc7f035af5efe0c40d8a033db83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000625_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 0.26735150 Before NNI: tree length is 0.26735150 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..bac4bec763412704050c72b2835b57d366403563 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.133251 0.487468 0.555087 0.131223 +1 0.133251 0.000001 0.477870 0.545489 0.041027 +2 0.487468 0.477870 0.000001 0.523258 0.475841 +3 0.555087 0.545489 0.523258 0.000001 0.543460 +4 0.131223 0.041027 0.475841 0.543460 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..72a46a023bde25ae91ca2f8ce2a7c5f4d884c7c4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002963 0.095437 0.065356 0.000001 +1 0.002963 0.000001 0.098143 0.068061 0.002963 +2 0.095437 0.098143 0.000001 0.113629 0.095437 +3 0.065356 0.068061 0.113629 0.000001 0.065356 +4 0.000001 0.002963 0.095437 0.065356 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000631_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/OG0000631_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..214e4846d17c5d8ce493a0f77a35580dad15e4eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000631_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 0.30013302 Before NNI: tree length is 0.30013300 + 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/OG0000632_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/OG0000632_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d6be1dd883e220b499eec7ee803cb45e3807fdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000632_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.373456 0.572169 0.531232 0.373456 +1 0.373456 0.000001 0.405845 0.364908 0.000001 +2 0.572169 0.405845 0.000001 0.070235 0.405845 +3 0.531232 0.364908 0.070235 0.000001 0.364908 +4 0.373456 0.000001 0.405845 0.364908 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000632_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/OG0000632_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1586f7482045c3a3c765c861ef437c5a263b0ee4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000632_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 0.69038450 Before NNI: tree length is 0.69038450 + 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/OG0000634_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/OG0000634_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..56ccc99d8d267e8816eb37e8817d4543b3b78eaa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000634_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010129 0.066110 0.129558 0.013353 +1 0.010129 0.000001 0.064931 0.128380 0.003371 +2 0.066110 0.064931 0.000001 0.129693 0.068155 +3 0.129558 0.128380 0.129693 0.000001 0.131604 +4 0.013353 0.003371 0.068155 0.131604 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000637_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/OG0000637_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..774b82c3e66e488828259c414aeb9da5d2de7160 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000637_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020310 0.083252 0.204607 0.000001 +1 0.020310 0.000001 0.080805 0.202160 0.020310 +2 0.083252 0.080805 0.000001 0.196246 0.083252 +3 0.204607 0.202160 0.196246 0.000001 0.204607 +4 0.000001 0.020310 0.083252 0.204607 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000637_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/OG0000637_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b29ed26f2939bb50829dd7978bca5552737e12a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000637_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 0.25098450 Before NNI: tree length is 0.25098450 + 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/OG0000638_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/OG0000638_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f3456134bdceafeed1c09392c5ea822dbd1fb7c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000638_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000039 0.013578 0.047547 0.003707 +1 0.000039 0.000001 0.013539 0.047509 0.003745 +2 0.013578 0.013539 0.000001 0.057802 0.017285 +3 0.047547 0.047509 0.057802 0.000001 0.051254 +4 0.003707 0.003745 0.017285 0.051254 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000643_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/OG0000643_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd020c3e2bfb9cf243beb62d3ae373ec1d4083c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000643_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 0.80621350 Before NNI: tree length is 0.80621350 + 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/OG0000644_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/OG0000644_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1338400ff8b3447f1fc1105e38ed2c253491067 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000644_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 0.61189121 Before NNI: tree length is 0.61189125 + 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/OG0000645_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/OG0000645_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1e7ae7406f17acecfcc921f7c32a6c784cdfa31a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.180074 0.480615 0.000001 +1 0.000001 0.000001 0.180074 0.480615 0.000001 +2 0.180074 0.180074 0.000001 0.406247 0.180074 +3 0.480615 0.480615 0.406247 0.000001 0.480615 +4 0.000001 0.000001 0.180074 0.480615 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000645_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/OG0000645_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c40fe7f374b536393ce66a67c123126c0989479c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000645_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 0.53346900 Before NNI: tree length is 0.53346900 + 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/OG0000648_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/OG0000648_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4710ff66be751c9875960d85e36de3b6f17c8c64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012500 0.196289 0.320924 0.000001 +1 0.012500 0.000001 0.194214 0.318850 0.012500 +2 0.196289 0.194214 0.000001 0.323691 0.196289 +3 0.320924 0.318850 0.323691 0.000001 0.320924 +4 0.000001 0.012500 0.196289 0.320924 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000648_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/OG0000648_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..025dab639621fb59a4996892c307a9e1339a78f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000648_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 0.42566522 Before NNI: tree length is 0.42566525 + 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/OG0000649_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/OG0000649_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..834919fb78828df43fea7e4ae370d459e79e140f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019524 0.345937 0.374579 0.010390 +1 0.019524 0.000001 0.341674 0.370316 0.013060 +2 0.345937 0.341674 0.000001 0.453621 0.339473 +3 0.374579 0.370316 0.453621 0.000001 0.368115 +4 0.010390 0.013060 0.339473 0.368115 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000650_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/OG0000650_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2ea5c0d8287e0df2fcc2c3351bec76ba9615a1de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.063723 0.142057 0.001907 +1 0.000001 0.000001 0.063723 0.142057 0.001907 +2 0.063723 0.063723 0.000001 0.158294 0.064166 +3 0.142057 0.142057 0.158294 0.000001 0.142500 +4 0.001907 0.001907 0.064166 0.142500 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000650_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/OG0000650_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..65df597694078f4101b79dfb68275911197cf095 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000650_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 0.18321250 Before NNI: tree length is 0.18321250 + 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/OG0000652_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/OG0000652_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36d7d29a512eec303ad4f2d50bb5caae5b7e753a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000652_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003593 0.203939 0.356331 0.020762 +1 0.003593 0.000001 0.200346 0.352738 0.017169 +2 0.203939 0.200346 0.000001 0.396841 0.196846 +3 0.356331 0.352738 0.396841 0.000001 0.349238 +4 0.020762 0.017169 0.196846 0.349238 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000654_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/OG0000654_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2d20d1f62aa3d664325d8e47a0d0e2c88d7d3288 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000654_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054865 0.191617 0.465183 0.030051 +1 0.054865 0.000001 0.192150 0.465716 0.061186 +2 0.191617 0.192150 0.000001 0.438039 0.197937 +3 0.465183 0.465716 0.438039 0.000001 0.471504 +4 0.030051 0.061186 0.197937 0.471504 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000655_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/OG0000655_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1cc5ed57dd05a857f790897e8036494264af3558 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000655_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.333699 0.777022 0.013442 +1 0.000001 0.000001 0.333699 0.777022 0.013442 +2 0.333699 0.333699 0.000001 0.808384 0.339307 +3 0.777022 0.777022 0.808384 0.000001 0.782629 +4 0.013442 0.013442 0.339307 0.782629 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000655_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/OG0000655_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e86ef58664508f85d855b69276d2dc29b250339a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000655_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 0.96907780 Before NNI: tree length is 0.96907775 + 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/OG0000657_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/OG0000657_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac82a9dc3218f8de8b10bff3c5cf88b39f3a8720 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000657_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 0.08745700 Before NNI: tree length is 0.08745700 + 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/OG0000658_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/OG0000658_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..75fb6147734e8536546dfd12605a03af48d36523 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000658_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003512 0.016287 0.005626 0.004599 +1 0.003512 0.000001 0.015583 0.004926 0.003895 +2 0.016287 0.015583 0.000001 0.017702 0.011688 +3 0.005626 0.004926 0.017702 0.000001 0.006014 +4 0.004599 0.003895 0.011688 0.006014 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000659_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/OG0000659_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8bdd37bc22c151767237362d906a401ba254be79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000659_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001969 0.013244 0.007917 0.007909 +1 0.001969 0.000001 0.011873 0.009243 0.009235 +2 0.013244 0.011873 0.000001 0.020518 0.020510 +3 0.007917 0.009243 0.020518 0.000001 0.007921 +4 0.007909 0.009235 0.020510 0.007921 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000660_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/OG0000660_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af8d831e24df5476d95e1e5aab2243f0964dce99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000660_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 0.09137633 Before NNI: tree length is 0.09137625 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3f00b7a4a02d0a545badbe8dc246e6d93ff6784 --- /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_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 0.15886500 Before NNI: tree length is 0.15886500 + 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/OG0000665_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/OG0000665_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9101b0050a9d7e45418cd4aa91c67fe26c436243 --- /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_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 0.71331029 Before NNI: tree length is 0.71331025 + 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/OG0000668_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/OG0000668_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f1c0267efb3d7607f38b97bd74db62213ba7d35d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000668_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006586 0.060826 0.170730 0.006361 +1 0.006586 0.000001 0.054240 0.164145 0.000224 +2 0.060826 0.054240 0.000001 0.154145 0.054464 +3 0.170730 0.164145 0.154145 0.000001 0.164369 +4 0.006361 0.000224 0.054464 0.164369 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000669_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/OG0000669_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6122646fd2ab45176d333f671154d106913f18ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013820 0.067755 0.167129 0.016154 +1 0.013820 0.000001 0.062752 0.162125 0.014397 +2 0.067755 0.062752 0.000001 0.178672 0.068332 +3 0.167129 0.162125 0.178672 0.000001 0.167706 +4 0.016154 0.014397 0.068332 0.167706 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000678_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/OG0000678_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f21aea664f7fee00f4e19f1958bdf62473a331a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011494 0.124960 0.209007 0.017296 +1 0.011494 0.000001 0.122276 0.206323 0.014612 +2 0.124960 0.122276 0.000001 0.207643 0.118574 +3 0.209007 0.206323 0.207643 0.000001 0.202622 +4 0.017296 0.014612 0.118574 0.202622 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000678_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/OG0000678_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa0dd06cdcb65c9a913c38f70a4907c41f514f68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000678_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 0.28066522 Before NNI: tree length is 0.28066525 + 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/OG0000683_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/OG0000683_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fec400906479bb04271f4496d33817f6990ca7a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000683_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007240 0.090658 0.323141 0.002363 +1 0.007240 0.000001 0.086197 0.318679 0.004877 +2 0.090658 0.086197 0.000001 0.330491 0.088296 +3 0.323141 0.318679 0.330491 0.000001 0.320778 +4 0.002363 0.004877 0.088296 0.320778 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000685_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/OG0000685_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d0c6094f6b13b39dc5bed03d685bf5027b59efe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000685_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 0.17522287 Before NNI: tree length is 0.17522288 + 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/OG0000689_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/OG0000689_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..65c80ffb21fb55432c73ada4aa01d20e7380d81a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000689_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 0.16519859 Before NNI: tree length is 0.16519863 + 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/OG0000690_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/OG0000690_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2658943ea4724189a68491122889bd5a2e7b1f1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005385 0.052017 0.232850 0.027237 +1 0.005385 0.000001 0.051751 0.232584 0.026970 +2 0.052017 0.051751 0.000001 0.225662 0.040678 +3 0.232850 0.232584 0.225662 0.000001 0.221511 +4 0.027237 0.026970 0.040678 0.221511 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000690_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/OG0000690_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..98103046a52e26f33d18567955d2d8216558f624 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000690_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 0.26577275 Before NNI: tree length is 0.26577275 + 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/OG0000691_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/OG0000691_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3ebcdb92a01bcb8c404a8b2dcf9fe760eaa0b721 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000691_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000174 0.056622 0.207188 0.000174 +1 0.000174 0.000001 0.056448 0.207014 0.000348 +2 0.056622 0.056448 0.000001 0.209622 0.056796 +3 0.207188 0.207014 0.209622 0.000001 0.207362 +4 0.000174 0.000348 0.056796 0.207362 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..92f668c78e94fc804c6c91fc99d2d81859c01df5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.038317 0.093392 0.000001 +1 0.000001 0.000001 0.038317 0.093392 0.000001 +2 0.038317 0.038317 0.000001 0.084091 0.038317 +3 0.093392 0.093392 0.084091 0.000001 0.093392 +4 0.000001 0.000001 0.038317 0.093392 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000693_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/OG0000693_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f75d937d443514ae47c573c8727a182665cc29c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000693_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 0.55930915 Before NNI: tree length is 0.55930912 + 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/OG0000694_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/OG0000694_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d6574ea9c6c4b88c4653f186fb365e0c1e00ad4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000694_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.094950 0.183114 0.311830 0.086292 +1 0.094950 0.000001 0.210955 0.339670 0.046988 +2 0.183114 0.210955 0.000001 0.351184 0.202296 +3 0.311830 0.339670 0.351184 0.000001 0.331012 +4 0.086292 0.046988 0.202296 0.331012 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000695_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/OG0000695_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..47f3d48dd6e61fe25fe424b013e7a234744eea56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000695_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.062769 0.168441 0.003637 +1 0.000001 0.000001 0.062769 0.168441 0.003637 +2 0.062769 0.062769 0.000001 0.186237 0.062200 +3 0.168441 0.168441 0.186237 0.000001 0.167872 +4 0.003637 0.003637 0.062200 0.167872 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000695_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/OG0000695_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d2636ed57e2352439c052f9f45dd944a8f553682 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000695_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 0.21025800 Before NNI: tree length is 0.21025800 + 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/OG0000696_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/OG0000696_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..877ab00f4044f2eec754de033bfae0117ebbcdfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000696_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.470429 0.214551 0.024443 +1 0.000001 0.000001 0.470429 0.214551 0.024443 +2 0.470429 0.470429 0.000001 0.558249 0.473329 +3 0.214551 0.214551 0.558249 0.000001 0.217451 +4 0.024443 0.024443 0.473329 0.217451 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000697_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/OG0000697_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..836680bdb06ddc438fd2a1c9030e767efe2e52dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000697_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.196442 0.366952 0.014726 +1 0.000001 0.000001 0.196442 0.366952 0.014726 +2 0.196442 0.196442 0.000001 0.340151 0.193333 +3 0.366952 0.366952 0.340151 0.000001 0.363843 +4 0.014726 0.014726 0.193333 0.363843 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000698_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/OG0000698_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cb79778b6c260bdaf4e39acfdb2a91c611dc94f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000698_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 0.87569150 Before NNI: tree length is 0.87569150 + 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/OG0000699_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/OG0000699_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fad183fe2d55f88be370401bcd9bfaa1d7db9f71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000699_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.027709 0.172093 0.002930 +1 0.000001 0.000001 0.027709 0.172093 0.002930 +2 0.027709 0.027709 0.000001 0.176772 0.029813 +3 0.172093 0.172093 0.176772 0.000001 0.174197 +4 0.002930 0.002930 0.029813 0.174197 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000701_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/OG0000701_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4050ca88800d0a2ddc586893da5a8e9adef2f734 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000701_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.084110 0.193143 0.000001 +1 0.000001 0.000001 0.084110 0.193143 0.000001 +2 0.084110 0.084110 0.000001 0.273514 0.084110 +3 0.193143 0.193143 0.273514 0.000001 0.193143 +4 0.000001 0.000001 0.084110 0.193143 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000702_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/OG0000702_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2070604c2d6da50016a88caf9b43a3a9bc2619f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000702_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 0.27045307 Before NNI: tree length is 0.27045300 + 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/OG0000703_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/OG0000703_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..79da005f5233e7f36328885eeb481e2abe63971c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000703_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005580 0.033536 0.077484 0.003984 +1 0.005580 0.000001 0.033838 0.077787 0.001596 +2 0.033536 0.033838 0.000001 0.080721 0.032242 +3 0.077484 0.077787 0.080721 0.000001 0.076190 +4 0.003984 0.001596 0.032242 0.076190 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000704_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/OG0000704_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6662dbde444e17159b00d32cdab0eaca3e3807c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000704_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 0.10442100 Before NNI: tree length is 0.10442100 + 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/OG0000706_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/OG0000706_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..154400260035b404609a61f98c4791d586e61cc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000706_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014676 0.022284 0.122677 0.014676 +1 0.014676 0.000001 0.028536 0.128929 0.000001 +2 0.022284 0.028536 0.000001 0.128091 0.028536 +3 0.122677 0.128929 0.128091 0.000001 0.128929 +4 0.014676 0.000001 0.028536 0.128929 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000707_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/OG0000707_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f843327230882b92c36243325abbea5716c5670f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000707_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 1.39806580 Before NNI: tree length is 1.39806575 + 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/OG0000710_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/OG0000710_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38a91bdd2b5e6aa8d2ab37293fe8ab94f06a750 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000710_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 0.69791139 Before NNI: tree length is 0.69791138 + 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/OG0000713_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/OG0000713_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7022d6341fc033bee67dbea3f68663a5e132854 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000713_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 0.66346052 Before NNI: tree length is 0.66346050 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f10222acfaec5e03e6935ce4ddfa4cac6d4da4d0 --- /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_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 0.15675661 Before NNI: tree length is 0.15675662 + 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/OG0000718_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/OG0000718_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4089c86611403fd654b522c968ea402a5052cbb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000718_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.118047 0.338354 0.000001 +1 0.000001 0.000001 0.118047 0.338354 0.000001 +2 0.118047 0.118047 0.000001 0.343124 0.118047 +3 0.338354 0.338354 0.343124 0.000001 0.338354 +4 0.000001 0.000001 0.118047 0.338354 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000721_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/OG0000721_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..459af97233407730eaebcc3694dc7770b73aefdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000721_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 0.29815800 Before NNI: tree length is 0.29815800 + 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/OG0000722_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/OG0000722_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7bd0d7388d9444c7dc781b2e7e1eac2204ce6b74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000577 0.069695 0.151171 0.000289 +1 0.000577 0.000001 0.070272 0.151748 0.000289 +2 0.069695 0.070272 0.000001 0.145311 0.069984 +3 0.151171 0.151748 0.145311 0.000001 0.151459 +4 0.000289 0.000289 0.069984 0.151459 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..741822497208efb303c603e5b247898fa0fe94d9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008880 0.364182 0.338667 0.002486 +1 0.008880 0.000001 0.363968 0.338453 0.007675 +2 0.364182 0.363968 0.000001 0.242025 0.362977 +3 0.338667 0.338453 0.242025 0.000001 0.337462 +4 0.002486 0.007675 0.362977 0.337462 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000727_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/OG0000727_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a18e992ad8bd71ceac62a9e3f64ee732c01156ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.070258 0.664230 0.734008 0.005861 +1 0.070258 0.000001 0.652198 0.721976 0.071297 +2 0.664230 0.652198 0.000001 0.626436 0.665269 +3 0.734008 0.721976 0.626436 0.000001 0.735047 +4 0.005861 0.071297 0.665269 0.735047 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000727_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/OG0000727_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81047d7f3eae9058928ec000bd4ace19ecffa5f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000727_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 1.04490000 Before NNI: tree length is 1.04490000 + 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/OG0000729_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/OG0000729_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..feb93e0b86833a1698c659b0c21c9dbd2a7120c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000729_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 0.23666479 Before NNI: tree length is 0.23666475 + 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/OG0000730_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/OG0000730_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6b45ae4bb5c6e10d2ea8e7cdd5e789441cb8fbb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.232611 0.477195 0.020978 +1 0.000001 0.000001 0.232611 0.477195 0.020978 +2 0.232611 0.232611 0.000001 0.466689 0.225743 +3 0.477195 0.477195 0.466689 0.000001 0.470327 +4 0.020978 0.020978 0.225743 0.470327 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000734_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/OG0000734_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5122af8f6e1e6959803a987eb8e27ac8893e3e5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000734_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 2.21498988 Before NNI: tree length is 2.21498987 + 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/OG0000735_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/OG0000735_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41a78e8a31daefb43956c7b6e314bbe0add21fd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000735_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 0.17650291 Before NNI: tree length is 0.17650288 + 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/OG0000737_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/OG0000737_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..020b1ff713ba0712993f610413f15e26eaa6a2ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000737_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 0.06898350 Before NNI: tree length is 0.06898350 + 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/OG0000738_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/OG0000738_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..879531d70841e08a0e115266e382b1afdfee9b0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000738_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 0.23468731 Before NNI: tree length is 0.23468725 + 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/OG0000741_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/OG0000741_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4f25634a04fab86232b9b220a11c2c84d25b3dad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000741_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008208 0.068337 0.045042 0.008208 +1 0.008208 0.000001 0.065101 0.041807 0.000001 +2 0.068337 0.065101 0.000001 0.079305 0.065101 +3 0.045042 0.041807 0.079305 0.000001 0.041807 +4 0.008208 0.000001 0.065101 0.041807 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000742_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/OG0000742_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c37c32115188e8fddca3f32b1eb14bf17801dfee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000742_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 0.22117225 Before NNI: tree length is 0.22117225 + 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/OG0000744_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/OG0000744_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a01dd290382740839732d7245ee626c1a326a286 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000744_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011268 0.043570 0.072458 0.011268 +1 0.011268 0.000001 0.048504 0.077392 0.000001 +2 0.043570 0.048504 0.000001 0.074253 0.048504 +3 0.072458 0.077392 0.074253 0.000001 0.077392 +4 0.011268 0.000001 0.048504 0.077392 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000748_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/OG0000748_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4dabeb35d8e43a2c4320815f87f647a60e2c8081 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000748_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 0.26493050 Before NNI: tree length is 0.26493050 + 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/OG0000751_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/OG0000751_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ca3862b210b517032939769f10a149e174be1d85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000751_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013720 0.044055 0.181155 0.000001 +1 0.013720 0.000001 0.046037 0.183137 0.013720 +2 0.044055 0.046037 0.000001 0.161617 0.044055 +3 0.181155 0.183137 0.161617 0.000001 0.181155 +4 0.000001 0.013720 0.044055 0.181155 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000752_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/OG0000752_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7b56cc4c5f09257187f1f062450b354118c52817 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000752_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002761 0.031541 0.056217 0.003882 +1 0.002761 0.000001 0.033791 0.058466 0.006644 +2 0.031541 0.033791 0.000001 0.056758 0.035424 +3 0.056217 0.058466 0.056758 0.000001 0.060099 +4 0.003882 0.006644 0.035424 0.060099 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000752_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/OG0000752_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ff0ba939e1afe4993489bafd6d78662aaae499a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000752_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 0.07864564 Before NNI: tree length is 0.07864562 + 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/OG0000753_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/OG0000753_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5ff79c0808d9bb5885b748088a9a83361c65ccf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000753_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 0.46398625 Before NNI: tree length is 0.46398625 + 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/OG0000755_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/OG0000755_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4256d4b410f476021e819ee1a36b4cdedd2357b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000755_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003316 0.105357 0.202055 0.015643 +1 0.003316 0.000001 0.106746 0.203444 0.017033 +2 0.105357 0.106746 0.000001 0.201782 0.109890 +3 0.202055 0.203444 0.201782 0.000001 0.206588 +4 0.015643 0.017033 0.109890 0.206588 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000756_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/OG0000756_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..776968fc3068df8864052bbd587e486c4b3d5322 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000756_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 0.45296510 Before NNI: tree length is 0.45296512 + 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/OG0000761_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/OG0000761_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5094ac64eabc9b1f561be8e1248bd473b0e0a995 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028740 0.105821 0.315907 0.018402 +1 0.028740 0.000001 0.102987 0.313073 0.030227 +2 0.105821 0.102987 0.000001 0.333064 0.107309 +3 0.315907 0.313073 0.333064 0.000001 0.317394 +4 0.018402 0.030227 0.107309 0.317394 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000761_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/OG0000761_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0dd3d21e645f49f73452a44dbc805bc4d018e66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000761_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 0.40029360 Before NNI: tree length is 0.40029362 + 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/OG0000762_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/OG0000762_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71148812b1e4df9e6eeb2766d29aaf33b5c1be4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008373 0.098774 0.234100 0.003298 +1 0.008373 0.000001 0.107147 0.242474 0.011671 +2 0.098774 0.107147 0.000001 0.229193 0.097346 +3 0.234100 0.242474 0.229193 0.000001 0.232673 +4 0.003298 0.011671 0.097346 0.232673 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000762_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/OG0000762_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3880be88d34e5ed7e5c5de7b397754f2e1e0ad08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000762_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 0.29034185 Before NNI: tree length is 0.29034188 + 