diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..83bb3333da7142638dc6979fe978d605a6506b07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000013 0.011589 0.012530 0.010518 +1 0.000013 0.000001 0.011576 0.000001 0.010506 +2 0.011589 0.011576 0.000001 0.007124 0.001883 +3 0.012530 0.000001 0.007124 0.000001 0.006054 +4 0.010518 0.010506 0.001883 0.006054 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca43ce6c3e6a19b6441704b42ef0c2e128d98995 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02938548 Before NNI: tree length is 0.02936100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.95399652 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f0565650cb9cfc16fcb6f72d97b9612228b482f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022822 0.148312 0.000001 0.148312 +1 0.022822 0.000001 0.317611 0.513123 0.317611 +2 0.148312 0.317611 0.000001 0.838499 0.000001 +3 0.000001 0.513123 0.838499 0.000001 0.838499 +4 0.148312 0.317611 0.000001 0.838499 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7aac2f3bb9ee027ecd2fa08db944c7149c124632 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.003834 0.007536 0.004318 +1 0.000001 0.000001 0.003834 0.378639 0.004318 +2 0.003834 0.003834 0.000001 0.408367 0.003811 +3 0.007536 0.378639 0.408367 0.000001 0.408852 +4 0.004318 0.004318 0.003811 0.408852 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..aa9cf4e01b4b0dbdd3e8038628c8088dd49fc1de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005140 0.013480 0.025864 0.001520 +1 0.005140 0.000001 0.016888 0.029272 0.003619 +2 0.013480 0.016888 0.000001 0.028732 0.013269 +3 0.025864 0.029272 0.028732 0.000001 0.025653 +4 0.001520 0.003619 0.013269 0.025653 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50ed2438a77313414a7f033748a7f8a764c0b01a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000015_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03831175 Before NNI: tree length is 0.03831175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..09e97eb94ac4acc6aa5015d079bf8ee601341597 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010081 1.018828 1.332099 0.016322 +1 0.010081 0.000001 1.027331 1.340602 0.006241 +2 1.018828 1.027331 0.000001 0.759249 1.021223 +3 1.332099 1.340602 0.759249 0.000001 1.334494 +4 0.016322 0.006241 1.021223 1.334494 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f38f3f023a8f7ddd7d6811f1abd6c7ffb57b635 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000018_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.56753375 Before NNI: tree length is 1.56753375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99996581 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2065ed5c86116dc4527a2fdd62b5af04776432cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027040 0.785285 1.033124 0.011176 +1 0.027040 0.000001 0.173219 0.535770 0.017275 +2 0.785285 0.173219 0.000001 0.540984 0.178632 +3 1.033124 0.535770 0.540984 0.000001 0.541183 +4 0.011176 0.017275 0.178632 0.541183 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42bf176132cc91b8d3a887bf9f86848fa256f9cd --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.42524874 Before NNI: tree length is 1.42524875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99979530 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dd7f1f3b189506ea216bb2b1090444987b2275ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.036435 0.033706 0.003459 +1 0.000001 0.000001 0.597354 0.159363 0.003459 +2 0.036435 0.597354 0.000001 0.007122 0.018907 +3 0.033706 0.159363 0.007122 0.000001 0.016178 +4 0.003459 0.003459 0.018907 0.016178 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..67652efb7e711dd64e4818d986762e46e1f8ac03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000022_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13555542 Before NNI: tree length is 0.11741950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.27042417 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d6f3166ecaa1b141fa74dfa8f7234286a80d028 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22198615 Before NNI: tree length is 0.22198612 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..954fb9485721d8264a7af99fd978de55412a210b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73264075 Before NNI: tree length is 0.73264075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb35e5758ccc98cd65f4ced464273aa2abb0821d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20151291 Before NNI: tree length is 0.20151288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9afe539ce9d589ce628036fdf667ac4927554ab4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004083 0.025657 0.359083 0.028635 +1 0.004083 0.000001 0.024680 0.360934 0.027658 +2 0.025657 0.024680 0.000001 0.382509 0.026153 +3 0.359083 0.360934 