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/OG0000763_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/OG0000763_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..329d943db34aa153ad936b26daaef589f45315cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007579 0.092925 0.218809 0.007479 +1 0.007579 0.000001 0.093781 0.219666 0.008336 +2 0.092925 0.093781 0.000001 0.191787 0.088959 +3 0.218809 0.219666 0.191787 0.000001 0.214844 +4 0.007479 0.008336 0.088959 0.214844 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000763_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/OG0000763_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4280458bf76be28ddf553d9143ca85431712f8c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000763_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 0.25773510 Before NNI: tree length is 0.25773513 + 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/OG0000764_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/OG0000764_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fef775303201f310f1a238afd9a3bdadc78e3a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000764_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 0.32366550 Before NNI: tree length is 0.32366550 + 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/OG0000765_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/OG0000765_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..803546e5c90b3cc4a3c9264bed05178884520743 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000765_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.015210 0.046341 0.000001 +1 0.000001 0.000001 0.015210 0.046341 0.000001 +2 0.015210 0.015210 0.000001 0.046162 0.015210 +3 0.046341 0.046341 0.046162 0.000001 0.046341 +4 0.000001 0.000001 0.015210 0.046341 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000766_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/OG0000766_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92ee1b1c198dbe1493eca1648a69ec4963b6d9b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000766_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 0.22318600 Before NNI: tree length is 0.22318600 + 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/OG0000768_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/OG0000768_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de346f388414c8f718cfa8c875593be52fd494b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000768_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024284 0.249140 0.704869 0.030213 +1 0.024284 0.000001 0.240812 0.696541 0.021140 +2 0.249140 0.240812 0.000001 0.666152 0.246741 +3 0.704869 0.696541 0.666152 0.000001 0.702470 +4 0.030213 0.021140 0.246741 0.702470 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000770_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/OG0000770_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b59a7ddaeb2620bd0d908da60f95542d45ba09a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000770_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 0.32814700 Before NNI: tree length is 0.32814700 + 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/OG0000771_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/OG0000771_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9419db3092d3ad49e1e505344c95e01558b5be07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000771_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010069 0.358256 0.926929 1.213367 +1 0.010069 0.000001 0.358405 0.927079 1.213517 +2 0.358256 0.358405 0.000001 0.954963 1.241401 +3 0.926929 0.927079 0.954963 0.000001 1.305983 +4 1.213367 1.213517 1.241401 1.305983 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000771_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/OG0000771_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..70c160a65a140b549661a3fdde9767aee46f3bce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000771_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 1.92139375 Before NNI: tree length is 1.92139375 + 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/OG0000772_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/OG0000772_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ce13f836698922cd011d865630aab0acba16175f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000772_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007898 0.321824 0.791030 1.044987 +1 0.007898 0.000001 0.318907 0.788113 1.042070 +2 0.321824 0.318907 0.000001 0.850167 1.104124 +3 0.791030 0.788113 0.850167 0.000001 1.130802 +4 1.044987 1.042070 1.104124 1.130802 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000773_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/OG0000773_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e15373311b8e38e1dbaa7b309e287d141d00ddfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000773_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035290 0.018250 0.315482 0.015897 +1 0.035290 0.000001 0.034033 0.320321 0.033547 +2 0.018250 0.034033 0.000001 0.314226 0.016508 +3 0.315482 0.320321 0.314226 0.000001 0.313740 +4 0.015897 0.033547 0.016508 0.313740 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000775_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/OG0000775_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72232d0fdb47114c88eb8a53c5e15a42a9c0ccec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000775_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 0.35513313 Before NNI: tree length is 0.35513313 + 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/OG0000776_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/OG0000776_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7d22e7d1e8e84140b0b50e0f213f5bf3740be45c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000776_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.206553 0.000001 0.287637 0.205826 +1 0.206553 0.000001 0.206553 0.246919 0.027097 +2 0.000001 0.206553 0.000001 0.287637 0.205826 +3 0.287637 0.246919 0.287637 0.000001 0.246192 +4 0.205826 0.027097 0.205826 0.246192 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000776_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/OG0000776_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02a699944f840aabc085a79ed3bb4640b765cf9a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000776_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 0.38374000 Before NNI: tree length is 0.38374000 + 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/OG0000778_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/OG0000778_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc429b584ede6eb925bbb7582dcb2d9ae048234b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000778_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020285 0.078044 0.092483 0.020285 +1 0.020285 0.000001 0.059762 0.074201 0.000001 +2 0.078044 0.059762 0.000001 0.125577 0.059762 +3 0.092483 0.074201 0.125577 0.000001 0.074201 +4 0.020285 0.000001 0.059762 0.074201 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000779_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/OG0000779_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bdc82464ab8bae6bd9dfe62e0ab84bd2007664c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000779_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 0.10216900 Before NNI: tree length is 0.10216900 + 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/OG0000780_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/OG0000780_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9cfcc809fe47bce7f163d4e4977aedac9ad63293 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000780_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 0.48410925 Before NNI: tree length is 0.48410925 + 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/OG0000782_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/OG0000782_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63c23143fb5b16fca206ed57f3716708b8018ec2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000782_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 0.11088137 Before NNI: tree length is 0.11088138 + 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/OG0000783_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/OG0000783_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9e24982f4889bbadec43bea13f323608eea49235 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000783_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022248 0.266975 0.412497 0.023549 +1 0.022248 0.000001 0.274470 0.419991 0.017632 +2 0.266975 0.274470 0.000001 0.481195 0.275772 +3 0.412497 0.419991 0.481195 0.000001 0.421293 +4 0.023549 0.017632 0.275772 0.421293 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000784_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/OG0000784_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c46c72fb96ec7d177fc02501a91e53ee6564874d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000784_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 0.95205450 Before NNI: tree length is 0.95205450 + 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/OG0000789_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/OG0000789_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c4fd69325cb6dfe39dc29b28410f15c22e841ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000789_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026921 0.347737 0.429313 0.024979 +1 0.026921 0.000001 0.356321 0.437897 0.019515 +2 0.347737 0.356321 0.000001 0.497069 0.354380 +3 0.429313 0.437897 0.497069 0.000001 0.435956 +4 0.024979 0.019515 0.354380 0.435956 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000789_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/OG0000789_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0424f0c2f6e0a0a0c643b49dd36efd8b554e5454 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000789_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 0.66359875 Before NNI: tree length is 0.66359875 + 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/OG0000790_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/OG0000790_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d3b9f13c5d71578c02a262eaf5ce8921baeb9640 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000790_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039037 0.251239 0.501483 0.044970 +1 0.039037 0.000001 0.233942 0.484185 0.037939 +2 0.251239 0.233942 0.000001 0.471656 0.250141 +3 0.501483 0.484185 0.471656 0.000001 0.500385 +4 0.044970 0.037939 0.250141 0.500385 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000790_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/OG0000790_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2bda29e81491830270b96d83b270817831f92d2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000790_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 0.64499479 Before NNI: tree length is 0.64499475 + 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/OG0000792_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/OG0000792_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b2cfc3c3eaeed6530b27ea8dc9d2e00895e96f1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004291 0.050138 0.147303 0.002500 +1 0.004291 0.000001 0.050726 0.147891 0.006365 +2 0.050138 0.050726 0.000001 0.141265 0.052211 +3 0.147303 0.147891 0.141265 0.000001 0.149377 +4 0.002500 0.006365 0.052211 0.149377 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000793_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/OG0000793_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3c641d286cd38737d6ffbbc2e50187a51744e8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000793_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013341 0.023371 0.033782 0.000096 +1 0.013341 0.000001 0.036712 0.047124 0.013437 +2 0.023371 0.036712 0.000001 0.023274 0.023275 +3 0.033782 0.047124 0.023274 0.000001 0.033686 +4 0.000096 0.013437 0.023275 0.033686 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000795_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/OG0000795_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..821c814fc5d13236cc32c163abdc099eb48d3c0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000795_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020231 0.169735 0.238436 0.009932 +1 0.020231 0.000001 0.157027 0.225729 0.011924 +2 0.169735 0.157027 0.000001 0.265523 0.161429 +3 0.238436 0.225729 0.265523 0.000001 0.230130 +4 0.009932 0.011924 0.161429 0.230130 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000797_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/OG0000797_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..814b9ec250215aa148fe3cfb496971a35bce12d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000797_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003635 0.062916 0.024617 0.002891 +1 0.003635 0.000001 0.062955 0.024655 0.000815 +2 0.062916 0.062955 0.000001 0.071810 0.062212 +3 0.024617 0.024655 0.071810 0.000001 0.023912 +4 0.002891 0.000815 0.062212 0.023912 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000799_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/OG0000799_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4361938d8e9bfd02b2b89f58d07056a0e314bd2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000799_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 0.79809131 Before NNI: tree length is 0.79809125 + 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/OG0000801_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/OG0000801_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0360fb6aa684afeb0b1e32b7839e6a7a1b0b998 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000801_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 0.43430075 Before NNI: tree length is 0.43430075 + 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/OG0000802_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/OG0000802_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3404915b91dfc8277fd8e32ed61393999500e07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000802_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 0.95997475 Before NNI: tree length is 0.95997475 + 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/OG0000804_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/OG0000804_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5f8b802194c840c3f61284f01b293b442f333565 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.007930 0.060279 0.000001 +1 0.000001 0.000001 0.007930 0.060279 0.000001 +2 0.007930 0.007930 0.000001 0.057762 0.007930 +3 0.060279 0.060279 0.057762 0.000001 0.060279 +4 0.000001 0.000001 0.007930 0.060279 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000804_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/OG0000804_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64802fa205445a209762ef5dbb63d4e93f5cbb68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000804_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 0.06298650 Before NNI: tree length is 0.06298650 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ceaf9f77fa059a3acf1d32cd817cbd6e5e75a8dd --- /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_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 0.15941066 Before NNI: tree length is 0.15941063 + 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/OG0000811_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/OG0000811_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed826c18f7de9e388784de344ca4df314bd75942 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000811_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 0.82204866 Before NNI: tree length is 0.82204863 + 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/OG0000813_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/OG0000813_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ec9e7469421b85053cfcf46adbbd6ab57384c535 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035321 0.446998 0.561876 0.000001 +1 0.035321 0.000001 0.464297 0.579174 0.035321 +2 0.446998 0.464297 0.000001 0.795464 0.446998 +3 0.561876 0.579174 0.795464 0.000001 0.561876 +4 0.000001 0.035321 0.446998 0.561876 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000814_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/OG0000814_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd96a35fff026b1bb85652497e5d4679c264fc60 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000814_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011373 0.141706 0.055811 0.011928 +1 0.011373 0.000001 0.146579 0.060684 0.016802 +2 0.141706 0.146579 0.000001 0.165885 0.143023 +3 0.055811 0.060684 0.165885 0.000001 0.057127 +4 0.011928 0.016802 0.143023 0.057127 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000815_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/OG0000815_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d1a77d6c3695bcb0c4b6b499eed437d0879d94a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000815_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007894 0.193447 0.263053 0.056638 +1 0.007894 0.000001 0.191356 0.260961 0.054547 +2 0.193447 0.191356 0.000001 0.284456 0.178853 +3 0.263053 0.260961 0.284456 0.000001 0.248458 +4 0.056638 0.054547 0.178853 0.248458 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000822_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/OG0000822_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f672e470611f1ea9021d1f941bb1df1db4ae66a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000822_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002726 0.022416 0.084501 0.003638 +1 0.002726 0.000001 0.019836 0.081921 0.000913 +2 0.022416 0.019836 0.000001 0.092898 0.020749 +3 0.084501 0.081921 0.092898 0.000001 0.082833 +4 0.003638 0.000913 0.020749 0.082833 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000824_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/OG0000824_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f38cda1b357af514e6a4694357b825079d0f520 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000824_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016991 0.154471 0.300467 0.015948 +1 0.016991 0.000001 0.159203 0.305199 0.017082 +2 0.154471 0.159203 0.000001 0.287203 0.158160 +3 0.300467 0.305199 0.287203 0.000001 0.304156 +4 0.015948 0.017082 0.158160 0.304156 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000827_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/OG0000827_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..28f67ebb34afd7674807057be7534f0989665bd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000827_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040023 0.236556 0.402335 0.005095 +1 0.040023 0.000001 0.246857 0.412636 0.045118 +2 0.236556 0.246857 0.000001 0.433871 0.241651 +3 0.402335 0.412636 0.433871 0.000001 0.407429 +4 0.005095 0.045118 0.241651 0.407429 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000827_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/OG0000827_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa55166c3f272deab3d5dd772b2142b2d1c7213f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000827_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 0.56663786 Before NNI: tree length is 0.56663788 + 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/OG0000829_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/OG0000829_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b838bc876d163c500cc8cc22c62d4254542a8b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006745 0.008155 0.080774 0.006745 +1 0.006745 0.000001 0.014900 0.087519 0.000001 +2 0.008155 0.014900 0.000001 0.084409 0.014900 +3 0.080774 0.087519 0.084409 0.000001 0.087519 +4 0.006745 0.000001 0.014900 0.087519 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000831_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/OG0000831_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9e34746d3a288ff954603d25715a79121639354 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000831_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.042638 0.067249 0.000001 +1 0.000001 0.000001 0.042638 0.067249 0.000001 +2 0.042638 0.042638 0.000001 0.053968 0.042638 +3 0.067249 0.067249 0.053968 0.000001 0.067249 +4 0.000001 0.000001 0.042638 0.067249 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000836_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/OG0000836_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a5340e2cb6daf62534011b86413c8e19ef12cf4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000836_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023040 0.061957 0.050345 0.000001 +1 0.023040 0.000001 0.051609 0.039997 0.023040 +2 0.061957 0.051609 0.000001 0.026728 0.061957 +3 0.050345 0.039997 0.026728 0.000001 0.050345 +4 0.000001 0.023040 0.061957 0.050345 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000836_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/OG0000836_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0612b558745332cf44156e912741b57a8cfa9ae7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000836_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 0.07586150 Before NNI: tree length is 0.07586150 + 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/OG0000846_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/OG0000846_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f411b58830ecbbcbd868cda0359a9b7e4845a303 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000846_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.081076 0.190490 0.000001 +1 0.000001 0.000001 0.081076 0.190490 0.000001 +2 0.081076 0.081076 0.000001 0.220497 0.081076 +3 0.190490 0.190490 0.220497 0.000001 0.190490 +4 0.000001 0.000001 0.081076 0.190490 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..bf87e081cea788da038645389188277dc7717c6a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.242713 0.327275 0.025949 +1 0.000001 0.000001 0.242713 0.327275 0.025949 +2 0.242713 0.242713 0.000001 0.324775 0.247589 +3 0.327275 0.327275 0.324775 0.000001 0.332151 +4 0.025949 0.025949 0.247589 0.332151 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000848_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/OG0000848_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d103f466f5279d8653d27f5d7978f4df3b88eba1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000848_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.485956 0.501867 0.094906 +1 0.000001 0.000001 0.485956 0.501867 0.094906 +2 0.485956 0.485956 0.000001 0.485167 0.509588 +3 0.501867 0.501867 0.485167 0.000001 0.525498 +4 0.094906 0.094906 0.509588 0.525498 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000849_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/OG0000849_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f704aa04694a5d1d96239f2cfc8c6c6f794fb78e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000849_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.021109 0.045281 0.000001 +1 0.000001 0.000001 0.021109 0.045281 0.000001 +2 0.021109 0.021109 0.000001 0.045409 0.021109 +3 0.045281 0.045281 0.045409 0.000001 0.045281 +4 0.000001 0.000001 0.021109 0.045281 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000849_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/OG0000849_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1727e566ffc96536764d42fcf762faaf1fb53f2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000849_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 0.05590050 Before NNI: tree length is 0.05590050 + 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/OG0000851_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/OG0000851_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ebe4baad3dac8c5d3b83ab36bd0486761ecd590a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.065967 0.155147 0.000001 +1 0.000001 0.000001 0.065967 0.155147 0.000001 +2 0.065967 0.065967 0.000001 0.134496 0.065967 +3 0.155147 0.155147 0.134496 0.000001 0.155147 +4 0.000001 0.000001 0.065967 0.155147 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000854_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/OG0000854_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6fe5ef54bb40a6aa3d282bb6f00a3381ecb709f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.148646 0.387601 0.017440 +1 0.000001 0.000001 0.148646 0.387601 0.017440 +2 0.148646 0.148646 0.000001 0.382154 0.162362 +3 0.387601 0.387601 0.382154 0.000001 0.401317 +4 0.017440 0.017440 0.162362 0.401317 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000856_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/OG0000856_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3edf55e7542d04a17056fa8e7c364d5be4fcbe3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000856_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 0.21968723 Before NNI: tree length is 0.21968725 + 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/OG0000857_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/OG0000857_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0c15bb2bce1e29ab713d81b6a1e4b2cbf4feec01 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000857_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.405260 0.519572 0.050262 +1 0.000001 0.000001 0.405260 0.519572 0.050262 +2 0.405260 0.405260 0.000001 0.540664 0.384328 +3 0.519572 0.519572 0.540664 0.000001 0.498640 +4 0.050262 0.050262 0.384328 0.498640 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000858_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/OG0000858_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f1707780c16618ee3f57941002040aacbcb13c4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000858_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004497 0.019922 2.799542 0.000001 +1 0.004497 0.000001 0.020682 2.800303 0.004497 +2 0.019922 0.020682 0.000001 2.803398 0.019922 +3 2.799542 2.800303 2.803398 0.000001 2.799542 +4 0.000001 0.004497 0.019922 2.799542 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000859_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/OG0000859_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8814d4b963ec61608740932a7d76fab133df2158 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000859_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036180 0.038939 1.392836 0.049978 +1 0.036180 0.000001 0.035492 1.389389 0.046532 +2 0.038939 0.035492 0.000001 1.367911 0.020409 +3 1.392836 1.389389 1.367911 0.000001 1.378950 +4 0.049978 0.046532 0.020409 1.378950 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000861_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/OG0000861_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..47d64d041932b9adbd6426911292e22b32f5da63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000861_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 0.77609375 Before NNI: tree length is 0.77609375 + 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/OG0000862_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/OG0000862_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d5ce9f448c61d3135ddccc89e4f1454c2bff2db2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000862_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012983 0.295277 0.679776 0.120156 +1 0.012983 0.000001 0.289468 0.673968 0.114348 +2 0.295277 0.289468 0.000001 0.611512 0.247972 +3 0.679776 0.673968 0.611512 0.000001 0.632471 +4 0.120156 0.114348 0.247972 0.632471 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000863_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/OG0000863_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eb65e27677b6fc7a52d05c2e6d390d907671dd5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000863_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009860 0.727712 1.187278 0.025868 +1 0.009860 0.000001 0.735463 1.195029 0.033619 +2 0.727712 0.735463 0.000001 1.494418 0.735282 +3 1.187278 1.195029 1.494418 0.000001 1.194848 +4 0.025868 0.033619 0.735282 1.194848 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..2ed10748b62b7adaa2aa547dd86b2da505fa6d6c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000573 0.023465 0.068908 0.000573 +1 0.000573 0.000001 0.024038 0.068336 0.001145 +2 0.023465 0.024038 0.000001 0.092373 0.022893 +3 0.068908 0.068336 0.092373 0.000001 0.069481 +4 0.000573 0.001145 0.022893 0.069481 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000867_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/OG0000867_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a0db4e291fa09917bea9dbfb84d7c19f15ccc58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000867_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002720 0.068233 0.331132 0.002147 +1 0.002720 0.000001 0.065512 0.328412 0.000573 +2 0.068233 0.065512 0.000001 0.298210 0.066085 +3 0.331132 0.328412 0.298210 0.000001 0.328985 +4 0.002147 0.000573 0.066085 0.328985 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000869_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/OG0000869_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c56977c9573fe606fa52102c553b730998eb01df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000869_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 0.13083825 Before NNI: tree length is 0.13083825 + 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/OG0000871_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/OG0000871_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ec02d7075199138bf82e71c53c4849cecbb4bd63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000871_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059074 0.055285 0.055048 0.002649 +1 0.059074 0.000001 0.054710 0.054473 0.056425 +2 0.055285 0.054710 0.000001 0.038442 0.052636 +3 0.055048 0.054473 0.038442 0.000001 0.052399 +4 0.002649 0.056425 0.052636 0.052399 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000871_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/OG0000871_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..13a529692d0da141a7b380288d65c1b9347c7fcc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000871_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 0.10363700 Before NNI: tree length is 0.10363700 + 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/OG0000873_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/OG0000873_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2946fa9bda8fe4d640d76c36c52d8d2fc651fc11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000873_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008920 0.026219 0.013907 0.018922 +1 0.008920 0.000001 0.017299 0.004987 0.010003 +2 0.026219 0.017299 0.000001 0.013275 0.018899 +3 0.013907 0.004987 0.013275 0.000001 0.006587 +4 0.018922 0.010003 0.018899 0.006587 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000873_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/OG0000873_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6505b42238b6e226708b3c520a4283b891a471bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000873_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 0.03250183 Before NNI: tree length is 0.03250175 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5176eedc648812aadc8d234c08ca68b0d9901a66 --- /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_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 0.05589266 Before NNI: tree length is 0.05589263 + 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/OG0000875_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/OG0000875_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5a169b64ae0df8a0b3a845c0fab6096a0b5787c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000875_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 0.47822830 Before NNI: tree length is 0.47822825 + 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/OG0000876_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/OG0000876_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..28ac53d3765356f5a9e54b094bbe0ebfff974fdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.541952 0.843296 1.173512 0.536343 +1 0.541952 0.000001 0.817336 1.147552 0.016647 +2 0.843296 0.817336 0.000001 1.234826 0.811726 +3 1.173512 1.147552 1.234826 0.000001 1.141943 +4 0.536343 0.016647 0.811726 1.141943 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000876_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/OG0000876_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ffe57a10108deb6b648a6a5580ca302aa7bb5df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000876_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 1.88933188 Before NNI: tree length is 1.88933187 + 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/OG0000877_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/OG0000877_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..19c1fe8e48a011a855b7669b8636721d29b28f13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007609 0.085253 0.295679 0.008889 +1 0.007609 0.000001 0.086395 0.296820 0.014643 +2 0.085253 0.086395 0.000001 0.267114 0.092287 +3 0.295679 0.296820 0.267114 0.000001 0.302713 +4 0.008889 0.014643 0.092287 0.302713 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000879_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/OG0000879_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9136908e8dec6f9ccde032193dd812183f855f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000879_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 0.13956337 Before NNI: tree length is 0.13956338 + 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/OG0000880_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/OG0000880_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b90231888d54f5e9cdb108ea41347d3befe471f --- /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_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 0.51050565 Before NNI: tree length is 0.51050562 + 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/OG0000883_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/OG0000883_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c44ea9b99236aa80104dac6a1f21618309e583de --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.106214 0.211728 0.003442 +1 0.000001 0.000001 0.106214 0.211728 0.003442 +2 0.106214 0.106214 0.000001 0.218401 0.105987 +3 0.211728 0.211728 0.218401 0.000001 0.211502 +4 0.003442 0.003442 0.105987 0.211502 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000887_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/OG0000887_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..acaaca8ce95d4ffaa1308d4e1626132c5dbaca0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000887_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009747 0.156664 0.290166 0.020704 +1 0.009747 0.000001 0.155751 0.289253 0.011050 +2 0.156664 0.155751 0.000001 0.319734 0.166708 +3 0.290166 0.289253 0.319734 0.000001 0.300210 +4 0.020704 0.011050 0.166708 0.300210 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9f0572ac79c02dbe80f8fa7186bffa69d9f8c5a7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063955 0.222640 0.465242 0.036465 +1 0.063955 0.000001 0.245722 0.488323 0.073212 +2 0.222640 0.245722 0.000001 0.497428 0.231897 +3 0.465242 0.488323 0.497428 0.000001 0.474499 +4 0.036465 0.073212 0.231897 0.474499 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000889_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/OG0000889_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e4d79fd958f1f291b287125fc5183c31dd6e13b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000889_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 0.39424975 Before NNI: tree length is 0.39424975 + 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/OG0000891_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/OG0000891_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b4b17667cb8f6b69579d63a3030cb3b76834ad8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000891_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 0.18054662 Before NNI: tree length is 0.18054662 + 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/OG0000892_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/OG0000892_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..37f0b4b68d0265eccc41bef5c31cec4338eaccd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032955 0.444118 0.399548 0.032459 +1 0.032955 0.000001 0.435610 0.391041 0.041744 +2 0.444118 0.435610 0.000001 0.542675 0.452906 +3 0.399548 0.391041 0.542675 0.000001 0.408337 +4 0.032459 0.041744 0.452906 0.408337 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000894_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/OG0000894_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9b6bbe51b888dbe546d34aa0f218ad88eb04f1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000894_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 0.09383300 Before NNI: tree length is 0.09383300 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cc8a790e216839804448393452f8e0d2579efab8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.113309 0.078793 0.000001 +1 0.000001 0.000001 0.113309 0.078793 0.000001 +2 0.113309 0.113309 0.000001 0.090516 0.113309 +3 0.078793 0.078793 0.090516 0.000001 0.078793 +4 0.000001 0.000001 0.113309 0.078793 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000896_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/OG0000896_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..43fdc06c580873eb7fb6f38fa426c16437aa3f04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000896_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 0.17914150 Before NNI: tree length is 0.17914150 + 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/OG0000897_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/OG0000897_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c4370bc6b301089b488c7933f6c4607026adbf06 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007663 0.215848 0.380343 0.007663 +1 0.007663 0.000001 0.218073 0.382569 0.000001 +2 0.215848 0.218073 0.000001 0.378102 0.218073 +3 0.380343 0.382569 0.378102 0.000001 0.382569 +4 0.007663 0.000001 0.218073 0.382569 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000898_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/OG0000898_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0212b2909a57a1cdf707318bd791c40360123ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000898_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 0.23408100 Before NNI: tree length is 0.23408100 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..da156084b6ed3fdc3997105d177b53b40c18f27d --- /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_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 1.07688576 Before NNI: tree length is 1.07688575 + 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/OG0000900_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/OG0000900_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..558d9d7dcf68ad91dccb2153288bfe09fe6a21d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000900_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 0.67323929 Before NNI: tree length is 0.67323925 + 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/OG0000901_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/OG0000901_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4fb6391c433a28eabaf1f239cfbf830bc3e7601a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000901_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 0.26933281 Before NNI: tree length is 0.26933275 + 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/OG0000902_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/OG0000902_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2e5b0b23e58dc0d5dcb8ab1b618be8c056075941 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000902_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009720 0.046305 0.112514 0.009968 +1 0.009720 0.000001 0.046008 0.112217 0.001711 +2 0.046305 0.046008 0.000001 0.110684 0.046255 +3 0.112514 0.112217 0.110684 0.000001 0.112464 +4 0.009968 0.001711 0.046255 0.112464 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000904_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/OG0000904_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..272a5f2aeab986be6cea370322c551d2842326ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000904_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 0.45089822 Before NNI: tree length is 0.45089825 + 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/OG0000906_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/OG0000906_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b7af19f0151d46274d849e17a179b0831caf000e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000906_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001384 0.323704 0.092737 0.004295 +1 0.001384 0.000001 0.322320 0.091353 0.002912 +2 0.323704 0.322320 0.000001 0.325246 0.319606 +3 0.092737 0.091353 0.325246 0.000001 0.088639 +4 0.004295 0.002912 0.319606 0.088639 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000907_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/OG0000907_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8fc2ceca1681b4861fb2a123be6a12441ae5fe66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000907_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008807 0.095388 0.125794 0.007853 +1 0.008807 0.000001 0.096074 0.126479 0.005200 +2 0.095388 0.096074 0.000001 0.123750 0.095120 +3 0.125794 0.126479 0.123750 0.000001 0.125525 +4 0.007853 0.005200 0.095120 0.125525 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000912_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/OG0000912_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..831d7976592a792ab5c1cd8caef5184c2c1c095d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000912_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 0.30293000 Before NNI: tree length is 0.30293000 + 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/OG0000914_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/OG0000914_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42c86a8ec23da5db3423950f93f847b1a00c5ee0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000914_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.124596 0.242397 0.062160 +1 0.000001 0.000001 0.124596 0.242397 0.062160 +2 0.124596 0.124596 0.000001 0.165245 0.169459 +3 0.242397 0.242397 0.165245 0.000001 0.287261 +4 0.062160 0.062160 0.169459 0.287261 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000917_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/OG0000917_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a2bfd8c208ac46c6d51a1f9ce6acb103ff4255f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.014463 0.039377 0.000001 +1 0.000001 0.000001 0.014463 0.039377 0.000001 +2 0.014463 0.014463 0.000001 0.044158 0.014463 +3 0.039377 0.039377 0.044158 0.000001 0.039377 +4 0.000001 0.000001 0.014463 0.039377 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000919_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/OG0000919_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b54a5a72b1e225e8e9f8da7d470a1cfaa2f8035f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000919_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007791 0.252681 0.619053 0.007791 +1 0.007791 0.000001 0.252664 0.619037 0.000001 +2 0.252681 0.252664 0.000001 0.597803 0.252664 +3 0.619053 0.619037 0.597803 0.000001 0.619037 +4 0.007791 0.000001 0.252664 0.619037 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000919_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/OG0000919_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..10cb8cf3b076a06b70faad5fdecb4d1b3ea6a92d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000919_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 0.73865630 Before NNI: tree length is 0.73865625 + 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/OG0000922_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/OG0000922_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2c764fb71ef52145bca24caf9a8f92fe5370985b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000922_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036847 0.272907 0.600938 0.036847 +1 0.036847 0.000001 0.283742 0.611773 0.000001 +2 0.272907 0.283742 0.000001 0.666966 0.283742 +3 0.600938 0.611773 0.666966 0.000001 0.611773 +4 0.036847 0.000001 0.283742 0.611773 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000923_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/OG0000923_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c1267366affdf580372bfb6d33efe3a7916c8eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000923_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032073 0.664973 1.218217 0.032073 +1 0.032073 0.000001 0.645460 1.198704 0.000001 +2 0.664973 0.645460 0.000001 1.249622 0.645460 +3 1.218217 1.198704 1.249622 0.000001 1.198704 +4 0.032073 0.000001 0.645460 1.198704 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000925_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/OG0000925_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..255d9d5b9948b5bc9ea60298fb898bb20e7902fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000925_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004924 0.036959 0.112363 0.005517 +1 0.004924 0.000001 0.036939 0.112343 0.001770 +2 0.036959 0.036939 0.000001 0.115608 0.037532 +3 0.112363 0.112343 0.115608 0.000001 0.112936 +4 0.005517 0.001770 0.037532 0.112936 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000926_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/OG0000926_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6dea98d917775e9951fa4a18d4a897cf5b659336 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011998 0.024342 0.221753 0.011998 +1 0.011998 0.000001 0.017714 0.221513 0.000001 +2 0.024342 0.017714 0.000001 0.233857 0.017714 +3 0.221753 0.221513 0.233857 0.000001 0.221513 +4 0.011998 0.000001 0.017714 0.221513 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000927_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/OG0000927_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6d4bd5138c293552662eb451972916ee4eaa340 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024748 0.043297 0.198562 0.024748 +1 0.024748 0.000001 0.044143 0.199408 0.000001 +2 0.043297 0.044143 0.000001 0.214134 0.044143 +3 0.198562 0.199408 0.214134 0.000001 0.199408 +4 0.024748 0.000001 0.044143 0.199408 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000932_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/OG0000932_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7d89bdc15f59e4bc981f1c9dad89f500a38cb30f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000932_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.033698 0.039838 0.000001 +1 0.000001 0.000001 0.033698 0.039838 0.000001 +2 0.033698 0.033698 0.000001 0.041019 0.033698 +3 0.039838 0.039838 0.041019 0.000001 0.039838 +4 0.000001 0.000001 0.033698 0.039838 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000932_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/OG0000932_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fac47c4093f63706968b45f489123294f2321abd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000932_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 0.05727850 Before NNI: tree length is 0.05727850 + 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/OG0000938_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/OG0000938_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6e1e143253709caaa9f0f893525b218807f48e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000938_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 0.12075450 Before NNI: tree length is 0.12075450 + 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/OG0000940_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/OG0000940_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2bbab33e518493cd691b7c4f0d4cc40cf748044f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000940_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.097829 0.241399 0.002899 +1 0.000001 0.000001 0.097829 0.241399 0.002899 +2 0.097829 0.097829 0.000001 0.248731 0.095673 +3 0.241399 0.241399 0.248731 0.000001 0.239243 +4 0.002899 0.002899 0.095673 0.239243 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000944_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/OG0000944_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ea22372fb87da03769843eaa5e520b5be103056d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000484 0.152110 0.249861 0.006328 +1 0.000484 0.000001 0.152594 0.250345 0.005843 +2 0.152110 0.152594 0.000001 0.287667 0.158437 +3 0.249861 0.250345 0.287667 0.000001 0.256189 +4 0.006328 0.005843 0.158437 0.256189 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000944_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/OG0000944_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f3361e3b2c3983f26f7ad874d43d68a0c016099 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000944_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 0.35114639 Before NNI: tree length is 0.35114638 + 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/OG0000949_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/OG0000949_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a173097ef640d57da0ef8da0a6294ededba7be4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000949_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 0.06012115 Before NNI: tree length is 0.06012112 + 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/OG0000951_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/OG0000951_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fdce8d8acb91154eb517063eab163e72d275ec5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000951_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 0.45957050 Before NNI: tree length is 0.45957050 + 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/OG0000953_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/OG0000953_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8dcf52aef8c2c50b679dca848473d9de8a99662e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000953_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023742 0.213376 0.298753 0.023742 +1 0.023742 0.000001 0.205906 0.291283 0.000001 +2 0.213376 0.205906 0.000001 0.327117 0.205906 +3 0.298753 0.291283 0.327117 0.000001 0.291283 +4 0.023742 0.000001 0.205906 0.291283 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000955_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/OG0000955_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2b7508c4142f2b0de903c88c50ab09be98d91e73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000955_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020529 0.079735 0.090102 0.020529 +1 0.020529 0.000001 0.078130 0.088497 0.000001 +2 0.079735 0.078130 0.000001 0.096900 0.078130 +3 0.090102 0.088497 0.096900 0.000001 0.088497 +4 0.020529 0.000001 0.078130 0.088497 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000956_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/OG0000956_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3af49d3710a7223f6151450e6cc53a630f06f470 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000956_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003763 0.097003 0.306241 0.003763 +1 0.003763 0.000001 0.096678 0.305915 0.000001 +2 0.097003 0.096678 0.000001 0.329143 0.096678 +3 0.306241 0.305915 0.329143 0.000001 0.305915 +4 0.003763 0.000001 0.096678 0.305915 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000958_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/OG0000958_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9eb0d31f8a266b8b1e2cf2b1e7e11c0537031010 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000958_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005814 0.304065 0.179378 0.005814 +1 0.005814 0.000001 0.305578 0.180891 0.000001 +2 0.304065 0.305578 0.000001 0.327514 0.305578 +3 0.179378 0.180891 0.327514 0.000001 0.180891 +4 0.005814 0.000001 0.305578 0.180891 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..e2ae3bd69cb424bce6fee899c608871c1aa3bd63 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001162 0.211907 0.408413 0.001162 +1 0.001162 0.000001 0.212088 0.408594 0.000001 +2 0.211907 0.212088 0.000001 0.398040 0.212088 +3 0.408413 0.408594 0.398040 0.000001 0.408594 +4 0.001162 0.000001 0.212088 0.408594 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000962_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/OG0000962_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2aa4a9cc82ab0886354e42123b0b33e307b12181 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000962_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.025311 0.106602 0.000001 +1 0.000001 0.000001 0.025311 0.106602 0.000001 +2 0.025311 0.025311 0.000001 0.108359 0.025311 +3 0.106602 0.106602 0.108359 0.000001 0.106602 +4 0.000001 0.000001 0.025311 0.106602 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000964_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/OG0000964_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..679db3cf9faa127ec5719c2e28a8afc78df47605 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000964_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 0.30874400 Before NNI: tree length is 0.30874400 + 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/OG0000968_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/OG0000968_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..041da578df37d71330200517667e192450ff7e4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000968_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.311222 0.405978 0.001586 +1 0.000001 0.000001 0.311222 0.405978 0.001586 +2 0.311222 0.311222 0.000001 0.490884 0.309636 +3 0.405978 0.405978 0.490884 0.000001 0.404392 +4 0.001586 0.001586 0.309636 0.404392 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000969_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/OG0000969_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..95965a72b90f8e93bd46f25b78446d6b1487f3e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000969_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006199 0.081190 0.255974 0.009578 +1 0.006199 0.000001 0.082903 0.257687 0.011291 +2 0.081190 0.082903 0.000001 0.249556 0.077857 +3 0.255974 0.257687 0.249556 0.000001 0.252642 +4 0.009578 0.011291 0.077857 0.252642 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000972_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/OG0000972_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2becd2845041542b5fd2b23db49a98f8b576bf95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000972_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.108770 0.143171 0.000001 +1 0.000001 0.000001 0.108770 0.143171 0.000001 +2 0.108770 0.108770 0.000001 0.104008 0.108770 +3 0.143171 0.143171 0.104008 0.000001 0.143171 +4 0.000001 0.000001 0.108770 0.143171 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000972_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/OG0000972_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8704355c18fa66aacb4cf1c2f4a6b086b1f7fb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000972_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 0.17797550 Before NNI: tree length is 0.17797550 + 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/OG0000974_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/OG0000974_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb5b61f9fed2e85a99d2ebd79b147ab0996c5467 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000974_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009697 0.094287 0.308918 0.009697 +1 0.009697 0.000001 0.092494 0.307126 0.000001 +2 0.094287 0.092494 0.000001 0.291719 0.092494 +3 0.308918 0.307126 0.291719 0.000001 0.307126 +4 0.009697 0.000001 0.092494 0.307126 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000975_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/OG0000975_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e6e513a78a0a4d8f0124d4d31ea6b31fb6dc1a27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035467 0.316997 0.362861 0.052127 +1 0.035467 0.000001 0.308994 0.354858 0.044123 +2 0.316997 0.308994 0.000001 0.360629 0.317267 +3 0.362861 0.354858 0.360629 0.000001 0.363130 +4 0.052127 0.044123 0.317267 0.363130 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000978_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/OG0000978_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c5fa502a8f1687ccdfb89701652665b8af404ca1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000978_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005575 0.040480 0.262944 0.004654 +1 0.005575 0.000001 0.045763 0.268226 0.010229 +2 0.040480 0.045763 0.000001 0.267998 0.045134 +3 0.262944 0.268226 0.267998 0.000001 0.267598 +4 0.004654 0.010229 0.045134 0.267598 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000979_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/OG0000979_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..88b8a33a41696330cb3dff1864eb4d886e286253 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000979_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 0.29584975 Before NNI: tree length is 0.29584975 + 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/OG0000980_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/OG0000980_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b6f8e679b9f40850aa62e7d09a9578c7e93a6b85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000980_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020529 0.097496 0.576106 0.055895 +1 0.020529 0.000001 0.085931 0.564540 0.044330 +2 0.097496 0.085931 0.000001 0.518337 0.041601 +3 0.576106 0.564540 0.518337 0.000001 0.520211 +4 0.055895 0.044330 0.041601 0.520211 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000981_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/OG0000981_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ebe635b8c6fdf2ed9dba42c0b6c87ffbf65f605 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000981_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 0.37327783 Before NNI: tree length is 0.37327775 + 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/OG0000985_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/OG0000985_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb365d698365716ca40974b22cfb4ee1547cc2a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000985_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019902 0.199900 0.537069 0.009682 +1 0.019902 0.000001 0.198738 0.535907 0.018659 +2 0.199900 0.198738 0.000001 0.562910 0.198658 +3 0.537069 0.535907 0.562910 0.000001 0.535827 +4 0.009682 0.018659 0.198658 0.535827 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000990_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/OG0000990_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c371b15cd1c4691f433f160c6d29a3e0187f5328 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000990_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 0.13465500 Before NNI: tree length is 0.13465500 + 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/OG0000991_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/OG0000991_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..780b4a80039f40b1f9f33f52224607a6ea445f25 --- /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_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 0.22117382 Before NNI: tree length is 0.22117375 + 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/OG0000994_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/OG0000994_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0dbe8c6e316865e2c77f93b1193fcf9f6367f1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000994_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 0.52470385 Before NNI: tree length is 0.52470387 + 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/OG0000995_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/OG0000995_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2599f1edd4f45bf46415729ba8f98cc76d906522 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000995_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030881 0.233359 0.705701 0.012402 +1 0.030881 0.000001 0.225336 0.697677 0.020617 +2 0.233359 0.225336 0.000001 0.664826 0.223096 +3 0.705701 0.697677 0.664826 0.000001 0.695438 +4 0.012402 0.020617 0.223096 0.695438 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000997_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/OG0000997_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4785bc657e7bffe87f521503158843ffb030dc89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000997_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040355 0.485486 0.773647 0.050291 +1 0.040355 0.000001 0.483055 0.771216 0.047861 +2 0.485486 0.483055 0.000001 0.825643 0.478600 +3 0.773647 0.771216 0.825643 0.000001 0.766761 +4 0.050291 0.047861 0.478600 0.766761 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001000_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/OG0001000_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f9d85e5bba0e5280aa99c3f108ba11ef626b62f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001000_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 0.08118700 Before NNI: tree length is 0.08118700 + 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/OG0001001_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/OG0001001_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..282f412961008345494f195cc3029460f79fa2a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001001_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025239 0.033660 0.128929 0.000001 +1 0.025239 0.000001 0.023819 0.119087 0.025239 +2 0.033660 0.023819 0.000001 0.119822 0.033660 +3 0.128929 0.119087 0.119822 0.000001 0.128929 +4 0.000001 0.025239 0.033660 0.128929 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001001_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/OG0001001_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3911a1ff959ff25d43766fba94ebb36a70c6f271 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001001_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 0.14890475 Before NNI: tree length is 0.14890475 + 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/OG0001003_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/OG0001003_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa77fc5409d707a1e664e3c4f710de1db8b5ab15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001003_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 0.21611150 Before NNI: tree length is 0.21611150 + 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/OG0001005_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/OG0001005_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3fe9342f2c028f8a63b9cde56de29f95295fe99c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001005_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028309 0.038325 0.064633 0.024021 +1 0.028309 0.000001 0.023348 0.049655 0.010626 +2 0.038325 0.023348 0.000001 0.033007 0.020642 +3 0.064633 0.049655 0.033007 0.000001 0.046950 +4 0.024021 0.010626 0.020642 0.046950 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001005_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/OG0001005_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f20d266d261231688257b1949167e29f36dce906 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001005_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 0.07781732 Before NNI: tree length is 0.07781725 + 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/OG0001006_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/OG0001006_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c29103d483d4a7fce2923d6987f24efbffbce08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001006_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 0.23854975 Before NNI: tree length is 0.23854975 + 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/OG0001008_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/OG0001008_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c1cce75fdd818bd601f586c983900c979e796ccd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023798 0.115878 0.257825 0.020191 +1 0.023798 0.000001 0.114309 0.256257 0.023412 +2 0.115878 0.114309 0.000001 0.250667 0.115492 +3 0.257825 0.256257 0.250667 0.000001 0.257440 +4 0.020191 0.023412 0.115492 0.257440 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001010_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/OG0001010_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..690a1922a8ac067e5fa368211f9fc4fe273b4a55 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001010_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019502 0.076581 0.253096 0.015813 +1 0.019502 0.000001 0.075332 0.251847 0.024094 +2 0.076581 0.075332 0.000001 0.240188 0.081173 +3 0.253096 0.251847 0.240188 0.000001 0.257688 +4 0.015813 0.024094 0.081173 0.257688 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001010_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/OG0001010_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca8d89698c18f319dee358e0571ade53efbf01b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001010_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 0.30426150 Before NNI: tree length is 0.30426150 + 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/OG0001011_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/OG0001011_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..38823f5e32d1544efeb4e053b78b258909529947 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001011_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030617 0.166122 0.716674 0.011413 +1 0.030617 0.000001 0.161732 0.712284 0.021605 +2 0.166122 0.161732 0.000001 0.724337 0.157110 +3 0.716674 0.712284 0.724337 0.000001 0.707662 +4 0.011413 0.021605 0.157110 0.707662 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001012_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/OG0001012_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..03c1118d0d7eca8be07c3d5402dc4b9133e2ebdd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001012_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021991 0.312656 0.175024 0.000001 +1 0.021991 0.000001 0.309181 0.171549 0.021991 +2 0.312656 0.309181 0.000001 0.434261 0.312656 +3 0.175024 0.171549 0.434261 0.000001 0.175024 +4 0.000001 0.021991 0.312656 0.175024 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6da66fcda8d179036941d2a8d37c5fe62898f783 --- /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_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 0.12576285 Before NNI: tree length is 0.12576287 + 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/OG0001014_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/OG0001014_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..67b0a7cc7bfbd8b3552ae139e07b4da7f96b7a0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001014_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002022 0.056382 0.190841 0.007282 +1 0.002022 0.000001 0.055172 0.189631 0.005260 +2 0.056382 0.055172 0.000001 0.178308 0.060432 +3 0.190841 0.189631 0.178308 0.000001 0.194891 +4 0.007282 0.005260 0.060432 0.194891 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001014_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/OG0001014_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cad68c4b45d968731ff96eab10949b37c178e7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001014_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 0.21843150 Before NNI: tree length is 0.21843150 + 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/OG0001015_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/OG0001015_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2274f3463cf2949cf520d7ed0962f6741dfb62c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001015_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 0.38609020 Before NNI: tree length is 0.38609025 + 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/OG0001017_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/OG0001017_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58dc8001810d92214cb5cd69a86efe44c3fc93ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001017_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 0.30602450 Before NNI: tree length is 0.30602450 + 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/OG0001018_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/OG0001018_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..881789f98ae70fb80fee998884882f9af8e49300 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001018_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 0.41807721 Before NNI: tree length is 0.41807725 + 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/OG0001021_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/OG0001021_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f8a42c6c9e5de3b21bfe22f86be65373d7d9cd71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001021_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 0.23054638 Before NNI: tree length is 0.23054637 + 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/OG0001023_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/OG0001023_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b18d5a281f4a0844950c5da1fe76cda228f9f599 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001023_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 0.10521460 Before NNI: tree length is 0.10521463 + 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/OG0001025_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/OG0001025_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..45ef77b0ce9795f333b80bc20cb8916d19470072 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001025_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 0.15331850 Before NNI: tree length is 0.15331850 + 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/OG0001026_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/OG0001026_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0576b46f5880e9d32f9a5d3c98a8d16bf608dcfc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001026_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010464 0.095538 0.228509 0.010464 +1 0.010464 0.000001 0.098659 0.231630 0.000001 +2 0.095538 0.098659 0.000001 0.222716 0.098659 +3 0.228509 0.231630 0.222716 0.000001 0.231630 +4 0.010464 0.000001 0.098659 0.231630 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001028_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/OG0001028_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c593df019155273651b90717173006d0f8f3d920 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001028_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.283654 0.780529 0.962120 0.261088 +1 0.283654 0.000001 0.709295 0.890886 0.027219 +2 0.780529 0.709295 0.000001 0.943086 0.686729 +3 0.962120 0.890886 0.943086 0.000001 0.868320 +4 0.261088 0.027219 0.686729 0.868320 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001031_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/OG0001031_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..71b45f97f0a4b17b7b09b16baf2f324a04a9694c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001031_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 0.46552438 Before NNI: tree length is 0.46552437 + 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/OG0001035_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/OG0001035_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..362d0d1168b53ff1c2f31dbf23074f770407b1d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001035_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031224 0.154077 0.306236 0.032604 +1 0.031224 0.000001 0.153290 0.305450 0.001380 +2 0.154077 0.153290 0.000001 0.339119 0.154670 +3 0.306236 0.305450 0.339119 0.000001 0.306829 +4 0.032604 0.001380 0.154670 0.306829 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001043_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/OG0001043_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ca697c7c94a5d2e6f8d4c803d21d3749440c7220 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001043_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.047912 0.198989 0.008004 +1 0.000001 0.000001 0.047912 0.198989 0.008004 +2 0.047912 0.047912 0.000001 0.219735 0.052580 +3 0.198989 0.198989 0.219735 0.000001 0.203657 +4 0.008004 0.008004 0.052580 0.203657 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001044_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/OG0001044_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e143033856b1faeef4935f522913a6eb3158969d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.097270 0.165026 0.000001 +1 0.000001 0.000001 0.097270 0.165026 0.000001 +2 0.097270 0.097270 0.000001 0.192842 0.097270 +3 0.165026 0.165026 0.192842 0.000001 0.165026 +4 0.000001 0.000001 0.097270 0.165026 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001046_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/OG0001046_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12fc80333e10d516b35fafade6b453f20a62a60d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001046_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 