0.382509 0.000001 0.385486 +4 0.028635 0.027658 0.026153 0.385486 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..745faa0a954db0ec5cc6146d944636dc4be9adc8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000032_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39974262 Before NNI: tree length is 0.39974262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000033_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000033_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dbeda17a3a87b7afb3362569ccd0b5b1d21ea7ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000033_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.12662600 Before NNI: tree length is 1.12662600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dbfa3c251ad205dc5de38eacda51a63e33893c6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014730 0.146767 0.136225 0.010087 +1 0.014730 0.000001 0.146558 0.136015 0.013429 +2 0.146767 0.146558 0.000001 0.147573 0.145467 +3 0.136225 0.136015 0.147573 0.000001 0.134924 +4 0.010087 0.013429 0.145467 0.134924 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc906db2042f2d9e19d92a811305351a127825fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000038_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22693587 Before NNI: tree length is 0.22693588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b897714f88a9716df1e3cf0da6bd035e2c66b5b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028543 0.006428 0.435282 0.002804 +1 0.028543 0.000001 0.951871 0.420019 0.025738 +2 0.006428 0.951871 0.000001 1.008051 0.964329 +3 0.435282 0.420019 1.008051 0.000001 0.432477 +4 0.002804 0.025738 0.964329 0.432477 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d0ca3b2aeb27f27c8453e41dedc4109a0f4bbe8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000046_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,36 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.85473917 Before NNI: tree length is 0.87252888 + NNI 1: new tree length is 0.83348363 + Performed 1 NNI(s). + + Before SPR: tree length is 0.87252888 + SPR 1: new tree length is 0.83348363 + Performed 1 SPR(s). + + Explained variance : 0.66328129 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5f34bc521bd6f8fb58e94586caedf3cd030f6060 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.068895 0.291112 0.067462 +1 0.000001 0.000001 0.068895 0.291112 0.067462 +2 0.068895 0.068895 0.000001 0.270294 0.010178 +3 0.291112 0.291112 0.270294 0.000001 0.268860 +4 0.067462 0.067462 0.010178 0.268860 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..832adf4dd173c4eca11042571e6515ad128a1007 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000048_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31952325 Before NNI: tree length is 0.31952325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5afebf74539b8dd2d67827c22b94febbaf10eb19 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18665575 Before NNI: tree length is 0.18665575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f29f40b4cc01e8f094e4360af95c616e722997d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004416 0.205676 0.790221 0.009196 +1 0.004416 0.000001 0.203306 0.787851 0.011831 +2 0.205676 0.203306 0.000001 0.471434 0.213092 +3 0.790221 0.787851 0.471434 0.000001 0.797637 +4 0.009196 0.011831 0.213092 0.797637 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b27db006ba72f05da8e696e19d728b8855ac5f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000058_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.74299425 Before NNI: tree length is 0.74299425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99028521 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..6bd7cafe12385c507aa26cff980a53b8f13ce9f8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035774 0.235500 0.259082 0.040374 +1 0.035774 0.000001 0.250692 0.274274 0.055567 +2 0.235500 0.250692 0.000001 0.224586 0.233992 +3 0.259082 0.274274 0.224586 0.000001 0.257574 +4 0.040374 0.055567 0.233992 0.257574 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000061_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000061_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c159315cd926ae011467f03346389b9687a34bdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000061_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18519500 Before NNI: tree length is 0.18519500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..83f9152c1c0050d25db822b4d052752059eec9dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.401021 0.438140 1.176019 0.401021 +1 0.401021 0.000001 0.084318 0.862964 0.000001 +2 0.438140 0.084318 0.000001 0.900083 0.084318 +3 1.176019 0.862964 0.900083 0.000001 0.862964 +4 0.401021 0.000001 0.084318 0.862964 