0.12542250 Before NNI: tree length is 0.12542250 + 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/OG0001049_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/OG0001049_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0efc0857fcd29d3277eba771d33505b18dea1435 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008932 0.057000 0.087483 0.009627 +1 0.008932 0.000001 0.059569 0.090051 0.001909 +2 0.057000 0.059569 0.000001 0.075478 0.060264 +3 0.087483 0.090051 0.075478 0.000001 0.090746 +4 0.009627 0.001909 0.060264 0.090746 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001051_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/OG0001051_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2e4180d71288d963f89daa47be01f46e3742c04d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001051_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.066860 0.132868 0.359416 0.055240 +1 0.066860 0.000001 0.155551 0.343608 0.011619 +2 0.132868 0.155551 0.000001 0.448108 0.143932 +3 0.359416 0.343608 0.448108 0.000001 0.331988 +4 0.055240 0.011619 0.143932 0.331988 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001051_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/OG0001051_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..132946df2f1996c319c3859b8abf0b47e1ff651d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001051_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 0.49572135 Before NNI: tree length is 0.49572137 + 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/OG0001052_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/OG0001052_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e2668a29fb238ca7d1f506964c3c9a7b295cf1af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001052_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013907 0.074948 0.087652 0.014789 +1 0.013907 0.000001 0.070266 0.082971 0.000882 +2 0.074948 0.070266 0.000001 0.094576 0.071148 +3 0.087652 0.082971 0.094576 0.000001 0.083853 +4 0.014789 0.000882 0.071148 0.083853 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001057_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/OG0001057_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..169e2d092a446f1c2aa24e7fe26685f0f2c88869 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001057_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 1.84479900 Before NNI: tree length is 1.84479900 + 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/OG0001058_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/OG0001058_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..059fcdb687ec54273e1398d5fd46a8068d82f3a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001058_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001896 0.302419 0.230561 0.001896 +1 0.001896 0.000001 0.304314 0.232457 0.000001 +2 0.302419 0.304314 0.000001 0.270781 0.304314 +3 0.230561 0.232457 0.270781 0.000001 0.232457 +4 0.001896 0.000001 0.304314 0.232457 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001062_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/OG0001062_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b658c81601faba51117da32c9d85f9128de676bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001062_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 0.17779370 Before NNI: tree length is 0.17779375 + 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/OG0001063_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/OG0001063_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..62669fc3d049255bb6aff0c72a877db115828619 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001063_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 0.35168000 Before NNI: tree length is 0.35168000 + 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/OG0001065_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/OG0001065_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..831b9e13194629b42f81107271b75dc97f118288 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001065_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025144 0.082109 0.193806 0.025144 +1 0.025144 0.000001 0.083368 0.195065 0.000001 +2 0.082109 0.083368 0.000001 0.199508 0.083368 +3 0.193806 0.195065 0.199508 0.000001 0.195065 +4 0.025144 0.000001 0.083368 0.195065 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001066_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/OG0001066_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab861b56d777613a62379779942f92299b3201d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001066_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 0.31093650 Before NNI: tree length is 0.31093650 + 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/OG0001067_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/OG0001067_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9ab400bd1110790e454abcff287dd1bc445703d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001067_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026120 0.191007 0.287758 0.026120 +1 0.026120 0.000001 0.189231 0.285982 0.000001 +2 0.191007 0.189231 0.000001 0.328260 0.189231 +3 0.287758 0.285982 0.328260 0.000001 0.285982 +4 0.026120 0.000001 0.189231 0.285982 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001068_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/OG0001068_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f73ecde157bdfd5d2971f599df2d4bf122ee9abe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001068_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009320 0.309857 0.746904 0.007718 +1 0.009320 0.000001 0.300537 0.737584 0.001602 +2 0.309857 0.300537 0.000001 0.717810 0.302139 +3 0.746904 0.737584 0.717810 0.000001 0.739186 +4 0.007718 0.001602 0.302139 0.739186 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001071_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/OG0001071_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d765c049a6b0e2d834ddf9ae045e0d5710e4cc20 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001071_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.130630 0.120796 0.000001 +1 0.000001 0.000001 0.130630 0.120796 0.000001 +2 0.130630 0.130630 0.000001 0.154254 0.130630 +3 0.120796 0.120796 0.154254 0.000001 0.120796 +4 0.000001 0.000001 0.130630 0.120796 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001071_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/OG0001071_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8f37b232201b2ad0e951a720806f0c461ad2937 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001071_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 0.20284100 Before NNI: tree length is 0.20284100 + 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/OG0001074_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/OG0001074_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..998a0ed29c93d6584a66d02b14f85c93f9b1dcc9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.210582 0.264950 0.000001 +1 0.000001 0.000001 0.210582 0.264950 0.000001 +2 0.210582 0.210582 0.000001 0.281250 0.210582 +3 0.264950 0.264950 0.281250 0.000001 0.264950 +4 0.000001 0.000001 0.210582 0.264950 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001074_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/OG0001074_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6457342094c1a01403027e818db3ed3f5df81eb8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001074_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 0.37839200 Before NNI: tree length is 0.37839200 + 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/OG0001077_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/OG0001077_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39234901659973d034cf099c8d8eb5d3492301a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001077_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010081 0.212029 0.331633 0.007746 +1 0.010081 0.000001 0.206834 0.326438 0.003203 +2 0.212029 0.206834 0.000001 0.282521 0.205150 +3 0.331633 0.326438 0.282521 0.000001 0.324755 +4 0.007746 0.003203 0.205150 0.324755 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001077_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/OG0001077_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..340a31c2e3d2f751934008ed172ca2fe5174b119 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001077_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 0.41596839 Before NNI: tree length is 0.41596838 + 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/OG0001078_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/OG0001078_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b65666a55b44e29bd9dd308a45c880fa84c5dc4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001078_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024957 0.298968 0.873391 0.024957 +1 0.024957 0.000001 0.291068 0.865491 0.000001 +2 0.298968 0.291068 0.000001 0.844112 0.291068 +3 0.873391 0.865491 0.844112 0.000001 0.865491 +4 0.024957 0.000001 0.291068 0.865491 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001079_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/OG0001079_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a60ddc68b5cb37b182c162fb984eec56b1bb17d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040332 0.261745 0.472190 0.040332 +1 0.040332 0.000001 0.287711 0.498156 0.000001 +2 0.261745 0.287711 0.000001 0.528066 0.287711 +3 0.472190 0.498156 0.528066 0.000001 0.498156 +4 0.040332 0.000001 0.287711 0.498156 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001079_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/OG0001079_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0c05c716b51be9e6dd436bf03747ca8f65b5bd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001079_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 0.66415000 Before NNI: tree length is 0.66415000 + 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/OG0001084_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/OG0001084_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..16352e17cbbb6da6f845b8aac25694afbcda8615 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001084_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 0.23947550 Before NNI: tree length is 0.23947550 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..3ae25a26aa58569d2acf71c20b3c7fff89620c1f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.186922 0.229600 0.000001 +1 0.000001 0.000001 0.186922 0.229600 0.000001 +2 0.186922 0.186922 0.000001 0.281497 0.186922 +3 0.229600 0.229600 0.281497 0.000001 0.229600 +4 0.000001 0.000001 0.186922 0.229600 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001089_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/OG0001089_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cafc1bfe995b5c566787ba0e1027829384267574 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001089_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.336440 0.640004 0.000001 +1 0.000001 0.000001 0.336440 0.640004 0.000001 +2 0.336440 0.336440 0.000001 0.786279 0.336440 +3 0.640004 0.640004 0.786279 0.000001 0.640004 +4 0.000001 0.000001 0.336440 0.640004 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001091_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/OG0001091_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbb6e3a82315c11527b64e3d1dc27919e7a74bb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001091_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.099957 0.248764 0.000001 +1 0.000001 0.000001 0.099957 0.248764 0.000001 +2 0.099957 0.099957 0.000001 0.259644 0.099957 +3 0.248764 0.248764 0.259644 0.000001 0.248764 +4 0.000001 0.000001 0.099957 0.248764 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001091_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/OG0001091_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c326ccba386e944d64298496d104d45773c0e640 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001091_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 0.30418350 Before NNI: tree length is 0.30418350 + 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/OG0001093_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/OG0001093_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32c67f81df984fdb3fb5e04cbe6bfe2b301eafac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001093_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 0.04448300 Before NNI: tree length is 0.04448300 + 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/OG0001096_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/OG0001096_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..488a78fcf110885f1a11045fdfc0ae3921eaba8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001096_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 0.30025420 Before NNI: tree length is 0.30025425 + 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/OG0001102_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/OG0001102_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..82f12c7c6fd97b17448b8f3410d313f869192c58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001102_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 0.36401125 Before NNI: tree length is 0.36401125 + 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/OG0001103_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/OG0001103_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2447cfbb3b4b9c9552d3052f29e8b49691ba7b38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001103_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017163 0.051511 0.187188 0.022857 +1 0.017163 0.000001 0.067260 0.202936 0.010249 +2 0.051511 0.067260 0.000001 0.185325 0.072954 +3 0.187188 0.202936 0.185325 0.000001 0.208630 +4 0.022857 0.010249 0.072954 0.208630 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001105_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/OG0001105_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..252b1f3f405bd199bdd975dca51dad67d580ece8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001105_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 0.28303575 Before NNI: tree length is 0.28303575 + 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/OG0001106_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/OG0001106_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..501e42802407685ac09166013259bc1c55e33fdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001106_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.066950 0.122686 0.226162 0.074916 +1 0.066950 0.000001 0.128461 0.231937 0.056458 +2 0.122686 0.128461 0.000001 0.178261 0.136427 +3 0.226162 0.231937 0.178261 0.000001 0.239902 +4 0.074916 0.056458 0.136427 0.239902 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001110_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/OG0001110_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d5a44bf538e929ae65deff1508538023fa60da68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001110_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003865 0.029051 0.015802 0.001624 +1 0.003865 0.000001 0.027552 0.014303 0.002241 +2 0.029051 0.027552 0.000001 0.036471 0.027426 +3 0.015802 0.014303 0.036471 0.000001 0.014177 +4 0.001624 0.002241 0.027426 0.014177 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001113_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/OG0001113_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21b5ead560f29c628b9d0df66988f8c1878a783d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001113_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 1.08744184 Before NNI: tree length is 1.08744187 + 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/OG0001114_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/OG0001114_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b3d30da8221932c7c2e9030f0f705a0be608afa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001114_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 0.17855000 Before NNI: tree length is 0.17855000 + 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/OG0001115_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/OG0001115_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6e9b4d9b86cc5635b87f75621c0c0535cb14f1c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001115_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003713 0.016819 0.075277 0.000001 +1 0.003713 0.000001 0.018315 0.076772 0.003713 +2 0.016819 0.018315 0.000001 0.086872 0.016819 +3 0.075277 0.076772 0.086872 0.000001 0.075277 +4 0.000001 0.003713 0.016819 0.075277 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001119_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/OG0001119_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd58933ed62c3d3c2656b80debad1de999675aa7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001119_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 0.39231285 Before NNI: tree length is 0.39231287 + 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/OG0001121_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/OG0001121_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9a4fcfa725b9790247339f219fc720e8da26424 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001121_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 0.33065425 Before NNI: tree length is 0.33065425 + 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/OG0001124_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/OG0001124_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8a7ab8746ea64c2e314ece9e2a196e602784ec8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001124_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 0.13023200 Before NNI: tree length is 0.13023200 + 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/OG0001125_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/OG0001125_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e15a12e0bb8e3bbcf0dbeb77613b39895f06972a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001125_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 0.10629970 Before NNI: tree length is 0.10629975 + 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/OG0001130_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/OG0001130_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..177fb838c6b1086ebb6f8e14e42be5887c54c8c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001130_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032938 0.276253 0.435514 0.052659 +1 0.032938 0.000001 0.298307 0.457569 0.074713 +2 0.276253 0.298307 0.000001 0.458159 0.266340 +3 0.435514 0.457569 0.458159 0.000001 0.425602 +4 0.052659 0.074713 0.266340 0.425602 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001131_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/OG0001131_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b32d745f6a89e318afe425c4fd7e4c287da4ffd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001131_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 0.53691486 Before NNI: tree length is 0.53691488 + 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/OG0001138_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/OG0001138_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a119ee0e6f6ed7191e4796be049c319fb292c550 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001138_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014129 0.119800 0.184570 0.013866 +1 0.014129 0.000001 0.117001 0.181772 0.007333 +2 0.119800 0.117001 0.000001 0.182021 0.116737 +3 0.184570 0.181772 0.182021 0.000001 0.181508 +4 0.013866 0.007333 0.116737 0.181508 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001138_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/OG0001138_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6a96b0670295e5923e85360564b9bd3ea188d13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001138_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 0.25239553 Before NNI: tree length is 0.25239550 + 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/OG0001140_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/OG0001140_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..76bfe51bc01eb4f3cc40b7b1768f85c2a8b07dfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001140_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 0.46883250 Before NNI: tree length is 0.46883250 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..54d66c6ec255968e1eec34bd95df6465c0bf7422 --- /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_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 0.48007150 Before NNI: tree length is 0.48007150 + 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/OG0001142_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/OG0001142_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c602b566ffce5fefb20f221c3c0b12fc2202f809 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059427 0.291082 0.785075 0.004899 +1 0.059427 0.000001 0.316361 0.810353 0.064325 +2 0.291082 0.316361 0.000001 0.807783 0.295981 +3 0.785075 0.810353 0.807783 0.000001 0.789973 +4 0.004899 0.064325 0.295981 0.789973 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001142_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/OG0001142_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc965c92712ff30040d3672b67f3a4fe9a96bb08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001142_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 0.98922140 Before NNI: tree length is 0.98922137 + 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/OG0001143_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/OG0001143_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a36b395589ad2c8dcd8570fada44a1b17909a11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001143_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 0.22179100 Before NNI: tree length is 0.22179100 + 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/OG0001145_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/OG0001145_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..793768a031b14f177554cd43caaf046e5d9ad862 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001145_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 1.09719350 Before NNI: tree length is 1.09719350 + 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/OG0001147_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/OG0001147_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a057168a2ee756708c439fc8b9fcdc9a1f029e0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001147_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034155 0.245922 0.408689 0.017036 +1 0.034155 0.000001 0.266655 0.429421 0.037769 +2 0.245922 0.266655 0.000001 0.378556 0.242121 +3 0.408689 0.429421 0.378556 0.000001 0.404888 +4 0.017036 0.037769 0.242121 0.404888 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001148_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/OG0001148_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e9d3441f04919bc351bc09b4d6ee700a6aa0b046 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001148_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.159954 0.260744 0.009702 +1 0.000001 0.000001 0.159954 0.260744 0.009702 +2 0.159954 0.159954 0.000001 0.293040 0.150253 +3 0.260744 0.260744 0.293040 0.000001 0.251042 +4 0.009702 0.009702 0.150253 0.251042 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001151_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/OG0001151_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f697420f5a7786830e5a42794945ed2a5dca470 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052466 0.097614 0.150835 0.009680 +1 0.052466 0.000001 0.114763 0.167983 0.055454 +2 0.097614 0.114763 0.000001 0.181216 0.100603 +3 0.150835 0.167983 0.181216 0.000001 0.153823 +4 0.009680 0.055454 0.100603 0.153823 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001151_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/OG0001151_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2914b4a49d30fd736a53ee51d08665613bb0af3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001151_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 0.25597389 Before NNI: tree length is 0.25597388 + 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/OG0001152_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/OG0001152_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de5ad5afc7fdd1ecf1fbebfd0b2ab6875505e9ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001152_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006704 0.269572 0.490335 0.000001 +1 0.006704 0.000001 0.268449 0.489211 0.006704 +2 0.269572 0.268449 0.000001 0.441533 0.269572 +3 0.490335 0.489211 0.441533 0.000001 0.490335 +4 0.000001 0.006704 0.269572 0.490335 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001152_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/OG0001152_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50d2bad0d8398bf7136ae40342ff99cd4caeeb98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001152_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 0.60351079 Before NNI: tree length is 0.60351075 + 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/OG0001159_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/OG0001159_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e5ad2f4f54eaa48eceff37f3c048635661e7f2bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012736 0.136605 0.372930 0.012736 +1 0.012736 0.000001 0.141089 0.377414 0.000001 +2 0.136605 0.141089 0.000001 0.447843 0.141089 +3 0.372930 0.377414 0.447843 0.000001 0.377414 +4 0.012736 0.000001 0.141089 0.377414 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001159_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/OG0001159_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab2e3eee57df4f01a424300ea2546e81097146a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001159_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 0.48729950 Before NNI: tree length is 0.48729950 + 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/OG0001162_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/OG0001162_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0046fc603e95c2a9ee000138b5ff0acc2b2432bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.113771 0.608460 1.303616 0.113771 +1 0.113771 0.000001 0.672178 1.367333 0.000001 +2 0.608460 0.672178 0.000001 1.614174 0.672178 +3 1.303616 1.367333 1.614174 0.000001 1.367333 +4 0.113771 0.000001 0.672178 1.367333 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001164_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/OG0001164_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4494a3c7ddb4b2f769aaff38d8798fc7138a954a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001164_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005408 0.149498 0.313703 0.000283 +1 0.005408 0.000001 0.154906 0.319111 0.005125 +2 0.149498 0.154906 0.000001 0.338193 0.149781 +3 0.313703 0.319111 0.338193 0.000001 0.313986 +4 0.000283 0.005125 0.149781 0.313986 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001168_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/OG0001168_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..510f0d97f14b70c92ae7a68e801e581a8c3971e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001168_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005875 0.057541 0.093108 0.004501 +1 0.005875 0.000001 0.057672 0.093240 0.008644 +2 0.057541 0.057672 0.000001 0.076172 0.060309 +3 0.093108 0.093240 0.076172 0.000001 0.095876 +4 0.004501 0.008644 0.060309 0.095876 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001173_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/OG0001173_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f11379f8f5273c268e0f526b0199e113de980a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001173_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 0.33854975 Before NNI: tree length is 0.33854975 + 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/OG0001174_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/OG0001174_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7100ff1727d2733f1f8f235dbdcb5db231cbaef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001174_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025714 0.103175 0.253325 0.025714 +1 0.025714 0.000001 0.105765 0.255915 0.000001 +2 0.103175 0.105765 0.000001 0.260233 0.105765 +3 0.253325 0.255915 0.260233 0.000001 0.255915 +4 0.025714 0.000001 0.105765 0.255915 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001174_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/OG0001174_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..43728be0c7ac4fe4cb7825b06556366cc975d4dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001174_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 0.32251900 Before NNI: tree length is 0.32251900 + 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/OG0001175_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/OG0001175_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ec63cd9a2138cbf0f8832465000f04fa097bb6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001175_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 0.56161277 Before NNI: tree length is 0.56161275 + 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/OG0001176_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/OG0001176_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae98c821e2ce407797d0109916c372aa4923191b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001176_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 0.55468800 Before NNI: tree length is 0.55468800 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..10fa724aa9f5c563fafa60e14a19243469f778a4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009926 0.086467 0.169307 0.001934 +1 0.009926 0.000001 0.089612 0.172452 0.011861 +2 0.086467 0.089612 0.000001 0.189980 0.088401 +3 0.169307 0.172452 0.189980 0.000001 0.171241 +4 0.001934 0.011861 0.088401 0.171241 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001179_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/OG0001179_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a7877a87e01eb9a1a55888f76d8b727caf698be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001179_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 0.32269395 Before NNI: tree length is 0.32269400 + 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/OG0001181_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/OG0001181_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af35348fd7d16811f6441df24592b62b5e171ff7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001181_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 0.06081750 Before NNI: tree length is 0.06081750 + 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/OG0001184_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/OG0001184_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..117a80c4f3895e358908b74726b91ff7c5330ff5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001184_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 0.20826150 Before NNI: tree length is 0.20826150 + 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/OG0001188_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/OG0001188_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5387e94262eec0ffebef67cc1abc4c8f94a837e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001188_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012872 0.088630 0.135430 0.013628 +1 0.012872 0.000001 0.088634 0.135434 0.013633 +2 0.088630 0.088634 0.000001 0.141028 0.087535 +3 0.135430 0.135434 0.141028 0.000001 0.134335 +4 0.013628 0.013633 0.087535 0.134335 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001190_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/OG0001190_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d3f4438ccdc98976579e8b4b49308b70b930e30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001190_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 0.46846350 Before NNI: tree length is 0.46846350 + 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/OG0001194_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/OG0001194_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..68576ba02e4ac3537292716e6510471c4235fd82 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001194_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 0.55273522 Before NNI: tree length is 0.55273525 + 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/OG0001198_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/OG0001198_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c202dafe3ebda2f5bbe09b4a366d54566a848480 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001198_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 0.90197913 Before NNI: tree length is 0.90197912 + 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/OG0001199_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/OG0001199_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8990c4abfc02968a0346276a9ee6f5549c26a0b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001199_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.263727 0.458471 0.372114 0.045467 +1 0.263727 0.000001 0.362316 0.407061 0.280598 +2 0.458471 0.362316 0.000001 0.601805 0.475342 +3 0.372114 0.407061 0.601805 0.000001 0.388985 +4 0.045467 0.280598 0.475342 0.388985 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001199_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/OG0001199_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..feb786e947bca9ec8c2c725a57bc238f60b49aa4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001199_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 0.83115000 Before NNI: tree length is 0.83115000 + 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/OG0001201_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/OG0001201_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dcc81e8320466ace34e8e13a94a6fdec82fab3de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.245847 0.239857 0.509443 0.037124 +1 0.245847 0.000001 0.270381 0.539967 0.258613 +2 0.239857 0.270381 0.000001 0.371442 0.252623 +3 0.509443 0.539967 0.371442 0.000001 0.522209 +4 0.037124 0.258613 0.252623 0.522209 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001201_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/OG0001201_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..563e37f4b84df2a4054a2d42ca1f24bae727802a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001201_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 0.72350150 Before NNI: tree length is 0.72350150 + 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/OG0001202_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/OG0001202_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..489242b79e31ac67f91a6d3ecf91910d5f50c9e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001202_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 0.20708000 Before NNI: tree length is 0.20708000 + 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/OG0001203_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/OG0001203_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b9dad25788167bd4bb68e08bd0c43079765a4ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001203_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 1.57157850 Before NNI: tree length is 1.57157850 + 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/OG0001204_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/OG0001204_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a9b00552c1ea99676897e25ebd72d2de018b2fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001204_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 0.01197750 Before NNI: tree length is 0.01197750 + 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/OG0001205_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/OG0001205_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c72f80e84fc9cc5cc3585a8ce815fd090fe2405d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001205_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.151448 0.338605 0.000001 +1 0.000001 0.000001 0.151448 0.338605 0.000001 +2 0.151448 0.151448 0.000001 0.358198 0.151448 +3 0.338605 0.338605 0.358198 0.000001 0.338605 +4 0.000001 0.000001 0.151448 0.338605 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001206_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/OG0001206_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d0b57da427f77ec2b0c53f5000ac567176fa746 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001206_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 0.98819150 Before NNI: tree length is 0.98819150 + 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/OG0001207_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/OG0001207_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bcf0ff45ca4df6227527fe7f6917d19777e3f3b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001207_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019564 0.225470 0.506846 0.007426 +1 0.019564 0.000001 0.216811 0.498188 0.012425 +2 0.225470 0.216811 0.000001 0.577521 0.218330 +3 0.506846 0.498188 0.577521 0.000001 0.499707 +4 0.007426 0.012425 0.218330 0.499707 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001209_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/OG0001209_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5b78a6981c96ae2dbdcdd29f1bc5993f0450974 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001209_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029218 0.339051 0.682254 0.011798 +1 0.029218 0.000001 0.363207 0.706410 0.017420 +2 0.339051 0.363207 0.000001 0.637979 0.345787 +3 0.682254 0.706410 0.637979 0.000001 0.688990 +4 0.011798 0.017420 0.345787 0.688990 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001210_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/OG0001210_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1fabe8289d3f5f054dee2eefef1b2b9f855bcceb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001210_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021599 0.590301 0.825144 0.000001 +1 0.021599 0.000001 0.596309 0.831151 0.021599 +2 0.590301 0.596309 0.000001 0.855878 0.590301 +3 0.825144 0.831151 0.855878 0.000001 0.825144 +4 0.000001 0.021599 0.590301 0.825144 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001211_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/OG0001211_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d232f1514802182ad49c823ca28b530b563d2f34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001211_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 0.99047300 Before NNI: tree length is 0.99047300 + 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/OG0001212_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/OG0001212_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a590f6210811d92335e99f3ee14a45111b632aee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001212_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011478 0.054868 0.137556 0.006344 +1 0.011478 0.000001 0.056165 0.138853 0.011924 +2 0.054868 0.056165 0.000001 0.142019 0.055314 +3 0.137556 0.138853 0.142019 0.000001 0.138002 +4 0.006344 0.011924 0.055314 0.138002 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001218_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/OG0001218_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..30eab28ae82ccb958db0cf942331248442301126 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001218_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 0.49130326 Before NNI: tree length is 0.49130325 + 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/OG0001219_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/OG0001219_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9900e3e8094f5b6808f299113c36f4ed0604dd2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001219_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 0.19539650 Before NNI: tree length is 0.19539650 + 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/OG0001220_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/OG0001220_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b94866697bc6214349093b553fcac00470c42d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026753 0.200491 0.048355 0.025239 +1 0.026753 0.000001 0.197673 0.045537 0.003505 +2 0.200491 0.197673 0.000001 0.213719 0.196160 +3 0.048355 0.045537 0.213719 0.000001 0.044024 +4 0.025239 0.003505 0.196160 0.044024 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001225_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/OG0001225_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3369e499762a378e69b369d456513799cb591f67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001225_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023579 0.248665 0.565315 0.023112 +1 0.023579 0.000001 0.247730 0.564380 0.010240 +2 0.248665 0.247730 0.000001 0.517291 0.247263 +3 0.565315 0.564380 0.517291 0.000001 0.563913 +4 0.023112 0.010240 0.247263 0.563913 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001229_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/OG0001229_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5cf8e55689321d91482cfa25c37a25d0fbabae80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001229_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005072 0.157493 0.320914 0.004236 +1 0.005072 0.000001 0.152421 0.315842 0.000837 +2 0.157493 0.152421 0.000001 0.331113 0.153258 +3 0.320914 0.315842 0.331113 0.000001 0.316679 +4 0.004236 0.000837 0.153258 0.316679 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001230_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/OG0001230_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2bd35b04d2215a8e8f4f3e2bf4ddd497edf53559 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005224 0.057293 0.527090 0.005215 +1 0.005224 0.000001 0.058477 0.528273 0.001736 +2 0.057293 0.058477 0.000001 0.510181 0.058468 +3 0.527090 0.528273 0.510181 0.000001 0.528264 +4 0.005215 0.001736 0.058468 0.528264 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001230_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/OG0001230_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..490c851e46f0d3f50e1445f288c65f1201208df5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001230_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 0.55134917 Before NNI: tree length is 0.55134925 + 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/OG0001231_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/OG0001231_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18bc18480b5d1c5273f056c6ffddd1072cd53a93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001231_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 0.30666750 Before NNI: tree length is 0.30666750 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d63026fb8f5c35e938425d42c0d6af1a59b9829f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008285 0.397854 1.191850 0.025891 +1 0.008285 0.000001 0.389569 1.183564 0.017606 +2 0.397854 0.389569 0.000001 1.280628 0.372515 +3 1.191850 1.183564 1.280628 0.000001 1.166510 +4 0.025891 0.017606 0.372515 1.166510 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001238_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/OG0001238_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5fd499245a89444a24cdf3b38d72aa4275b87e9b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001238_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 0.44978725 Before NNI: tree length is 0.44978725 + 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/OG0001239_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/OG0001239_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..224609c98c6b9dfb15033e95787e9fdbe81e6aa3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001239_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013147 0.155618 0.380174 0.009403 +1 0.013147 0.000001 0.157429 0.381985 0.013468 +2 0.155618 0.157429 0.000001 0.396383 0.155938 +3 0.380174 0.381985 0.396383 0.000001 0.380495 +4 0.009403 0.013468 0.155938 0.380495 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001239_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/OG0001239_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58dfcab8d9400ed573157a459739b6db4978cfa8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001239_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 0.47842840 Before NNI: tree length is 0.47842838 + 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/OG0001240_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/OG0001240_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a599f8ede02a66440dcf109b988f89e1d0e6070e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001240_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018471 0.331980 0.719993 0.039218 +1 0.018471 0.000001 0.332126 0.720138 0.039364 +2 0.331980 0.332126 0.000001 0.580079 0.311969 +3 0.719993 0.720138 0.580079 0.000001 0.699981 +4 0.039218 0.039364 0.311969 0.699981 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001241_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/OG0001241_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d55c50f4152c681a6e229168e2c03c3f21beee38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001241_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 0.30434040 Before NNI: tree length is 0.30434037 + 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/OG0001242_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/OG0001242_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4e5147581570caf2fc7a725e1619258bc73c4a83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003571 0.063152 0.056733 0.003571 +1 0.003571 0.000001 0.060269 0.053850 0.000001 +2 0.063152 0.060269 0.000001 0.070046 0.060269 +3 0.056733 0.053850 0.070046 0.000001 0.053850 +4 0.003571 0.000001 0.060269 0.053850 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001243_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/OG0001243_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88325ab7fbb15952ff349e265c552fcb6815122c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001243_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005386 0.081629 0.023672 0.009112 +1 0.005386 0.000001 0.079773 0.021816 0.004014 +2 0.081629 0.079773 0.000001 0.088535 0.083499 +3 0.023672 0.021816 0.088535 0.000001 0.025542 +4 0.009112 0.004014 0.083499 0.025542 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001245_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/OG0001245_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a11f33b19b1a7a309dd5eab2138ff31aa7a23e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001245_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013932 0.066047 0.437598 0.000001 +1 0.013932 0.000001 0.063704 0.435254 0.013932 +2 0.066047 0.063704 0.000001 0.413451 0.066047 +3 0.437598 0.435254 0.413451 0.000001 0.437598 +4 0.000001 0.013932 0.066047 0.437598 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001245_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/OG0001245_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d3ee0b109470bb65725fc9ceb81bc46d148defe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001245_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 0.46434282 Before NNI: tree length is 0.46434275 + 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/OG0001249_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/OG0001249_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d61e3f3f65e879f2db1aea7e24bedff1e29a6af1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001249_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001102 0.109259 0.224629 0.000001 +1 0.001102 0.000001 0.108918 0.224288 0.001102 +2 0.109259 0.108918 0.000001 0.246072 0.109259 +3 0.224629 0.224288 0.246072 0.000001 0.224629 +4 0.000001 0.001102 0.109259 0.224629 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001251_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/OG0001251_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e4f3496e0ebd679043ee44b44a74c93781a1f943 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001251_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001588 0.176675 0.267816 0.001588 +1 0.001588 0.000001 0.175161 0.266302 0.000001 +2 0.176675 0.175161 0.000001 0.300585 0.175161 +3 0.267816 0.266302 0.300585 0.000001 0.266302 +4 0.001588 0.000001 0.175161 0.266302 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001251_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/OG0001251_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0b213bbb2f06df943e5d6b4d5603e9bacd48be2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001251_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 0.37257550 Before NNI: tree length is 0.37257550 + 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/OG0001252_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/OG0001252_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9b77496d499d4fe5a70da01b7445ad2e97eff12 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001252_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 0.27870171 Before NNI: tree length is 0.27870175 + 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/OG0001253_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/OG0001253_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f49348edca1e09428e6f14172b56fb716f904a7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001253_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006203 0.182880 0.326984 0.010869 +1 0.006203 0.000001 0.179462 0.323566 0.007452 +2 0.182880 0.179462 0.000001 0.332045 0.180621 +3 0.326984 0.323566 0.332045 0.000001 0.324725 +4 0.010869 0.007452 0.180621 0.324725 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001254_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/OG0001254_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e11696259a28cdcf8c3c3b063139b6c8390e8e47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001254_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 1.30208150 Before NNI: tree length is 1.30208150 + 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/OG0001255_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/OG0001255_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94e9a508159536a376c939e28a177d6f024160b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001255_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 0.25418600 Before NNI: tree length is 0.25418600 + 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/OG0001257_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/OG0001257_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c602452416ea3f1121b08c1447720f1357703cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001257_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 0.34607700 Before NNI: tree length is 0.34607700 + 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/OG0001258_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/OG0001258_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f131b98b6cbf53aaff57abe171c66367b54715c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001258_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 0.24419100 Before NNI: tree length is 0.24419100 + 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/OG0001263_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/OG0001263_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f3c0aa0517f64c2c2eebbb8534fb5ea0804d358b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001263_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.111594 0.226865 0.036441 +1 0.000001 0.000001 0.111594 0.226865 0.036441 +2 0.111594 0.111594 0.000001 0.234239 0.102639 +3 0.226865 0.226865 0.234239 0.000001 0.217909 +4 0.036441 0.036441 0.102639 0.217909 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001263_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/OG0001263_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e00d0e251d6814b4a2ebcbbff937b9b558c99c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001263_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 0.30009229 Before NNI: tree length is 0.30009225 + 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/OG0001265_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/OG0001265_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..89769d6d9c1818774d79769998da490cd6420bb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001265_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 1.26389466 Before NNI: tree length is 1.26389463 + 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/OG0001268_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/OG0001268_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b85e64a646f9f498da889031ed36d3c37a574e42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001268_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 0.52382775 Before NNI: tree length is 0.52382775 + 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/OG0001270_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/OG0001270_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..607064381d4ddb3be6277d7b2499bd71dcc316ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001270_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 0.27079850 Before NNI: tree length is 0.27079850 + 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/OG0001271_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/OG0001271_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ef4a42d90e2f10e87691334d081500d2984dd32 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001271_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009592 0.025264 0.136856 0.009592 +1 0.009592 0.000001 0.026851 0.138442 0.000001 +2 0.025264 0.026851 0.000001 0.138683 0.026851 +3 0.136856 0.138442 0.138683 0.000001 0.138442 +4 0.009592 0.000001 0.026851 0.138442 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001272_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/OG0001272_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..230e2d15287701fd87f20a007bb553be02577b7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001272_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 0.37436950 Before NNI: tree length is 0.37436950 + 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/OG0001274_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/OG0001274_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6e76a2f67dd9d39fba725a0e225cbd408547c300 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001274_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013277 0.119815 0.179659 0.004176 +1 0.013277 0.000001 0.120470 0.180314 0.009102 +2 0.119815 0.120470 0.000001 0.120537 0.115640 +3 0.179659 0.180314 0.120537 0.000001 0.175484 +4 0.004176 0.009102 0.115640 0.175484 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001275_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/OG0001275_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..80afd15db5f36c15bbba712c8fc45f4d7138c549 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001275_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006412 0.037854 0.074642 0.007648 +1 0.006412 0.000001 0.033564 0.070352 0.003358 +2 0.037854 0.033564 0.000001 0.073339 0.031636 +3 0.074642 0.070352 0.073339 0.000001 0.068424 +4 0.007648 0.003358 0.031636 0.068424 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001276_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/OG0001276_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..477fbd296a22e1ef119c30089c662186f7b9322e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001276_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014783 0.093087 0.201959 0.020318 +1 0.014783 0.000001 0.100450 0.209322 0.012838 +2 0.093087 0.100450 0.000001 0.191825 0.105984 +3 0.201959 0.209322 0.191825 0.000001 0.214857 +4 0.020318 0.012838 0.105984 0.214857 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001277_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/OG0001277_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c30aacfb35f02fa1ce6eb27c1e29cc81b06bf10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001277_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 0.09440550 Before NNI: tree length is 0.09440550 + 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/OG0001279_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/OG0001279_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8352195cc79eef258d9a8c3e41c4fce5d3c4385 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001279_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008800 0.092545 0.197760 0.011064 +1 0.008800 0.000001 0.091299 0.196514 0.004636 +2 0.092545 0.091299 0.000001 0.219925 0.093563 +3 0.197760 0.196514 0.219925 0.000001 0.198778 +4 0.011064 0.004636 0.093563 0.198778 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001279_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/OG0001279_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3450c52f9e6aba79d0e0cab1c09f24b6be6c065 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001279_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 0.26234200 Before NNI: tree length is 0.26234200 + 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/OG0001282_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/OG0001282_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbc868bf6e9ab8d22a1018461202df7600b8e028 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001282_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 0.32673200 Before NNI: tree length is 0.32673200 + 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/OG0001283_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/OG0001283_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba609bc666621e9cd5fc3956268c92b5329625da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001283_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 1.03243081 Before NNI: tree length is 1.03243075 + 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/OG0001286_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/OG0001286_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5663fdf5d242e755900fbc38adb40a437e1cf0eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001286_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 0.21927629 Before NNI: tree length is 0.21927625 + 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/OG0001288_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/OG0001288_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..069ef8cce0f488278532b206cc244edb7bf36a7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001288_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 0.89873515 Before NNI: tree length is 0.89873512 + 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/OG0001289_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/OG0001289_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..312c5adbad6e67c850c333e7cd371fd4f4dd7016 --- /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_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 0.40262497 Before NNI: tree length is 0.40262500 + 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/OG0001292_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/OG0001292_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b6f62b7cc6cd2bc1930e6feff9ccf2bbfee1852 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001292_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001321 0.097752 0.018337 0.001497 +1 0.001321 0.000001 0.096431 0.017016 0.000177 +2 0.097752 0.096431 0.000001 0.109231 0.096255 +3 0.018337 0.017016 0.109231 0.000001 0.016839 +4 0.001497 0.000177 0.096255 0.016839 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001293_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/OG0001293_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b304bc31075e3aacb20cf51e282817e90493ec8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001293_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024120 0.216320 0.025461 0.029285 +1 0.024120 0.000001 0.214957 0.024097 0.005166 +2 0.216320 0.214957 0.000001 0.198979 0.220122 +3 0.025461 0.024097 0.198979 0.000001 0.029263 +4 0.029285 0.005166 0.220122 0.029263 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001297_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/OG0001297_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a1d863f1583997c21719765a308b25cf3ec7753d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005671 0.280187 0.242399 0.000001 +1 0.005671 0.000001 0.278580 0.240792 0.005671 +2 0.280187 0.278580 0.000001 0.355127 0.280187 +3 0.242399 0.240792 0.355127 0.000001 0.242399 +4 0.000001 0.005671 0.280187 0.242399 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001300_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/OG0001300_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fa79acce2b11a7c136ec8dfc0154ce1c189d0880 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001300_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 1.031694 0.062638 0.032885 +1 0.000001 0.000001 1.031694 0.062638 0.032885 +2 1.031694 1.031694 0.000001 0.969055 1.006718 +3 0.062638 0.062638 0.969055 0.000001 0.037663 +4 0.032885 0.032885 1.006718 0.037663 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001301_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/OG0001301_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46243d79220eae6af8f1fe3c3931733c4f943d27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001301_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004145 0.015255 0.014321 0.006905 +1 0.004145 0.000001 0.017588 0.016654 0.007367 +2 0.015255 0.017588 0.000001 0.003670 0.020348 +3 0.014321 0.016654 0.003670 0.000001 0.019414 +4 0.006905 0.007367 0.020348 0.019414 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001302_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/OG0001302_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7ad327cbcc97ebd552259b1b6a14fe39eb7742c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001302_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033542 0.066040 0.065032 0.033829 +1 0.033542 0.000001 0.096529 0.095521 0.006536 +2 0.066040 0.096529 0.000001 0.030869 0.096815 +3 0.065032 0.095521 0.030869 0.000001 0.095807 +4 0.033829 0.006536 0.096815 0.095807 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001302_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/OG0001302_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b56fcbb7147e674eb1a4e0cd197fa3c7f7b17f13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001302_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 0.11639725 Before NNI: tree length is 0.11639725 + 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/OG0001303_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/OG0001303_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..86cd09487bb40381f85300d50608b91717f029f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001303_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003782 0.096044 0.024270 0.000001 +1 0.003782 0.000001 0.092739 0.020964 0.003782 +2 0.096044 0.092739 0.000001 0.092298 0.096044 +3 0.024270 0.020964 0.092298 0.000001 0.024270 +4 0.000001 0.003782 0.096044 0.024270 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..454f431877d0e1a7511296f0e75d8e8dff1d55b1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.076612 0.054014 0.081076 0.070986 +1 0.076612 0.000001 0.068388 0.076849 0.054698 +2 0.054014 0.068388 0.000001 0.072852 0.062761 +3 0.081076 0.076849 0.072852 0.000001 0.071223 +4 0.070986 0.054698 0.062761 0.071223 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001311_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/OG0001311_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..365669b7c1ce4d8da0927dd49626f0aa4b38a0d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001311_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 0.58806513 Before NNI: tree length is 0.58806512 + 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/OG0001312_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/OG0001312_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..52c78514626a1309c76216eb34340380143586ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001312_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028813 0.143232 0.365197 0.023313 +1 0.028813 0.000001 0.128532 0.350497 0.017866 +2 0.143232 0.128532 0.000001 0.355144 0.132285 +3 0.365197 0.350497 0.355144 0.000001 0.354250 +4 0.023313 0.017866 0.132285 0.354250 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001312_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/OG0001312_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..603d638e9b892844761a8ece9201c914d749c795 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001312_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 0.44502600 Before NNI: tree length is 0.44502600 + 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/OG0001314_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/OG0001314_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb0932d267198cb67d4d4c051a836c91ceebd367 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001314_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 0.15486772 Before NNI: tree length is 0.15486775 + 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/OG0001316_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/OG0001316_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fdacf3e6a3aa5c02a09d7271150b46b033b62fbd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001316_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016412 0.279801 0.259307 0.010529 +1 0.016412 0.000001 0.286989 0.266495 0.022049 +2 0.279801 0.286989 0.000001 0.307411 0.285438 +3 0.259307 0.266495 0.307411 0.000001 0.264944 +4 0.010529 0.022049 0.285438 0.264944 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001319_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/OG0001319_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..274695c6e53d943a7ed3fe8a6920ad08f5ebcd1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001319_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.055342 0.070025 0.004190 +1 0.000001 0.000001 0.055342 0.070025 0.004190 +2 0.055342 0.055342 0.000001 0.069598 0.059486 +3 0.070025 0.070025 0.069598 0.000001 0.074170 +4 0.004190 0.004190 0.059486 0.074170 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001320_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/OG0001320_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d44d73544c19408dc1618156f0f692b2909d03e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001320_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.118786 0.780699 0.937817 0.155802 +1 0.118786 0.000001 0.727863 0.884981 0.230824 +2 0.780699 0.727863 0.000001 0.988056 0.892737 +3 0.937817 0.884981 0.988056 0.000001 1.049855 +4 0.155802 0.230824 0.892737 1.049855 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001322_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/OG0001322_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..53d6f4008fc0e44fc23c003dea46df38f23bfc0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001322_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 0.78743625 Before NNI: tree length is 0.78743625 + 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/OG0001324_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/OG0001324_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd5dcd36259d9b06b1b9408424b33c742eeb3045 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001324_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 2.20206535 Before NNI: tree length is 2.20206538 + 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/OG0001325_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/OG0001325_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f268814c508634a5fbd90d63bafc3c91f0f72c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001325_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 0.35012675 Before NNI: tree length is 0.35012675 + 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/OG0001329_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/OG0001329_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af2231133e216769972d65bad537bdae7e3ad7af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001329_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010105 0.123747 0.321515 0.011784 +1 0.010105 0.000001 0.123920 0.321688 0.016323 +2 0.123747 0.123920 0.000001 0.322025 0.129965 +3 0.321515 0.321688 0.322025 0.000001 0.327734 +4 0.011784 0.016323 0.129965 0.327734 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001332_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/OG0001332_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..83e0534252a3fdaefe50583c74e15f2cfaf271e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001332_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024111 0.247111 0.401886 0.012966 +1 0.024111 0.000001 0.237835 0.392609 0.014872 +2 0.247111 0.237835 0.000001 0.369509 0.237873 +3 0.401886 0.392609 0.369509 0.000001 0.392648 +4 0.012966 0.014872 0.237873 0.392648 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001335_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/OG0001335_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..825d9fbfb4777d6bc5a86f5def7c8a575216b86e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001335_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 0.24307772 Before NNI: tree length is 0.24307775 + 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/OG0001336_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/OG0001336_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..60b328cc1589de0bdcfafc937ee9526e155d30bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001336_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008159 0.008182 0.021766 0.008135 +1 0.008159 0.000001 0.000023 0.013608 0.000023 +2 0.008182 0.000023 0.000001 0.013584 0.000046 +3 0.021766 0.013608 0.013584 0.000001 0.013631 +4 0.008135 0.000023 0.000046 0.013631 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001338_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/OG0001338_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0a67c87b65fea57312074475b93dadf3965a7d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001338_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 0.16772028 Before NNI: tree length is 0.16772025 + 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/OG0001339_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/OG0001339_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2208d73a3baf95a2bbe7ab8d57118441c075dea7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013561 0.093514 0.012329 0.014743 +1 0.013561 0.000001 0.084378 0.016477 0.015418 +2 0.093514 0.084378 0.000001 0.096431 0.095371 +3 0.012329 0.016477 0.096431 0.000001 0.017660 +4 0.014743 0.015418 0.095371 0.017660 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001340_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/OG0001340_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71ec44a03cf4fb4678ce21652fd1ad85da33314a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063983 0.207512 0.088592 0.036589 +1 0.063983 0.000001 0.193362 0.108616 0.038992 +2 0.207512 0.193362 0.000001 0.252144 0.182521 +3 0.088592 0.108616 0.252144 0.000001 0.081222 +4 0.036589 0.038992 0.182521 0.081222 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001340_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/OG0001340_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7e4d18a9b6b3c3a08fb7e171fd208672cefa75d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001340_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 0.30483986 Before NNI: tree length is 0.30483987 + 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/OG0001342_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/OG0001342_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a861d2a91e8e40135099bb1760eabbdb1929ca1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001342_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011606 0.276279 0.325380 0.010137 +1 0.011606 0.000001 0.281137 0.330238 0.014995 +2 0.276279 0.281137 0.000001 0.179915 0.274721 +3 0.325380 0.330238 0.179915 0.000001 0.323822 +4 0.010137 0.014995 0.274721 0.323822 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001345_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/OG0001345_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d834dd2e874e9860ea2a936c8b392c275ed0948b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039273 0.144684 0.382528 0.039273 +1 0.039273 0.000001 0.130397 0.368241 0.000001 +2 0.144684 0.130397 0.000001 0.373423 0.130397 +3 0.382528 0.368241 0.373423 0.000001 0.368241 +4 0.039273 0.000001 0.130397 0.368241 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001347_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/OG0001347_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..964d28c3c8141719ab8ad67128a7df60f904d454 