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c237535d8d43675c41046cfeddffb1b5270e2a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.06146400 Before NNI: tree length is 1.06146400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000068_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000068_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0544bccd4932d0f7d1d2c34261808dfefa671f08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000068_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.47013200 Before NNI: tree length is 1.47013200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99985478 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000069_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000069_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd142bf3045351d0fe8b93684851419d684abb76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000069_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50239825 Before NNI: tree length is 0.50239825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..471e38b338234a3180fe115d61504d1c6634b4e4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50496022 Before NNI: tree length is 0.50496025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4e19ea890a19a9ad248e887f475d87dc9e6121a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32155566 Before NNI: tree length is 0.32155563 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000078_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000078_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f2b1762f7c08d234325cf1f492ce5e406549f429 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000078_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019107 0.403153 0.357627 0.014092 +1 0.019107 0.000001 0.409944 0.364418 0.005167 +2 0.403153 0.409944 0.000001 0.421098 0.404929 +3 0.357627 0.364418 0.421098 0.000001 0.359403 +4 0.014092 0.005167 0.404929 0.359403 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..aeda68da4d33e49a801b2b7b4ed8ed1b1e5acc5c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005019 0.076384 0.122841 0.008106 +1 0.005019 0.000001 0.074230 0.120686 0.005952 +2 0.076384 0.074230 0.000001 0.149981 0.074489 +3 0.122841 0.120686 0.149981 0.000001 0.120945 +4 0.008106 0.005952 0.074489 0.120945 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7006f0318f0d88b7eb4e0438986152dcbeb40eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.206442 1.441622 2.769540 0.003058 +1 0.206442 0.000001 1.396978 2.724896 0.209499 +2 1.441622 1.396978 0.000001 1.456016 1.444679 +3 2.769540 2.724896 1.456016 0.000001 2.772597 +4 0.003058 0.209499 1.444679 2.772597 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be26eb4914544eb85547bc9d3dd69a42052431e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000089_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19795975 Before NNI: tree length is 0.19795975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000090_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000090_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..538b3c846d9b569e9ad01659b9d179ba6b66cd9b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000090_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14871017 Before NNI: tree length is 0.14871025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d02b7700cf95bd3d25f40fe5fc18ebea9e6258dd --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33318263 Before NNI: tree length is 0.33318263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000098_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000098_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df28ccb0563cf19c25690ada1b4295a133d014db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000098_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.274700 0.248109 0.311144 0.278398 +1 0.274700 0.000001 0.019992 0.048181 0.011210 +2 0.248109 0.019992 0.000001 0.056435 0.023689 +3 0.311144 0.048181 0.056435 0.000001 0.051878 +4 0.278398 0.011210 0.023689 0.051878 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1b8af30486d8eaa76d5a8abdedb606a27930a53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23977575 Before NNI: tree length is 0.23977575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5d1a4fddf60459e9cd8bdc56171828409125b7e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000878 0.135849 0.235692 0.002160 +1 0.000878 0.000001 0.134971 0.234814 0.003038 +2 0.135849 0.134971 0.000001 0.258580 0.138009 +3 0.235692 0.234814 0.258580 0.000001 0.237852 +4 0.002160 0.003038 0.138009 0.237852 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c6286e4fd4bd3019a7d8f2e78302f25d078912b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000102_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31722050 Before NNI: tree length is 