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001347_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019749 0.018818 0.119433 0.009835 +1 0.019749 0.000001 0.026651 0.112064 0.023070 +2 0.018818 0.026651 0.000001 0.126335 0.022138 +3 0.119433 0.112064 0.126335 0.000001 0.122754 +4 0.009835 0.023070 0.022138 0.122754 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001349_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/OG0001349_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28ba58c7567e4eaed734c770fe0d4abc1dae96e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001349_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 0.30904400 Before NNI: tree length is 0.30904400 + 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/OG0001350_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/OG0001350_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c9174ccf459d9222d9af58061ed67326961fe75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001350_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009994 0.124837 0.394095 0.038269 +1 0.009994 0.000001 0.133259 0.402517 0.046691 +2 0.124837 0.133259 0.000001 0.382697 0.120835 +3 0.394095 0.402517 0.382697 0.000001 0.390093 +4 0.038269 0.046691 0.120835 0.390093 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001351_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/OG0001351_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8053d968d32aa7d35dacba35eac63bd81c501289 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001351_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 0.65308110 Before NNI: tree length is 0.65308113 + 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/OG0001352_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/OG0001352_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbb2390bf51c22fd23a541992fae0004b80e407b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001352_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 0.67570100 Before NNI: tree length is 0.67570100 + 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/OG0001353_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/OG0001353_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..984aa8f051b79cb70a49afd86ffb0990a4895b6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.059540 0.221006 0.003976 +1 0.000001 0.000001 0.059540 0.221006 0.003976 +2 0.059540 0.059540 0.000001 0.227995 0.060593 +3 0.221006 0.221006 0.227995 0.000001 0.222060 +4 0.003976 0.003976 0.060593 0.222060 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001354_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/OG0001354_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4110fa258127f9cee19003b0767f7db10b051a8b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001354_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006160 0.302865 0.698143 0.042480 +1 0.006160 0.000001 0.300573 0.695851 0.040188 +2 0.302865 0.300573 0.000001 0.708423 0.286742 +3 0.698143 0.695851 0.708423 0.000001 0.682019 +4 0.042480 0.040188 0.286742 0.682019 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fdd0b856eb60fe57a3aa7861d593fb140acf4fd --- /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_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 0.32914500 Before NNI: tree length is 0.32914500 + 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/OG0001358_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/OG0001358_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a20ed665ad887df9573b4f38751037ca816feb38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001358_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 0.52946050 Before NNI: tree length is 0.52946050 + 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/OG0001362_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/OG0001362_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f0f3c44ada138e14145aef729c673a168d8b4e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009950 0.057600 0.057256 0.000001 +1 0.009950 0.000001 0.056723 0.056379 0.009950 +2 0.057600 0.056723 0.000001 0.074589 0.057600 +3 0.057256 0.056379 0.074589 0.000001 0.057256 +4 0.000001 0.009950 0.057600 0.057256 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001362_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/OG0001362_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..38ced075767d5b334feaf1060cb27bc07bca49f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001362_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 0.09925950 Before NNI: tree length is 0.09925950 + 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/OG0001363_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/OG0001363_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..221d3c1a7dcf028d8b9fbc9e6d78313a45a7489f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000060 0.014987 0.057720 0.005181 +1 0.000060 0.000001 0.014927 0.057660 0.005241 +2 0.014987 0.014927 0.000001 0.042733 0.020168 +3 0.057720 0.057660 0.042733 0.000001 0.062901 +4 0.005181 0.005241 0.020168 0.062901 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001364_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/OG0001364_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9036b05d676a5c18746e040a2f063ffd1cb34f5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001364_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025499 0.172040 0.423974 0.016453 +1 0.025499 0.000001 0.178022 0.429956 0.016773 +2 0.172040 0.178022 0.000001 0.392766 0.168976 +3 0.423974 0.429956 0.392766 0.000001 0.420910 +4 0.016453 0.016773 0.168976 0.420910 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001365_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/OG0001365_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0d618951119b8e44e0b2c1557ea77c11744b3b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001365_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 0.15764700 Before NNI: tree length is 0.15764700 + 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/OG0001366_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/OG0001366_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..20f0dc242a7f936231f9d6aaa5b665fe0f513ff9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001366_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006211 0.016528 0.061041 0.004744 +1 0.006211 0.000001 0.018442 0.062955 0.004695 +2 0.016528 0.018442 0.000001 0.049686 0.016974 +3 0.061041 0.062955 0.049686 0.000001 0.061487 +4 0.004744 0.004695 0.016974 0.061487 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001377_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/OG0001377_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be795c058e0c8103f9a8203aaa855868a2f7aff5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001377_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006524 0.024040 0.028408 0.006524 +1 0.006524 0.000001 0.019664 0.024032 0.000001 +2 0.024040 0.019664 0.000001 0.039479 0.019664 +3 0.028408 0.024032 0.039479 0.000001 0.024032 +4 0.006524 0.000001 0.019664 0.024032 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001377_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/OG0001377_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..250079edf3b2de4b9f31efad93817e69898a2f8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001377_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 0.04703800 Before NNI: tree length is 0.04703800 + 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/OG0001378_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/OG0001378_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0f16d744af9ec771703ef40e5f75399cd6542a4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.069349 0.056760 0.136688 0.069349 +1 0.069349 0.000001 0.030020 0.089247 0.000001 +2 0.056760 0.030020 0.000001 0.097359 0.030020 +3 0.136688 0.089247 0.097359 0.000001 0.089247 +4 0.069349 0.000001 0.030020 0.089247 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001378_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/OG0001378_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f75cb240fba789a4bd23fb643a76bff51520aaf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001378_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 0.15635800 Before NNI: tree length is 0.15635800 + 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/OG0001380_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/OG0001380_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..643fd0d9eb35163a55a38e6d93a591746da84bbe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001380_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 0.03935350 Before NNI: tree length is 0.03935350 + 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/OG0001382_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/OG0001382_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b17c5fe8c7cf472a94efa6a82a957b37396ef14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001382_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 0.01475450 Before NNI: tree length is 0.01475450 + 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/OG0001383_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/OG0001383_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2980a24d53eee235e396381fbb74552d6c18657b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001383_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 0.15845550 Before NNI: tree length is 0.15845550 + 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/OG0001384_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/OG0001384_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c932c6535903d17f2a46dd995fec53f14dea6084 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001384_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.027977 0.107420 0.000001 +1 0.000001 0.000001 0.027977 0.107420 0.000001 +2 0.027977 0.027977 0.000001 0.123899 0.027977 +3 0.107420 0.107420 0.123899 0.000001 0.107420 +4 0.000001 0.000001 0.027977 0.107420 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001384_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/OG0001384_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..88f4ff173e4d6f31a8125760c3bfa5156eb3867b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001384_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 0.12964900 Before NNI: tree length is 0.12964900 + 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/OG0001385_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/OG0001385_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0fa2c2290da37803e36f50121f060f566d418eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001385_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 0.02325650 Before NNI: tree length is 0.02325650 + 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/OG0001387_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/OG0001387_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0f6edb7debfeeba9f6f0baed0be2b945851be4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001387_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 0.02437050 Before NNI: tree length is 0.02437050 + 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/OG0001388_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/OG0001388_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74968325ab523994ccb0938669b23b70feadb32a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001388_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.005222 0.000001 +1 0.000001 0.000001 0.000001 0.005222 0.000001 +2 0.000001 0.000001 0.000001 0.005222 0.000001 +3 0.005222 0.005222 0.005222 0.000001 0.005222 +4 0.000001 0.000001 0.000001 0.005222 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001390_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/OG0001390_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed7536fd8cb55e71bf0be113369c9508bf9e5f91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001390_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 0.07935750 Before NNI: tree length is 0.07935750 + 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/OG0001392_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/OG0001392_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..176052d23673120f6c215bc93476cf7fae81f749 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001392_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011124 0.021431 0.031702 0.000030 +1 0.011124 0.000001 0.032555 0.042826 0.011154 +2 0.021431 0.032555 0.000001 0.034639 0.021401 +3 0.031702 0.042826 0.034639 0.000001 0.031671 +4 0.000030 0.011154 0.021401 0.031671 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001394_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/OG0001394_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1814594d7afe8b4c3afbf934fe4e0aa5d25f9475 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001394_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016448 0.264852 0.454450 0.000001 +1 0.016448 0.000001 0.261497 0.451095 0.016448 +2 0.264852 0.261497 0.000001 0.387367 0.264852 +3 0.454450 0.451095 0.387367 0.000001 0.454450 +4 0.000001 0.016448 0.264852 0.454450 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001396_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/OG0001396_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58685998754aeb2bb82a7696e5932e7b64b29b38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001396_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003306 0.014325 0.024934 0.000095 +1 0.003306 0.000001 0.017632 0.028241 0.003402 +2 0.014325 0.017632 0.000001 0.021380 0.014230 +3 0.024934 0.028241 0.021380 0.000001 0.024839 +4 0.000095 0.003402 0.014230 0.024839 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..86e76bdc6f93e0f61c37f229ed30402f29fa996e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004141 0.012498 0.012498 0.004141 +1 0.004141 0.000001 0.012498 0.012498 0.000001 +2 0.012498 0.012498 0.000001 0.008333 0.012498 +3 0.012498 0.012498 0.008333 0.000001 0.012498 +4 0.004141 0.000001 0.012498 0.012498 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001403_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/OG0001403_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..032c3562db5627ea27a416686c8d0a229ef71adb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001403_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006349 0.026869 0.083183 0.006349 +1 0.006349 0.000001 0.022717 0.079030 0.000001 +2 0.026869 0.022717 0.000001 0.068996 0.022717 +3 0.083183 0.079030 0.068996 0.000001 0.079030 +4 0.006349 0.000001 0.022717 0.079030 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001403_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/OG0001403_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..96bffcfe1964423cde09f761002158c105c08251 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001403_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 0.09062268 Before NNI: tree length is 0.09062275 + 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/OG0001404_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/OG0001404_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b12eb97c6a0a9200fde1fd3326c2128f2d7b6fa2 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004744 0.019956 0.100657 0.003391 +1 0.004744 0.000001 0.024700 0.105401 0.008136 +2 0.019956 0.024700 0.000001 0.094260 0.019990 +3 0.100657 0.105401 0.094260 0.000001 0.100691 +4 0.003391 0.008136 0.019990 0.100691 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001409_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/OG0001409_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fb2c36829a54bf5ea824a1721682debc79d8c45a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001409_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017495 0.104347 0.227518 0.027826 +1 0.017495 0.000001 0.102817 0.225988 0.026295 +2 0.104347 0.102817 0.000001 0.186246 0.097054 +3 0.227518 0.225988 0.186246 0.000001 0.220225 +4 0.027826 0.026295 0.097054 0.220225 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001409_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/OG0001409_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc7198158eeb794ac11a218d6a6e49da8434f33a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001409_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 0.27730425 Before NNI: tree length is 0.27730425 + 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/OG0001411_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/OG0001411_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94f3a40a6225d1528c8cc677c36653f505a7b0de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001411_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 0.93094375 Before NNI: tree length is 0.93094375 + 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/OG0001412_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/OG0001412_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6bf3325ee2cb28d7fd8ce68922817344ac9105a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001412_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 0.10957300 Before NNI: tree length is 0.10957300 + 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/OG0001413_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/OG0001413_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..14b5774d01df4fcf2d8adb672c5467aeff9c0668 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001413_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009933 0.346224 1.197808 0.007318 +1 0.009933 0.000001 0.356158 1.207741 0.005426 +2 0.346224 0.356158 0.000001 1.224205 0.353542 +3 1.197808 1.207741 1.224205 0.000001 1.205126 +4 0.007318 0.005426 0.353542 1.205126 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001414_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/OG0001414_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63b3756c23d7ad1c619f39eb05d4d9b72b6a5f62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001414_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 0.41191100 Before NNI: tree length is 0.41191100 + 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/OG0001415_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/OG0001415_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3df884b051ece7763a07f96dd1ac35852c596a88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001415_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.109116 0.222386 0.000001 +1 0.000001 0.000001 0.109116 0.222386 0.000001 +2 0.109116 0.109116 0.000001 0.222984 0.109116 +3 0.222386 0.222386 0.222984 0.000001 0.222386 +4 0.000001 0.000001 0.109116 0.222386 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001416_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/OG0001416_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d6f0f543a85a51b1fba2a4fd20755c14dbb855dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001416_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.038370 0.137276 0.000001 +1 0.000001 0.000001 0.038370 0.137276 0.000001 +2 0.038370 0.038370 0.000001 0.098906 0.038370 +3 0.137276 0.137276 0.098906 0.000001 0.137276 +4 0.000001 0.000001 0.038370 0.137276 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001418_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/OG0001418_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..288d6105f3e248e7943c9dce1378dfbfebda2256 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001418_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.284597 0.520392 0.013141 +1 0.000001 0.000001 0.284597 0.520392 0.013141 +2 0.284597 0.284597 0.000001 0.477027 0.282698 +3 0.520392 0.520392 0.477027 0.000001 0.518493 +4 0.013141 0.013141 0.282698 0.518493 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001419_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/OG0001419_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3177cc64958cd30ef998b7c7c8ee3976b8ff480a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001419_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.188429 0.458802 0.011164 +1 0.000001 0.000001 0.188429 0.458802 0.011164 +2 0.188429 0.188429 0.000001 0.481483 0.179897 +3 0.458802 0.458802 0.481483 0.000001 0.450270 +4 0.011164 0.011164 0.179897 0.450270 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001420_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/OG0001420_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..060c020563c4740eba537ce7de32785c0d494f74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001420_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 0.34609750 Before NNI: tree length is 0.34609750 + 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/OG0001422_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/OG0001422_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..826db4176c8e769269cdccc043bbe3d244df9b87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001422_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 0.31783700 Before NNI: tree length is 0.31783700 + 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/OG0001423_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/OG0001423_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..917d938610de86c36cef30032d73a69a19c47dd5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001423_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.141884 0.372323 0.036634 +1 0.000001 0.000001 0.141884 0.372323 0.036634 +2 0.141884 0.141884 0.000001 0.373343 0.164540 +3 0.372323 0.372323 0.373343 0.000001 0.394979 +4 0.036634 0.036634 0.164540 0.394979 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001425_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/OG0001425_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c29ece019fda40481f7bdd3d8788d48d890fcfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001425_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.153454 0.270538 0.015067 +1 0.000001 0.000001 0.153454 0.270538 0.015067 +2 0.153454 0.153454 0.000001 0.276084 0.155046 +3 0.270538 0.270538 0.276084 0.000001 0.272130 +4 0.015067 0.015067 0.155046 0.272130 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001425_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/OG0001425_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d52c026746d9e1d82aaaeef1001d316b1169087c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001425_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 0.35836800 Before NNI: tree length is 0.35836800 + 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/OG0001426_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/OG0001426_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d909d30991d5b9fadf10754d38ac1711381acdae --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000325 0.120150 0.327376 0.014963 +1 0.000325 0.000001 0.120475 0.327701 0.014638 +2 0.120150 0.120475 0.000001 0.309902 0.135113 +3 0.327376 0.327701 0.309902 0.000001 0.342339 +4 0.014963 0.014638 0.135113 0.342339 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001427_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/OG0001427_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8b72ecf56d6c104c00a46d2b5fe276371168874 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001427_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 0.26653400 Before NNI: tree length is 0.26653400 + 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/OG0001430_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/OG0001430_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..303640349c63dfcbb1869539a187c1b437b9a0e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.127949 0.686018 0.011881 +1 0.000001 0.000001 0.127949 0.686018 0.011881 +2 0.127949 0.127949 0.000001 0.736885 0.125314 +3 0.686018 0.686018 0.736885 0.000001 0.683383 +4 0.011881 0.011881 0.125314 0.683383 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001430_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/OG0001430_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bbfe3aa2fd35b05f75dab226e89dbd119d0404b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001430_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 0.78004950 Before NNI: tree length is 0.78004950 + 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3e253ca72d5c43ecda33a6d76818331ac91fc23 --- /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_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 0.14822873 Before NNI: tree length is 0.14822875 + 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/OG0001432_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/OG0001432_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5dcb1feb647cd77b060d6267d3480560eacc8ba3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001432_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002706 0.184823 0.137462 0.003270 +1 0.002706 0.000001 0.184417 0.137056 0.001853 +2 0.184823 0.184417 0.000001 0.214730 0.184981 +3 0.137462 0.137056 0.214730 0.000001 0.137619 +4 0.003270 0.001853 0.184981 0.137619 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001432_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/OG0001432_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5daa4acf16b435d41851c5212293a876a359b0f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001432_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 0.27086588 Before NNI: tree length is 0.27086588 + 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/OG0001433_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/OG0001433_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..59f813179aba63a165a50232eac7b3b87e02dca2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001433_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006508 0.115097 0.279837 0.012881 +1 0.006508 0.000001 0.113928 0.278667 0.011711 +2 0.115097 0.113928 0.000001 0.271364 0.115736 +3 0.279837 0.278667 0.271364 0.000001 0.280476 +4 0.012881 0.011711 0.115736 0.280476 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001433_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/OG0001433_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e0a49d6c7259b1684b1f1d32ed9c20809c79772 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001433_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 0.34257810 Before NNI: tree length is 0.34257812 + 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/OG0001434_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/OG0001434_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e1485cafee26290c9eabf1599133b9150d4ee69d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.050085 0.148315 0.390454 0.040323 +1 0.050085 0.000001 0.144097 0.386235 0.029710 +2 0.148315 0.144097 0.000001 0.366382 0.134335 +3 0.390454 0.386235 0.366382 0.000001 0.376474 +4 0.040323 0.029710 0.134335 0.376474 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001435_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/OG0001435_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..174d61a651593ea3d85b9cdfaf9f2b41702e4ca8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001435_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029722 0.233745 0.982666 0.014807 +1 0.029722 0.000001 0.262385 1.011306 0.032035 +2 0.233745 0.262385 0.000001 0.960669 0.247471 +3 0.982666 1.011306 0.960669 0.000001 0.996392 +4 0.014807 0.032035 0.247471 0.996392 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001437_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/OG0001437_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..47138574141c279e8d8447a0ccf83fb5f033c07d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001437_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025080 0.178697 0.496015 0.025080 +1 0.025080 0.000001 0.167993 0.485311 0.000001 +2 0.178697 0.167993 0.000001 0.510321 0.167993 +3 0.496015 0.485311 0.510321 0.000001 0.485311 +4 0.025080 0.000001 0.167993 0.485311 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001438_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/OG0001438_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18c45d0828575212d21f6c8c5a86b3a36f5d389e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001438_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 0.34669100 Before NNI: tree length is 0.34669100 + 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/OG0001439_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/OG0001439_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..51024c76eedb24129edd5e7154b383029e90e350 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001439_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 0.32322300 Before NNI: tree length is 0.32322300 + 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/OG0001440_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/OG0001440_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41a3a257f6802f921dec925b44e1671f7909c393 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001440_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 0.17882463 Before NNI: tree length is 0.17882463 + 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/OG0001444_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/OG0001444_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5c6b79af49b3c96708c967e07a11ff250307f981 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024716 0.253895 0.435782 0.030114 +1 0.024716 0.000001 0.239061 0.420947 0.008280 +2 0.253895 0.239061 0.000001 0.410569 0.244458 +3 0.435782 0.420947 0.410569 0.000001 0.426345 +4 0.030114 0.008280 0.244458 0.426345 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001446_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/OG0001446_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab6363458440122968c9e0ae22e30173186335c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001446_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 0.29304287 Before NNI: tree length is 0.29304287 + 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/OG0001449_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/OG0001449_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9df3fc92772e8f7a06944d655553099a7e7f9cdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001449_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 0.25730700 Before NNI: tree length is 0.25730700 + 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/OG0001450_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/OG0001450_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55f03e87080db5774ef5be70e87da3cb837c0c59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001450_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009784 0.037077 0.275025 0.007755 +1 0.009784 0.000001 0.035955 0.273903 0.003272 +2 0.037077 0.035955 0.000001 0.278913 0.033927 +3 0.275025 0.273903 0.278913 0.000001 0.271875 +4 0.007755 0.003272 0.033927 0.271875 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001451_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/OG0001451_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21c9b70a15437be70cd3e6e154e82b2c1f16ddc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001451_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 0.31186100 Before NNI: tree length is 0.31186100 + 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/OG0001453_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/OG0001453_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..743e95771c18766422cd7a2439a9ab69ac88092e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001453_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 0.04399639 Before NNI: tree length is 0.04399637 + 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/OG0001454_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/OG0001454_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9bf3a667dbf1645585ecd29031094bc46a56ed86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001454_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063908 0.071551 0.022402 0.034373 +1 0.063908 0.000001 0.028675 0.061359 0.073331 +2 0.071551 0.028675 0.000001 0.069002 0.080973 +3 0.022402 0.061359 0.069002 0.000001 0.023960 +4 0.034373 0.073331 0.080973 0.023960 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001455_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/OG0001455_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..51a78c0854b5889c4fffac49094ccb858569b1ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001455_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 0.29376259 Before NNI: tree length is 0.29376262 + 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/OG0001460_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/OG0001460_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ba14a871a82dabb5b72c4695fe905a3a1d9370cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001460_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031006 0.129619 0.238225 0.046596 +1 0.031006 0.000001 0.141223 0.249828 0.016902 +2 0.129619 0.141223 0.000001 0.283987 0.156813 +3 0.238225 0.249828 0.283987 0.000001 0.265419 +4 0.046596 0.016902 0.156813 0.265419 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001462_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/OG0001462_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8018b3a7b746f630a48bb0a88e17f8a79c3b6ad0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001462_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 0.30237621 Before NNI: tree length is 0.30237625 + 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/OG0001463_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/OG0001463_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7345b15b317250fdead986c6ee3d870e2b5e80cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001463_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011773 0.157655 0.218967 0.012392 +1 0.011773 0.000001 0.160442 0.221754 0.015179 +2 0.157655 0.160442 0.000001 0.193945 0.154406 +3 0.218967 0.221754 0.193945 0.000001 0.215718 +4 0.012392 0.015179 0.154406 0.215718 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001468_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/OG0001468_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e98a8cbbbb7b7c81f0a8a9bbfffd699bbc6a242b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001468_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 0.14666361 Before NNI: tree length is 0.14666362 + 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/OG0001469_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/OG0001469_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..86a6f79a3cb66d9afd6b752ee788c09bdbb3d2c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029721 0.251403 0.240931 0.013644 +1 0.029721 0.000001 0.258643 0.248172 0.026647 +2 0.251403 0.258643 0.000001 0.271296 0.248329 +3 0.240931 0.248172 0.271296 0.000001 0.237857 +4 0.013644 0.026647 0.248329 0.237857 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001469_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/OG0001469_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a80c093e6fad8864290ae79dccdd068178f95ad8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001469_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 0.40558075 Before NNI: tree length is 0.40558075 + 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/OG0001470_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/OG0001470_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..05b010a11106cf6342fc2e5e8054e893717dbca7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001470_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044227 0.138725 0.283210 0.000001 +1 0.044227 0.000001 0.151446 0.295930 0.044227 +2 0.138725 0.151446 0.000001 0.256586 0.138725 +3 0.283210 0.295930 0.256586 0.000001 0.283210 +4 0.000001 0.044227 0.138725 0.283210 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001471_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/OG0001471_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a00f0c71788718f56174ba2ff024f1e3a7afc1e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001471_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059456 0.162180 0.526752 0.000001 +1 0.059456 0.000001 0.130579 0.495151 0.059456 +2 0.162180 0.130579 0.000001 0.519226 0.162180 +3 0.526752 0.495151 0.519226 0.000001 0.526752 +4 0.000001 0.059456 0.162180 0.526752 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001471_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/OG0001471_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f6d28b1eee7e45fd4dcedb4409df85dc0a2af4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001471_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 0.61800700 Before NNI: tree length is 0.61800700 + 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/OG0001472_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/OG0001472_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2a02c16b5558e89b0513a79fb74084ac925c5f29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023054 0.178861 0.234988 0.014585 +1 0.023054 0.000001 0.181754 0.237880 0.020341 +2 0.178861 0.181754 0.000001 0.272181 0.176149 +3 0.234988 0.237880 0.272181 0.000001 0.232275 +4 0.014585 0.020341 0.176149 0.232275 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001474_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/OG0001474_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f0a9c69e38856b3f5187ed115395e0f006757860 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001474_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.145587 0.387110 0.839374 0.029777 +1 0.145587 0.000001 0.298939 0.751202 0.146209 +2 0.387110 0.298939 0.000001 0.830474 0.387733 +3 0.839374 0.751202 0.830474 0.000001 0.839997 +4 0.029777 0.146209 0.387733 0.839997 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001475_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/OG0001475_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8ad1c241d648eb1d76cb6f97d421358d9437bf9c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001475_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043485 0.294540 0.598871 0.000001 +1 0.043485 0.000001 0.305181 0.609512 0.043485 +2 0.294540 0.305181 0.000001 0.627415 0.294540 +3 0.598871 0.609512 0.627415 0.000001 0.598871 +4 0.000001 0.043485 0.294540 0.598871 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001477_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/OG0001477_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ce5bc425445f2ed788d590fe95933e6cb587ca9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001477_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029287 0.260894 0.612108 0.047547 +1 0.029287 0.000001 0.253214 0.604428 0.039866 +2 0.260894 0.253214 0.000001 0.540657 0.257226 +3 0.612108 0.604428 0.540657 0.000001 0.608440 +4 0.047547 0.039866 0.257226 0.608440 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001478_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/OG0001478_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ee50db0a6c93a5401fe6d66c02e9d38b523f2ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001478_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 0.64144603 Before NNI: tree length is 0.64144600 + 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/OG0001481_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/OG0001481_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8b68e6b02255a15e5c106f5212d4eb6c1c1ecf23 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001481_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.102152 0.227551 1.276604 0.124702 +1 0.102152 0.000001 0.211612 1.260665 0.115398 +2 0.227551 0.211612 0.000001 1.288858 0.240797 +3 1.276604 1.260665 1.288858 0.000001 1.289850 +4 0.124702 0.115398 0.240797 1.289850 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001483_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/OG0001483_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e2049c384d3a60245b06a2e5ead263ab97ed2409 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001483_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011641 0.079819 0.243648 0.008801 +1 0.011641 0.000001 0.085285 0.249115 0.003875 +2 0.079819 0.085285 0.000001 0.257999 0.082446 +3 0.243648 0.249115 0.257999 0.000001 0.246275 +4 0.008801 0.003875 0.082446 0.246275 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001485_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/OG0001485_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..252fc2ade4a4451214069ef484ae7e5849d00924 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001485_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044694 0.317858 0.549708 0.044694 +1 0.044694 0.000001 0.338517 0.570367 0.000001 +2 0.317858 0.338517 0.000001 0.607417 0.338517 +3 0.549708 0.570367 0.607417 0.000001 0.570367 +4 0.044694 0.000001 0.338517 0.570367 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001487_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/OG0001487_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..45e9ff3d582fca59bc061a1b83d25aa0503c065d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001487_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 0.14777750 Before NNI: tree length is 0.14777750 + 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/OG0001488_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/OG0001488_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..13141643a00855049b2286fc22eac500efe7d92c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001488_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007416 0.087419 0.355019 0.013731 +1 0.007416 0.000001 0.091848 0.359448 0.018160 +2 0.087419 0.091848 0.000001 0.351487 0.087937 +3 0.355019 0.359448 0.351487 0.000001 0.355537 +4 0.013731 0.018160 0.087937 0.355537 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001489_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/OG0001489_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..88426ab106cd159d5b1b3a53fa89d733490a521b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001489_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 0.55473821 Before NNI: tree length is 0.55473825 + 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/OG0001490_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/OG0001490_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..795e99257e634bc110b19274455ba0c40c562356 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001490_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 0.51324850 Before NNI: tree length is 0.51324850 + 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/OG0001491_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/OG0001491_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0c6bd0e8b9ef4adceceb4870779b55416c1f3f91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001491_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.087241 0.425071 0.000001 +1 0.000001 0.000001 0.087241 0.425071 0.000001 +2 0.087241 0.087241 0.000001 0.444500 0.087241 +3 0.425071 0.425071 0.444500 0.000001 0.425071 +4 0.000001 0.000001 0.087241 0.425071 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001492_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/OG0001492_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f7b2dc80574001c7e47c3eacaf8da467338f88ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018943 0.355990 0.678744 0.060492 +1 0.018943 0.000001 0.374933 0.697687 0.079435 +2 0.355990 0.374933 0.000001 0.684168 0.365346 +3 0.678744 0.697687 0.684168 0.000001 0.688101 +4 0.060492 0.079435 0.365346 0.688101 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001494_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/OG0001494_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af08f45b3a02b2fbb88c2ba4d3863234207486be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001494_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032884 0.413881 0.838383 0.018592 +1 0.032884 0.000001 0.411235 0.835737 0.038091 +2 0.413881 0.411235 0.000001 0.775577 0.419088 +3 0.838383 0.835737 0.775577 0.000001 0.843590 +4 0.018592 0.038091 0.419088 0.843590 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001498_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/OG0001498_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d264b5ba66663be86ca7129bab6f0879bc7b813 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001498_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032993 0.296991 0.602410 0.000001 +1 0.032993 0.000001 0.298819 0.604239 0.032993 +2 0.296991 0.298819 0.000001 0.656515 0.296991 +3 0.602410 0.604239 0.656515 0.000001 0.602410 +4 0.000001 0.032993 0.296991 0.602410 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001499_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/OG0001499_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..727563bdcab4c22253d7cefe39af69adc7bc6f28 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001499_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 0.19734150 Before NNI: tree length is 0.19734150 + 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/OG0001500_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/OG0001500_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0419ad6965034acef76b3053d2e9436fcbaf0286 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009155 0.089249 0.214326 0.008197 +1 0.009155 0.000001 0.088009 0.213087 0.010627 +2 0.089249 0.088009 0.000001 0.227032 0.090720 +3 0.214326 0.213087 0.227032 0.000001 0.215797 +4 0.008197 0.010627 0.090720 0.215797 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001500_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/OG0001500_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dfb55953608e9d76d9b4815abb7b7e71650e9b50 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001500_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 0.27409545 Before NNI: tree length is 0.27409550 + 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/OG0001503_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/OG0001503_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc5df1ce282e4aaf6c26fd067b092a90ba559a78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001503_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 0.54698900 Before NNI: tree length is 0.54698900 + 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/OG0001507_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/OG0001507_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8868fd4a5657a5269b1e72afbd64aa2f619e6f4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001507_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 1.23331675 Before NNI: tree length is 1.23331675 + 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/OG0001509_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/OG0001509_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f3b08253b749183230fbb19ce7c8559c1c7e978b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001509_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004746 0.117665 0.140220 0.006858 +1 0.004746 0.000001 0.113923 0.136478 0.009974 +2 0.117665 0.113923 0.000001 0.164408 0.122893 +3 0.140220 0.136478 0.164408 0.000001 0.145448 +4 0.006858 0.009974 0.122893 0.145448 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001509_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/OG0001509_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..71fad68e47df0d1a72dd8ef9a2bb2423d9f90911 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001509_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 0.21769150 Before NNI: tree length is 0.21769150 + 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/OG0001512_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/OG0001512_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a07ef867d15aba5a96e37a06b79d327e9ad494a8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001512_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.144284 0.294908 0.002033 +1 0.000001 0.000001 0.144284 0.294908 0.002033 +2 0.144284 0.144284 0.000001 0.338796 0.144820 +3 0.294908 0.294908 0.338796 0.000001 0.295445 +4 0.002033 0.002033 0.144820 0.295445 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001513_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/OG0001513_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5ef09c9cdebba6c383504cd6bbf218b59c9dd9d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001513_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018836 0.475744 0.703421 0.096229 +1 0.018836 0.000001 0.460880 0.688557 0.081365 +2 0.475744 0.460880 0.000001 0.830612 0.482652 +3 0.703421 0.688557 0.830612 0.000001 0.710329 +4 0.096229 0.081365 0.482652 0.710329 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001514_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/OG0001514_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9d79c8eaeb652a204f6ea62974dcf769f4dbfe0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001514_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 0.38382896 Before NNI: tree length is 0.38382900 + 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/OG0001516_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/OG0001516_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d25a5ce61cefe693a9b162d9e7ef9a1ba90ec8bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001516_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.155243 0.606101 0.164761 +1 0.000001 0.000001 0.155243 0.606101 0.164761 +2 0.155243 0.155243 0.000001 0.618740 0.017570 +3 0.606101 0.606101 0.618740 0.000001 0.628259 +4 0.164761 0.164761 0.017570 0.628259 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001518_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/OG0001518_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28ef18acc1eb00234d4f750bca6a657e23d7a584 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001518_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 0.44434075 Before NNI: tree length is 0.44434075 + 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/OG0001520_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/OG0001520_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4145d70d50ed3968a00e49e6658320c607bd4d02 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001520_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 0.66103450 Before NNI: tree length is 0.66103450 + 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/OG0001524_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/OG0001524_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7fc35f3e9f1e95136c62a854c6db103603eb880b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001524_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035789 0.248676 0.383266 0.000001 +1 0.035789 0.000001 0.251407 0.385997 0.035789 +2 0.248676 0.251407 0.000001 0.359851 0.248676 +3 0.383266 0.385997 0.359851 0.000001 0.383266 +4 0.000001 0.035789 0.248676 0.383266 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001526_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/OG0001526_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f387217ee32f6c9256d8c7ce54791c707dac0e72 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001526_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 0.80896350 Before NNI: tree length is 0.80896350 + 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/OG0001528_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/OG0001528_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88272313397de989374abc08f2fbde1561665cac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001528_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.123567 0.200144 0.508639 0.121925 +1 0.123567 0.000001 0.154996 0.463492 0.013146 +2 0.200144 0.154996 0.000001 0.461702 0.153354 +3 0.508639 0.463492 0.461702 0.000001 0.461850 +4 0.121925 0.013146 0.153354 0.461850 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001531_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/OG0001531_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cf89291bd98164725922854a74d07abaa4181740 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001531_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007513 0.047348 0.120304 0.003890 +1 0.007513 0.000001 0.046442 0.119398 0.005280 +2 0.047348 0.046442 0.000001 0.114855 0.045115 +3 0.120304 0.119398 0.114855 0.000001 0.118071 +4 0.003890 0.005280 0.045115 0.118071 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001537_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/OG0001537_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ec0d803fce4d8cd09edf50a9e8561087ab27c15a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001537_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.056262 0.181256 0.320083 0.023501 +1 0.056262 0.000001 0.137395 0.276223 0.049063 +2 0.181256 0.137395 0.000001 0.255090 0.174057 +3 0.320083 0.276223 0.255090 0.000001 0.312885 +4 0.023501 0.049063 0.174057 0.312885 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001537_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/OG0001537_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a7699d0188668a80b8414b4f6e65077066ff9e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001537_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 0.39256635 Before NNI: tree length is 0.39256637 + 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/OG0001538_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/OG0001538_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3fba4a00dcc067b89e23c33d44a606c8cc950075 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001538_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.082034 0.336331 0.627288 0.101674 +1 0.082034 0.000001 0.351234 0.642191 0.019639 +2 0.336331 0.351234 0.000001 0.651341 0.370873 +3 0.627288 0.642191 0.651341 0.000001 0.661830 +4 0.101674 0.019639 0.370873 0.661830 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6bfb0749732dc09e988779c4ab7427e01fb3fb8a --- /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_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 1.63692700 Before NNI: tree length is 1.63692700 + 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/OG0001542_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/OG0001542_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1b4961679b84ab660d52fcda5a9f93eff26a397 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001542_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 0.05638550 Before NNI: tree length is 0.05638550 + 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/OG0001544_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/OG0001544_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..292ee1d916bd9fcc58f7699f0532871c399a88be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001544_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 0.03557625 Before NNI: tree length is 0.03557625 + 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/OG0001548_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/OG0001548_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74735b93b1e3628a1c3c26b513b6a06b0ca373fc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007707 0.127476 0.381153 0.016061 +1 0.007707 0.000001 0.135183 0.388860 0.023768 +2 0.127476 0.135183 0.000001 0.405904 0.117786 +3 0.381153 0.388860 0.405904 0.000001 0.371464 +4 0.016061 0.023768 0.117786 0.371464 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001551_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/OG0001551_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bcc44ad9080aebbe45659c05c9346a645193dcc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001551_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 1.75549600 Before NNI: tree length is 1.75549600 + 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/OG0001554_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/OG0001554_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3b7d1999e58684a61bdabcd97ce8efb16ef8a436 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001554_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017114 0.253017 0.393456 0.023830 +1 0.017114 0.000001 0.245049 0.385487 0.015861 +2 0.253017 0.245049 0.000001 0.392049 0.247141 +3 0.393456 0.385487 0.392049 0.000001 0.387579 +4 0.023830 0.015861 0.247141 0.387579 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001555_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/OG0001555_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..69b0211abd8987388cf58e0bcbf1a2973367f150 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001555_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 1.31660050 Before NNI: tree length is 1.31660050 + 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/OG0001556_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/OG0001556_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b8d0018ae691b51549a7a6cb7c531e3cc4c503f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001556_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000624 0.278001 0.270605 0.008153 +1 0.000624 0.000001 0.277377 0.269980 0.008777 +2 0.278001 0.277377 0.000001 0.253497 0.286154 +3 0.270605 0.269980 0.253497 0.000001 0.278757 +4 0.008153 0.008777 0.286154 0.278757 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001556_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/OG0001556_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae3aefb7367f9ec4e1e63ff6f31487c60a6c2255 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001556_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 0.40920412 Before NNI: tree length is 0.40920412 + 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/OG0001557_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/OG0001557_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c629e8161f4841c65b9a1463de5cc408405a9341 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001557_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020803 0.343745 0.968561 0.031220 +1 0.020803 0.000001 0.328191 0.953007 0.015665 +2 0.343745 0.328191 0.000001 0.927024 0.324805 +3 0.968561 0.953007 0.927024 0.000001 0.949621 +4 0.031220 0.015665 0.324805 0.949621 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001557_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/OG0001557_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..79c8eacce6b86167148a81b397537fec2bf45399 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001557_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 1.12842925 Before NNI: tree length is 1.12842925 + 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/OG0001558_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/OG0001558_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f9c0fd87f4b72866311e9489bc0566c089c6d92c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001558_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025435 0.240662 0.312557 0.029196 +1 0.025435 0.000001 0.229446 0.301342 0.017981 +2 0.240662 0.229446 0.000001 0.327129 0.223587 +3 0.312557 0.301342 0.327129 0.000001 0.295482 +4 0.029196 0.017981 0.223587 0.295482 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001559_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/OG0001559_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a94f70c93616f89bc84a7f999dc06d83db3d66c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001559_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 0.58915650 Before NNI: tree length is 0.58915650 + 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/OG0001563_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/OG0001563_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..61f28cc8c518abe2da427cdea933693c9b2e2ea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012096 0.317152 0.673616 0.000001 +1 0.012096 0.000001 0.317915 0.674379 0.012096 +2 0.317152 0.317915 0.000001 0.658862 0.317152 +3 0.673616 0.674379 0.658862 0.000001 0.673616 +4 0.000001 0.012096 0.317152 0.673616 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001564_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/OG0001564_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad2c3e5038c8f6753e1155302d57cc5d4e8cc2cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001564_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 0.95458500 Before NNI: tree length is 0.95458500 + 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/OG0001566_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/OG0001566_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b545606f4ec6eb6711c739ed94542ced370807b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001566_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018269 0.089687 0.020303 0.019456 +1 0.018269 0.000001 0.089908 0.020525 0.002913 +2 0.089687 0.089908 0.000001 0.089793 0.091096 +3 0.020303 0.020525 0.089793 0.000001 0.021712 +4 0.019456 0.002913 0.091096 0.021712 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001567_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/OG0001567_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d385888011a3128c42e2438cc934ca0d507c0c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001567_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 0.04661509 Before NNI: tree length is 0.04661513 + 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/OG0001569_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/OG0001569_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a49bb61917e96a3fca6d87c5d6bad6c72395eeca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001569_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 0.06284150 Before NNI: tree length is 0.06284150 + 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/OG0001572_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/OG0001572_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec9b876723c36ec091e45ab53704a27bb2737fd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001572_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 0.99646975 Before NNI: tree length is 0.99646975 + 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/OG0001573_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/OG0001573_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef35c07ec0f18e1040ead456cc7a7794bafa82c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041952 0.046146 0.437274 0.056094 +1 0.041952 0.000001 0.038928 0.430056 0.035641 +2 0.046146 0.038928 0.000001 0.428944 0.053071 +3 0.437274 0.430056 0.428944 0.000001 0.444199 +4 0.056094 0.035641 0.053071 0.444199 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001574_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/OG0001574_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f77ef91c6823f26488f62d6954ce37cbd9b80c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001574_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 0.59647641 Before NNI: tree length is 0.59647638 + 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/OG0001575_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/OG0001575_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df1e197b33ba350b7bc0bee2e4225200dfef11e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001575_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020627 0.035408 0.362255 0.012620 +1 0.020627 0.000001 0.036968 0.363815 0.018523 +2 0.035408 0.036968 0.000001 0.355875 0.033303 +3 0.362255 0.363815 0.355875 0.000001 0.360150 +4 0.012620 0.018523 0.033303 0.360150 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001575_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/OG0001575_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..de0b865412feb06ebfa18c91b0e8c7e9a9aa8013 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001575_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 0.39312025 Before NNI: tree length is 0.39312025 + 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/OG0001576_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/OG0001576_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bee2243419c4f06abe6f15ec0d469f728507f55b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001576_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 0.74277889 Before NNI: tree length is 0.74277887 + 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/OG0001579_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/OG0001579_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c30b42aa65fdeb7a75bd0a7767762202518d7d11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001579_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 0.46936117 Before NNI: tree length is 0.46936125 + 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/OG0001581_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/OG0001581_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f1fefaa8e292fa18b48a760b86cf5aa20df4719 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001581_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 0.26954833 Before NNI: tree length is 0.26954825 + 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/OG0001582_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/OG0001582_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8a8f89cbd544e1dcc7f40a4e37b82c4d49baad6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001582_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 0.32992950 Before NNI: tree length is 0.32992950 + 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/OG0001583_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/OG0001583_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a1bd5d826769f731f1b3c351939a3dd6ba541033 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001583_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000465 0.571436 0.011532 0.000232 +1 0.000465 0.000001 0.570971 0.011997 0.000232 +2 0.571436 0.570971 0.000001 0.582968 0.571204 +3 0.011532 0.011997 0.582968 0.000001 0.011765 +4 0.000232 0.000232 0.571204 0.011765 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001584_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/OG0001584_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..49923a4f2c807c01d779440fb92bf3147ebe821a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001584_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007032 0.090745 0.013396 0.000001 +1 0.007032 0.000001 0.087930 0.010581 0.007032 +2 0.090745 0.087930 0.000001 0.092439 0.090745 +3 0.013396 0.010581 0.092439 0.000001 0.013396 +4 0.000001 0.007032 0.090745 0.013396 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001589_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/OG0001589_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cdfe4fb2e71717f5fde2fb0beaffbd31fedb785b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001589_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015292 0.324411 0.108403 0.017888 +1 0.015292 0.000001 0.320746 0.104738 0.011977 +2 0.324411 0.320746 0.000001 0.345870 0.323342 +3 0.108403 0.104738 0.345870 0.000001 0.107334 +4 0.017888 0.011977 0.323342 0.107334 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001590_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/OG0001590_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..61ce415b3f6df4e9f36a8b129a3a5be8f809e72e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001590_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 0.08225090 Before NNI: tree length is 0.08225088 + 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/OG0001593_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/OG0001593_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58213de76717f4ad98a93809b2437d155ae1603c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001593_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021042 0.214893 0.230070 0.011953 +1 0.021042 0.000001 0.232329 0.247505 0.009089 +2 0.214893 0.232329 0.000001 0.055168 0.223240 +3 0.230070 0.247505 0.055168 0.000001 0.238416 +4 0.011953 0.009089 0.223240 0.238416 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001596_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/OG0001596_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..200fdce784aa63755e9b4b0fbdfa679d99a3e883 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001596_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 0.56155600 Before NNI: tree length is 0.56155600 + 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/OG0001597_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/OG0001597_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42320e8182a3c6ad56fb4535e5d6638f4ba4a367 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001597_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020374 0.090852 0.271764 0.019086 +1 0.020374 0.000001 0.090913 0.271825 0.032354 +2 0.090852 0.090913 0.000001 0.250417 0.102831 +3 0.271764 0.271825 0.250417 0.000001 0.283743 +4 0.019086 0.032354 0.102831 0.283743 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001597_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/OG0001597_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b450b9a0a2cb37d051ebce263b18ce44a0999079 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001597_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 0.33226675 Before NNI: tree length is 0.33226675 + 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/OG0001604_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/OG0001604_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..955a34b4b046636922b8de9e176f186a67f5ff6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001604_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.038197 0.070546 0.125744 0.028249 +1 0.038197 0.000001 0.045819 0.142965 0.022409 +2 0.070546 0.045819 0.000001 0.175314 0.054759 +3 0.125744 0.142965 0.175314 0.000001 0.133017 +4 0.028249 0.022409 0.054759 0.133017 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001604_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/OG0001604_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c25b13eb1f8d27fa385a9336ce1b274e67c33c1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001604_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 0.19876775 Before NNI: tree length is 0.19876775 + 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..4fdaaf82289aebf37ab6582bfadfb8c08dd8fa11 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010540 0.068354 0.139366 0.015827 +1 0.010540 0.000001 0.063124 0.134136 0.010597 +2 0.068354 0.063124 0.000001 0.133338 0.060574 +3 0.139366 0.134136 0.133338 0.000001 0.131586 +4 0.015827 0.010597 0.060574 0.131586 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001608_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/OG0001608_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb21cf3afd4429b7c2200988461dc015c1b6c1ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001608_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 0.07631967 Before NNI: tree length is 0.07631975 + 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/OG0001610_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/OG0001610_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bcf9408eb841a9e39fac84b12a5a73725420fc3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001610_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 0.59577963 Before NNI: tree length is 0.59577963 + 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/OG0001612_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/OG0001612_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4884a4348fab0eae86b8727cf67a06825aaf122f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001612_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 0.43098225 Before NNI: tree length is 0.43098225 + 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/OG0001613_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/OG0001613_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c219e761bcb0f7ca898cc716813bbb58315cd6f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001613_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 0.15159100 Before NNI: tree length is 0.15159100 + 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/OG0001615_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/OG0001615_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8ff984ab303fac11d4aa7fa536aaf239d63d11d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001615_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.075541 1.086355 2.018619 0.106964 +1 0.075541 0.000001 1.139884 2.072147 0.105007 +2 1.086355 1.139884 0.000001 1.494951 1.171307 +3 2.018619 2.072147 1.494951 0.000001 2.103571 +4 0.106964 0.105007 1.171307 2.103571 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001617_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/OG0001617_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50d0f4d3840be9766086683000f681587769528f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001617_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 0.05178850 Before NNI: tree length is 0.05178850 + 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/OG0001618_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/OG0001618_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1887be5ca8cf5e8afacb47291796620c2e90cec9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001618_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.193879 