0.31722050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..376b3c4df50d8a82d65a9805074d635cde3f0d81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002597 0.535937 1.790285 0.031104 +1 0.002597 0.000001 0.538517 1.792864 0.033684 +2 0.535937 0.538517 0.000001 0.997111 0.534015 +3 1.790285 1.792864 0.997111 0.000001 1.788362 +4 0.031104 0.033684 0.534015 1.788362 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa297c0ddbceddffc74fc4c7a723dec547d65687 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000103_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.67884567 Before NNI: tree length is 1.67884563 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99000889 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..e8c086d77279da7ded744c5f20fc12e7dc38d985 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.376939 0.664289 1.161939 0.391366 +1 0.376939 0.000001 0.660513 1.174519 0.093802 +2 0.664289 0.660513 0.000001 1.755656 0.674940 +3 1.161939 1.174519 1.755656 0.000001 1.090075 +4 0.391366 0.093802 0.674940 1.090075 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..80bc553e9c8d68c2a7ccd7475c3001913d050317 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.269861 0.075681 0.122738 0.019185 +1 0.269861 0.000001 0.318390 0.365447 0.252025 +2 0.075681 0.318390 0.000001 0.109497 0.067714 +3 0.122738 0.365447 0.109497 0.000001 0.114772 +4 0.019185 0.252025 0.067714 0.114772 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02a4b494daf4f84b8edff0867b533eb2a023aa64 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08948650 Before NNI: tree length is 1.08948650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d1a83f0375f88c5b9fe965ac3e04b1a95c911ab3 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027965 0.056417 0.213468 0.029906 +1 0.027965 0.000001 0.059789 0.216840 0.033278 +2 0.056417 0.059789 0.000001 0.214056 0.055862 +3 0.213468 0.216840 0.214056 0.000001 0.212913 +4 0.029906 0.033278 0.055862 0.212913 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000113_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000113_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a01a11447f2fc76cb9f4ed867ffe6309fdd64d99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000113_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 1.862112 0.088068 0.000001 +1 0.000001 0.000001 1.862112 0.088068 0.000001 +2 1.862112 1.862112 0.000001 1.919826 1.862112 +3 0.088068 0.088068 1.919826 0.000001 0.088068 +4 0.000001 0.000001 1.862112 0.088068 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f4262db94656955a36c336464d1f7eb172f9cab --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.09283350 Before NNI: tree length is 1.09283350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000116_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000116_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c942ecaaa969d8671f88ae67af26574f01c2cb3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000116_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.14884490 Before NNI: tree length is 1.14884487 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b2327a82b1e1bdd0dea0e722d8c0487bb34d93b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007246 0.073818 0.221118 0.007667 +1 0.007246 0.000001 0.066572 0.213872 0.000420 +2 0.073818 0.066572 0.000001 0.233031 0.066151 +3 0.221118 0.213872 0.233031 0.000001 0.213452 +4 0.007667 0.000420 0.066151 0.213452 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed8d54785ce8c5bdfa1150c6cefd0ad8807cf8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000120_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26398345 Before NNI: tree length is 0.26398350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..afbcd7ac8c466f2c1cf466867d8f06bdecfba5e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16214250 Before NNI: tree length is 0.16214250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2281a4e9af8f28ae8104b7cf2a2963fd87ef0e15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32316900 Before NNI: tree length is 0.32316900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..70e4d998a24717537bd9b93cdc71838f4afc1e60 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013170 0.106356 0.305973 0.013170 +1 0.013170 0.000001 0.099934 0.299551 0.000001 +2 0.106356 0.099934 0.000001 0.304512 0.099934 +3 0.305973 0.299551 0.304512 0.000001 0.299551 +4 0.013170 0.000001 0.099934 0.299551 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8277665d0dda2cbbf44bb940003a79b61a527e46 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.070822 0.201679 0.212012 0.048019 +1 0.070822 0.000001 0.230896 0.241228 0.058657 +2 0.201679 0.230896 0.000001 0.267068 0.208093 +3 0.212012 0.241228 0.267068 0.000001 0.218425 +4 0.048019 0.058657 0.208093 0.218425 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..807440a2846ca1a4d2374a032eeaef5848201f8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007608 0.089054 0.180971 0.003887 +1 0.007608 0.000001 0.084821 0.176738 0.008576 +2 0.089054 0.084821 0.000001 0.171370 0.090021 +3 0.180971 0.176738 0.171370 0.000001 0.181938 +4 0.003887 0.008576 0.090021 0.181938 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ade29c8b038fb1c59fd6bd217f99da256c497bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000131_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22481225 Before NNI: tree length is 0.22481225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbb9d8631c285876a5c02f00d3f2fc4ee2ac3ca1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37198700 Before NNI: tree length is 0.37198700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..0cdbc15a2c23420ed7e3fb4a870d2e9807a73b7b --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.325346 0.388866 0.011481 0.011189 +1 0.325346 0.000001 0.031247 0.334959 0.334666 +2 0.388866 0.031247 0.000001 0.398478 0.398186 +3 0.011481 0.334959 0.398478 0.000001 0.014546 +4 0.011189 0.334666 0.398186 0.014546 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5889786f53e51b840802ff49c456e5eb465e22f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004540 0.000001 0.210036 0.000001 +1 0.004540 0.000001 0.004540 1.640673 0.004540 +2 0.000001 0.004540 0.000001 1.639618 0.000001 +3 0.210036 1.640673 1.639618 0.000001 1.639618 +4 0.000001 0.004540 0.000001 1.639618 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..836798df3008cf939bfb2ab0aa8cfb9d9b93c14e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000136_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,36 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.92878683 Before NNI: tree length is 0.92893200 + NNI 1: new tree length is 0.92849650 + Performed 1 NNI(s). + + Before SPR: tree length is 0.92893200 + SPR 1: new tree length is 0.92849650 + Performed 1 SPR(s). + + Explained variance : 0.66713103 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..17dd8ee4b955cf9b26fd8119c007063cd9492b39 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59149050 Before NNI: tree length is 0.59049213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.74484275 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7be4387f906cd22c8dd16606cce7e680006db723 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004222 0.035362 0.029261 0.024481 +1 0.004222 0.000001 0.036384 0.030284 0.025503 +2 0.035362 0.036384 0.000001 0.006100 0.036779 +3 0.029261 0.030284 0.006100 0.000001 0.030678 +4 0.024481 0.025503 0.036779 0.030678 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..481a01a1e230fe8ee90589b261685b08daa93b58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000140_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05093258 Before NNI: tree length is 0.05093263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..dd20071ce312f2131b361eede5891a78c16f6bb4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023136 0.163950 0.422362 0.023136 +1 0.023136 0.000001 0.172495 0.430906 0.000001 +2 0.163950 0.172495 0.000001 0.463345 0.172495 +3 0.422362 0.430906 0.463345 0.000001 0.430906 +4 0.023136 0.000001 0.172495 0.430906 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000144_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000144_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e8cd777a5e58f0537961d722f14183f19796fc45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000144_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027716 0.226401 0.338002 0.038711 +1 0.027716 0.000001 0.234220 0.345821 0.046530 +2 0.226401 0.234220 0.000001 0.289038 0.228147 +3 0.338002 0.345821 0.289038 0.000001 0.339748 +4 0.038711 0.046530 0.228147 0.339748 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9767cfc20748d5fb1d0ce0b592925faf288b3d54 --- /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_fastme_stat.txt @@ -0,0 +1,36 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.14113950 Before NNI: tree length is 1.15763963 + NNI 1: new tree length is 1.11211163 + Performed 1 NNI(s). + + Before SPR: tree length is 1.15763963 + SPR 1: new tree length is 1.11211162 + Performed 1 SPR(s). + + Explained variance : 0.67392284 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000147_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000147_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71431bad03f8f4cd3c458ddc87a5a85e701b9edb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000147_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.121998 0.213453 0.026331 +1 0.000001 0.000001 0.121998 0.213453 0.026331 +2 0.121998 0.121998 0.000001 0.199822 0.132025 +3 0.213453 0.213453 0.199822 0.000001 0.223479 +4 0.026331 