0.154457 0.000001 +1 0.000001 0.000001 0.193879 0.154457 0.000001 +2 0.193879 0.193879 0.000001 0.286731 0.193879 +3 0.154457 0.154457 0.286731 0.000001 0.154457 +4 0.000001 0.000001 0.193879 0.154457 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001619_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/OG0001619_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..031357696a93c19c81c26d9ce031d3cd8fbfefdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001619_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.055632 0.849719 0.000001 +1 0.000001 0.000001 0.055632 0.849719 0.000001 +2 0.055632 0.055632 0.000001 0.830210 0.055632 +3 0.849719 0.849719 0.830210 0.000001 0.849719 +4 0.000001 0.000001 0.055632 0.849719 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001619_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/OG0001619_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d57b396b958e37a217876de5130cc3a68db68ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001619_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 0.86778150 Before NNI: tree length is 0.86778150 + 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/OG0001620_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/OG0001620_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0292c14b8d161eb7264aafa018de63c1df4c1e77 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001620_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002663 0.056467 0.011821 0.011670 +1 0.002663 0.000001 0.057389 0.012744 0.012592 +2 0.056467 0.057389 0.000001 0.057582 0.054774 +3 0.011821 0.012744 0.057582 0.000001 0.012786 +4 0.011670 0.012592 0.054774 0.012786 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001620_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/OG0001620_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..97a9b6e99cba0e20ea12692769f3070fb8656afc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001620_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 0.06971647 Before NNI: tree length is 0.06971650 + 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/OG0001622_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/OG0001622_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cac97282ebf744d8c0299fccfd95fa62555343ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001622_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028694 0.230970 0.024428 0.028694 +1 0.028694 0.000001 0.237073 0.018131 0.000001 +2 0.230970 0.237073 0.000001 0.232806 0.237073 +3 0.024428 0.018131 0.232806 0.000001 0.018131 +4 0.028694 0.000001 0.237073 0.018131 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001623_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/OG0001623_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..91140e3cfecb568f4558af657d72d450a4e8d9ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001623_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006485 0.112452 0.085363 0.006485 +1 0.006485 0.000001 0.113510 0.086422 0.000001 +2 0.112452 0.113510 0.000001 0.170237 0.113510 +3 0.085363 0.086422 0.170237 0.000001 0.086422 +4 0.006485 0.000001 0.113510 0.086422 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001625_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/OG0001625_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dca70e4317136facbafe6aae8ce692533051a41c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001625_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008979 0.283832 0.361842 0.007379 +1 0.008979 0.000001 0.291301 0.369312 0.014849 +2 0.283832 0.291301 0.000001 0.292003 0.276453 +3 0.361842 0.369312 0.292003 0.000001 0.354463 +4 0.007379 0.014849 0.276453 0.354463 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001626_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/OG0001626_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..188330d343242fadf378d3437019810c69606dc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001626_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 0.55292325 Before NNI: tree length is 0.55292325 + 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/OG0001633_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/OG0001633_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a985bfcf31c0f08a9841836a3cfac1ce62b323df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000666 0.013156 0.005256 0.000001 +1 0.000666 0.000001 0.012490 0.004616 0.000666 +2 0.013156 0.012490 0.000001 0.017106 0.013156 +3 0.005256 0.004616 0.017106 0.000001 0.005256 +4 0.000001 0.000666 0.013156 0.005256 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001635_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/OG0001635_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..20f4f6230b24602046a5ffebb37f1499dac3e594 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001635_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.020061 0.026926 0.004506 +1 0.000001 0.000001 0.020061 0.026926 0.004506 +2 0.020061 0.020061 0.000001 0.018096 0.023863 +3 0.026926 0.026926 0.018096 0.000001 0.030728 +4 0.004506 0.004506 0.023863 0.030728 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001636_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/OG0001636_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2dce7c8d2699cfe66fc405013c91e38ad91e6beb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001636_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 0.02285600 Before NNI: tree length is 0.02285600 + 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/OG0001637_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/OG0001637_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ad08db06e1d12aa3c0d9b33ad70120ac2ff6f98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001637_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 0.02623575 Before NNI: tree length is 0.02623575 + 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/OG0001643_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/OG0001643_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d9c5eb56673252edfcc32c14e206938bac14c3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001643_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 0.30468411 Before NNI: tree length is 0.30468412 + 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/OG0001644_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/OG0001644_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4693210957a821bc97c18b85f5c009883e633ee2 --- /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_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 1.22325000 Before NNI: tree length is 1.22325000 + 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/OG0001646_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/OG0001646_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3fdbd94d3d89e996cbd3721c8676b40740dd20c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001646_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.136102 0.188692 0.002323 +1 0.000001 0.000001 0.136102 0.188692 0.002323 +2 0.136102 0.136102 0.000001 0.168940 0.133779 +3 0.188692 0.188692 0.168940 0.000001 0.186369 +4 0.002323 0.002323 0.133779 0.186369 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001647_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/OG0001647_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..027b5205aea48fa1e967e2d70abe8b2699ca3134 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001647_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 0.53024850 Before NNI: tree length is 0.53024850 + 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/OG0001648_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/OG0001648_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3af953cdf9a6a1d932f904b0011798f54d916374 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001648_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 0.56586525 Before NNI: tree length is 0.56586525 + 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/OG0001650_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/OG0001650_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..db4b185c42a1ce7d6cd9e9e88cef8d175b4064c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001650_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 0.43968182 Before NNI: tree length is 0.43968175 + 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/OG0001652_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/OG0001652_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..68b0cbdbe377ec427a8878421658c667e25ade56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001652_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017183 0.225735 0.288354 0.040369 +1 0.017183 0.000001 0.226742 0.289360 0.041375 +2 0.225735 0.226742 0.000001 0.393374 0.230543 +3 0.288354 0.289360 0.393374 0.000001 0.293161 +4 0.040369 0.041375 0.230543 0.293161 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001653_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/OG0001653_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..56184de4bac9caca4adc54b305e043056d25c3b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001653_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.062093 0.180213 0.395903 0.029478 +1 0.062093 0.000001 0.190041 0.405731 0.056054 +2 0.180213 0.190041 0.000001 0.377164 0.174175 +3 0.395903 0.405731 0.377164 0.000001 0.389864 +4 0.029478 0.056054 0.174175 0.389864 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001658_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/OG0001658_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4b59445f1882880da442af5670eafd2e4641afb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001658_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 0.55181050 Before NNI: tree length is 0.55181050 + 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/OG0001659_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/OG0001659_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..917a4f55f01cc600771fda971193b57b9a6b952d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001659_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 0.13044150 Before NNI: tree length is 0.13044150 + 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/OG0001660_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/OG0001660_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbc749125888e8a3c3d6ba2a263a98bbd08455f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001660_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 0.11331500 Before NNI: tree length is 0.11331500 + 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/OG0001661_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/OG0001661_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0ab4df94350b26466751a4771a1d02a20d931396 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001661_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055321 0.192167 0.332639 0.050492 +1 0.055321 0.000001 0.148675 0.289148 0.025515 +2 0.192167 0.148675 0.000001 0.355890 0.162360 +3 0.332639 0.289148 0.355890 0.000001 0.302833 +4 0.050492 0.025515 0.162360 0.302833 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001663_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/OG0001663_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aef378f9eafc4262216cbd3cea8758ee42421a9d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001663_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 0.10997338 Before NNI: tree length is 0.10997338 + 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/OG0001665_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/OG0001665_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc236a2ec2494812eb7ff370032990b3f0b83b96 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001665_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 0.01663193 Before NNI: tree length is 0.01663200 + 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/OG0001666_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/OG0001666_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..306cd705c4f1db16071a203d66236bbfae1eed69 --- /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_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 0.10698226 Before NNI: tree length is 0.10698225 + 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/OG0001667_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/OG0001667_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..01c19c3518232a58ae68bf11121c95d0d328901a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001667_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013670 0.012022 0.038295 0.030983 +1 0.013670 0.000001 0.024857 0.051130 0.043818 +2 0.012022 0.024857 0.000001 0.041517 0.035001 +3 0.038295 0.051130 0.041517 0.000001 0.061274 +4 0.030983 0.043818 0.035001 0.061274 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001668_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/OG0001668_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f1a96faaedc855dd4fa3284e4cb95d778be3ad3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001668_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 0.08158300 Before NNI: tree length is 0.08158300 + 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/OG0001675_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/OG0001675_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0345030c1c05e8cfb1deac25b5c14e5213e9d973 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001675_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000102 0.076791 0.311675 0.001942 +1 0.000102 0.000001 0.076689 0.311572 0.002045 +2 0.076791 0.076689 0.000001 0.269655 0.078734 +3 0.311675 0.311572 0.269655 0.000001 0.313617 +4 0.001942 0.002045 0.078734 0.313617 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001677_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/OG0001677_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b43ed764c709a710b9312778c92354971a7d0fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001677_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 0.25469700 Before NNI: tree length is 0.25469700 + 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/OG0001681_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/OG0001681_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fab66f2f3e4b9259ed6ab75ee8d9c5abbc806ede --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.067579 0.185114 0.150611 0.072055 +1 0.067579 0.000001 0.209607 0.175103 0.005418 +2 0.185114 0.209607 0.000001 0.166034 0.214082 +3 0.150611 0.175103 0.166034 0.000001 0.179579 +4 0.072055 0.005418 0.214082 0.179579 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001681_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/OG0001681_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e93ffe909af46620a24e08d9af3d483ed23e46d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001681_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 0.30186213 Before NNI: tree length is 0.30186213 + 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/OG0001682_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/OG0001682_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7b42fcf756f081c83d2d7117752591291247ab6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001682_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013707 0.155703 0.134065 0.014537 +1 0.013707 0.000001 0.150879 0.129241 0.013504 +2 0.155703 0.150879 0.000001 0.134261 0.155501 +3 0.134065 0.129241 0.134261 0.000001 0.133863 +4 0.014537 0.013504 0.155501 0.133863 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001684_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/OG0001684_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f09e808dffdd91bfad068cc4aacfb6878388ec5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001684_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 0.45976050 Before NNI: tree length is 0.45976050 + 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/OG0001686_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/OG0001686_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b4546e2272201da2de3b87ea7974509d0515789 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001686_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034763 0.404289 0.316610 0.042784 +1 0.034763 0.000001 0.412019 0.324341 0.015036 +2 0.404289 0.412019 0.000001 0.284493 0.420041 +3 0.316610 0.324341 0.284493 0.000001 0.332362 +4 0.042784 0.015036 0.420041 0.332362 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001689_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/OG0001689_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a56deef559a3259965b63128d93d313999b18ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054418 0.487426 0.689867 0.048314 +1 0.054418 0.000001 0.523007 0.725447 0.029613 +2 0.487426 0.523007 0.000001 0.711722 0.516904 +3 0.689867 0.725447 0.711722 0.000001 0.719344 +4 0.048314 0.029613 0.516904 0.719344 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001691_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/OG0001691_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4df033f94a78412572faddf37246a9b2b6b170a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001691_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022118 0.665409 1.025653 0.000001 +1 0.022118 0.000001 0.675144 1.035388 0.022118 +2 0.665409 0.675144 0.000001 1.240429 0.665409 +3 1.025653 1.035388 1.240429 0.000001 1.025653 +4 0.000001 0.022118 0.665409 1.025653 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001692_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/OG0001692_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0269dd590719fc045c3dc302430e5baf57c79c3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001692_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012113 0.228908 0.346203 0.012565 +1 0.012113 0.000001 0.216795 0.334090 0.000453 +2 0.228908 0.216795 0.000001 0.353082 0.216343 +3 0.346203 0.334090 0.353082 0.000001 0.333637 +4 0.012565 0.000453 0.216343 0.333637 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001692_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/OG0001692_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c1e655c96a78c2704f862fe45af795b8b7f35e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001692_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 0.46409653 Before NNI: tree length is 0.46409650 + 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/OG0001693_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/OG0001693_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..227d7587fffdc8db902273ba34d8c28f8b97ae09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001693_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055629 0.395668 0.711584 0.055629 +1 0.055629 0.000001 0.394525 0.710440 0.000001 +2 0.395668 0.394525 0.000001 0.643088 0.394525 +3 0.711584 0.710440 0.643088 0.000001 0.710440 +4 0.055629 0.000001 0.394525 0.710440 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001693_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/OG0001693_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f0eb22f5497bc8bdfe2e517fcbca8ad5305aadf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001693_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 0.90241321 Before NNI: tree length is 0.90241325 + 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/OG0001695_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/OG0001695_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8af7a4041d7bb3b5a0abf4e1a613369063503a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001695_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045562 0.452356 0.616614 0.044383 +1 0.045562 0.000001 0.457377 0.621635 0.028931 +2 0.452356 0.457377 0.000001 0.664150 0.456198 +3 0.616614 0.621635 0.664150 0.000001 0.620456 +4 0.044383 0.028931 0.456198 0.620456 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001703_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/OG0001703_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d0f6183a2e484ce0f35560730beecfd9f206fcc6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001703_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011807 0.181457 0.472718 0.035372 +1 0.011807 0.000001 0.191494 0.482755 0.045409 +2 0.181457 0.191494 0.000001 0.471892 0.193899 +3 0.472718 0.482755 0.471892 0.000001 0.485160 +4 0.035372 0.045409 0.193899 0.485160 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001704_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/OG0001704_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a228e925dc5ae0450184ffb1e7d123d623b30d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001704_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019068 0.201448 0.320714 0.019664 +1 0.019068 0.000001 0.190813 0.310079 0.014310 +2 0.201448 0.190813 0.000001 0.337244 0.196690 +3 0.320714 0.310079 0.337244 0.000001 0.315955 +4 0.019664 0.014310 0.196690 0.315955 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c93356dde26f6ad7fe0f03311761178a4dd8d208 --- /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_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 0.67595913 Before NNI: tree length is 0.67595912 + 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/OG0001709_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/OG0001709_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..37412304eab8260a191648227f69ebff1f139e88 --- /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_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 0.41430600 Before NNI: tree length is 0.41430600 + 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/OG0001710_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/OG0001710_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1acdfee12ef9d62a82ad006b177654ca6c9efd67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001710_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011108 0.265134 0.537417 0.018985 +1 0.011108 0.000001 0.263830 0.536114 0.013207 +2 0.265134 0.263830 0.000001 0.512675 0.271707 +3 0.537417 0.536114 0.512675 0.000001 0.543990 +4 0.018985 0.013207 0.271707 0.543990 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001712_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/OG0001712_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d227a6203285fc248349ebe444f1ed64e897839f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001712_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 0.60668259 Before NNI: tree length is 0.60668262 + 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/OG0001717_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/OG0001717_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..87650c716484fa5612cfb683f0825fde498ca62f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001717_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 0.84809650 Before NNI: tree length is 0.84809650 + 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/OG0001721_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/OG0001721_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..05ee34f48b2e4416c5e0fd0433fcceb99cb7f26e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001721_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 0.77024175 Before NNI: tree length is 0.77024175 + 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/OG0001722_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/OG0001722_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5728bd8137d9a8565a441f6860e9b515217a6814 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001722_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 1.27027938 Before NNI: tree length is 1.27027938 + 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/OG0001727_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/OG0001727_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..25cb960e1c62bc464cdbfb2951fb797eb5564fea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001727_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 1.75782250 Before NNI: tree length is 1.75782250 + 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/OG0001731_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/OG0001731_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1ce59518706b77133446980904352390d228db6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008176 0.029296 0.017546 0.008158 +1 0.008176 0.000001 0.021120 0.009370 0.000018 +2 0.029296 0.021120 0.000001 0.021120 0.021138 +3 0.017546 0.009370 0.021120 0.000001 0.009388 +4 0.008158 0.000018 0.021138 0.009388 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001732_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/OG0001732_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e5974d1cb82e3d00b340b5b880772635988fdbd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.061563 0.057023 0.000001 +1 0.000001 0.000001 0.061563 0.057023 0.000001 +2 0.061563 0.061563 0.000001 0.049774 0.061563 +3 0.057023 0.057023 0.049774 0.000001 0.057023 +4 0.000001 0.000001 0.061563 0.057023 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001735_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/OG0001735_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf28da283830f755b51b10c6500e1e4677cca6c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001735_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009741 0.021372 0.303918 0.009464 +1 0.009741 0.000001 0.016970 0.299516 0.003439 +2 0.021372 0.016970 0.000001 0.295633 0.016693 +3 0.303918 0.299516 0.295633 0.000001 0.299238 +4 0.009464 0.003439 0.016693 0.299238 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001736_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/OG0001736_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ce3cf805e96fe0e96011f92397f391e83647a394 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001736_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002274 0.016486 0.021304 0.006407 +1 0.002274 0.000001 0.016208 0.021025 0.006129 +2 0.016486 0.016208 0.000001 0.028106 0.017019 +3 0.021304 0.021025 0.028106 0.000001 0.021836 +4 0.006407 0.006129 0.017019 0.021836 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001736_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/OG0001736_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b1deea35531cf49a6d6081aa2f7a4bfa29aba37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001736_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 0.03741563 Before NNI: tree length is 0.03741563 + 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/OG0001738_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/OG0001738_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c79efb7aec1527dc7e0ae0ba283f82a38561bd41 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001738_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 0.42301332 Before NNI: tree length is 0.42301325 + 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/OG0001739_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/OG0001739_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..25836a2a3edd7c6b27f7ff57e3270bf11132bef3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001739_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023918 0.060835 0.256318 0.012329 +1 0.023918 0.000001 0.063608 0.259092 0.026422 +2 0.060835 0.063608 0.000001 0.257387 0.063339 +3 0.256318 0.259092 0.257387 0.000001 0.258822 +4 0.012329 0.026422 0.063339 0.258822 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001739_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/OG0001739_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..33344919c848a280890b99f8b177066c94ed4284 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001739_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 0.30803219 Before NNI: tree length is 0.30803225 + 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/OG0001740_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/OG0001740_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d5ccaa33c70c8a5ffda7eac9eb91b8a679b67c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001740_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 0.20766580 Before NNI: tree length is 0.20766575 + 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/OG0001741_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/OG0001741_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e555d372d99ac10d177de6040e851d005a5635b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001741_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 0.00685050 Before NNI: tree length is 0.00685050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999998 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001742_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/OG0001742_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..902d52155aad915c4f66071b8297db4a99198503 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001742_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008097 0.113951 0.183475 0.016060 +1 0.008097 0.000001 0.116223 0.185747 0.018333 +2 0.113951 0.116223 0.000001 0.233539 0.113130 +3 0.183475 0.185747 0.233539 0.000001 0.182654 +4 0.016060 0.018333 0.113130 0.182654 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001743_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/OG0001743_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b3c5fd17739acfa55e315540b6641219926cb3d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001743_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.023161 0.060453 0.000001 +1 0.000001 0.000001 0.023161 0.060453 0.000001 +2 0.023161 0.023161 0.000001 0.039112 0.023161 +3 0.060453 0.060453 0.039112 0.000001 0.060453 +4 0.000001 0.000001 0.023161 0.060453 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001743_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/OG0001743_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd5235aab0571a335eee653468a8987555aa7bff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001743_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 0.06136400 Before NNI: tree length is 0.06136400 + 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/OG0001744_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/OG0001744_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6cf92f777c4a25a5461e5d1389a11110d4fe7400 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001744_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021623 0.163410 0.366366 0.014315 +1 0.021623 0.000001 0.161924 0.364880 0.007308 +2 0.163410 0.161924 0.000001 0.376019 0.154616 +3 0.366366 0.364880 0.376019 0.000001 0.357571 +4 0.014315 0.007308 0.154616 0.357571 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001747_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/OG0001747_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd99087ba01abc84b8fffa50acfac7d2073ce9c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001747_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011960 0.037259 0.088163 0.005679 +1 0.011960 0.000001 0.039832 0.090735 0.006344 +2 0.037259 0.039832 0.000001 0.092435 0.033550 +3 0.088163 0.090735 0.092435 0.000001 0.084453 +4 0.005679 0.006344 0.033550 0.084453 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1dc14a9774f984bb270d57ffaee2d75420f7367c --- /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_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 0.19744130 Before NNI: tree length is 0.19744125 + 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/OG0001750_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/OG0001750_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e52e18679ce6c8590097848bf816a4292930efd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001750_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.146278 0.807535 0.787707 0.156788 +1 0.146278 0.000001 0.797179 0.777350 0.076076 +2 0.807535 0.797179 0.000001 1.350010 0.807689 +3 0.787707 0.777350 1.350010 0.000001 0.787861 +4 0.156788 0.076076 0.807689 0.787861 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001751_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/OG0001751_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0163112452b66909e4b7a13a47af125fa5431562 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.064379 0.135838 0.000001 +1 0.000001 0.000001 0.064379 0.135838 0.000001 +2 0.064379 0.064379 0.000001 0.104337 0.064379 +3 0.135838 0.135838 0.104337 0.000001 0.135838 +4 0.000001 0.000001 0.064379 0.135838 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001751_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/OG0001751_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e3da5bab4e0602d383f3193a18e9d4545e7939e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001751_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 0.15227800 Before NNI: tree length is 0.15227800 + 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/OG0001754_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/OG0001754_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c04b6a1af9d67c9e3a3d26354ff1d1c47a04df2d --- /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_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 0.57493136 Before NNI: tree length is 0.57493138 + 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/OG0001755_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/OG0001755_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a057cc048756eae0e5e3e089f0f09874842cea6d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001755_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.053275 0.027350 0.150518 0.055500 +1 0.053275 0.000001 0.072154 0.157317 0.006421 +2 0.027350 0.072154 0.000001 0.169398 0.074380 +3 0.150518 0.157317 0.169398 0.000001 0.159542 +4 0.055500 0.006421 0.074380 0.159542 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001755_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/OG0001755_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e80b636f09d86a54f7bf1052799af7621c36fd58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001755_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 0.20799289 Before NNI: tree length is 0.20799287 + 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/OG0001756_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/OG0001756_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..93a5238e08849d8951648d1aa78d3258087ef780 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001756_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.032268 0.168500 0.007634 +1 0.000001 0.000001 0.032268 0.168500 0.007634 +2 0.032268 0.032268 0.000001 0.179258 0.029743 +3 0.168500 0.168500 0.179258 0.000001 0.165974 +4 0.007634 0.007634 0.029743 0.165974 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001756_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/OG0001756_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f6fe86ff308243854d7eff1ca286683f6fca325 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001756_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 0.19256781 Before NNI: tree length is 0.19256775 + 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/OG0001757_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/OG0001757_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..92c4f6e80a7a091d9df3c81b304efa1c6671bdc6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001757_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045653 0.131952 0.593076 0.045653 +1 0.045653 0.000001 0.123800 0.584924 0.000001 +2 0.131952 0.123800 0.000001 0.621335 0.123800 +3 0.593076 0.584924 0.621335 0.000001 0.584924 +4 0.045653 0.000001 0.123800 0.584924 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001758_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/OG0001758_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5fdf4909a2989bca5fc96b05663e166ba369e3a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001758_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.044137 0.051998 0.000001 +1 0.000001 0.000001 0.044137 0.051998 0.000001 +2 0.044137 0.044137 0.000001 0.036756 0.044137 +3 0.051998 0.051998 0.036756 0.000001 0.051998 +4 0.000001 0.000001 0.044137 0.051998 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001758_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/OG0001758_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0cbb1194b14d665d75ccf91b62c70b885e008dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001758_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 0.06644650 Before NNI: tree length is 0.06644650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000