0.026331 0.132025 0.223479 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..970716cfbdd6986261f3130b773cd6647690cbd8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028792 0.195158 0.369900 0.014560 +1 0.028792 0.000001 0.194794 0.369537 0.040938 +2 0.195158 0.194794 0.000001 0.374420 0.207303 +3 0.369900 0.369537 0.374420 0.000001 0.382046 +4 0.014560 0.040938 0.207303 0.382046 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7eeb4e467bb069508efa3c6f55b9fdc3111f6c14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009896 0.093914 0.238804 0.000001 +1 0.009896 0.000001 0.089888 0.234777 0.009896 +2 0.093914 0.089888 0.000001 0.202573 0.093914 +3 0.238804 0.234777 0.202573 0.000001 0.238804 +4 0.000001 0.009896 0.093914 0.238804 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1fea349d5b98376d5948d0bb227fb88c6452f14 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53203650 Before NNI: tree length is 0.53203650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.89138389 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dce5078016b3d9e8cf4b447cc7e010cacc336e5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026670 0.075044 0.062518 0.018394 +1 0.026670 0.000001 0.084484 0.071957 0.024797 +2 0.075044 0.084484 0.000001 0.085002 0.076209 +3 0.062518 0.071957 0.085002 0.000001 0.063682 +4 0.018394 0.024797 0.076209 0.063682 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81bcf2b3ee6701e144505b4f4998873afe9f6768 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000157_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13759751 Before NNI: tree length is 0.13759750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fefc53febf8252baa7ccb72cdcd89fd3a1e23c9 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.77111637 Before NNI: tree length is 1.77111638 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cbd5760bfc124fcdc63f70f033ad100389bf6266 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031906 0.036785 0.018469 0.037868 +1 0.031906 0.000001 0.053416 0.035099 0.054499 +2 0.036785 0.053416 0.000001 0.029765 0.038522 +3 0.018469 0.035099 0.029765 0.000001 0.030848 +4 0.037868 0.054499 0.038522 0.030848 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..f6bc186f4356110c3f4c3395b7e66311e4ca92fc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.078662 0.256652 0.004901 +1 0.000001 0.000001 0.078662 0.256652 0.004901 +2 0.078662 0.078662 0.000001 0.270496 0.074970 +3 0.256652 0.256652 0.270496 0.000001 0.252960 +4 0.004901 0.004901 0.074970 0.252960 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000164_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000164_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a833e59301d4a1c8915c1b7b1f1e2572a91183f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000164_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39426750 Before NNI: tree length is 0.39426750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39bbe6ddae86013b41b5b3046b42294ceb34a0ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021364 0.277929 0.309077 0.032957 +1 0.021364 0.000001 0.257824 0.288972 0.024586 +2 0.277929 0.257824 0.000001 0.368423 0.281151 +3 0.309077 0.288972 0.368423 0.000001 0.312299 +4 0.032957 0.024586 0.281151 0.312299 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..14dbfdcd1a5635e294a60d5172a8598922970f47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000166_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49643350 Before NNI: tree length is 0.49643350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..03024e65d31370aad1130b47a681868bf911a67f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06560800 Before NNI: tree length is 0.06560800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50ccbb32ab7050b4e9e496538b98a5136daf9c51 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52807225 Before NNI: tree length is 0.52807225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c98548d1fc5c8b2133629a8c7143737d71c49e58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008747 0.071380 0.145067 0.007764 +1 0.008747 0.000001 0.073852 0.147539 0.011975 +2 0.071380 0.073852 0.000001 0.143714 0.074608 +3 0.145067 0.147539 0.143714 0.000001 0.148295 +4 0.007764 0.011975 0.074608 0.148295 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4206180e338efee46b759caef9c65a06c40a4063 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020745 0.087515 0.163866 0.031532 +1 0.020745 0.000001 0.094853 0.171204 0.038869 +2 0.087515 0.094853 0.000001 0.169979 0.089849 +3 0.163866 0.171204 0.169979 0.000001 0.166200 +4 0.031532 0.038869 0.089849 0.166200 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..0671a85db8090478e379165bf3732e265fe09a57 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.074563 0.116982 0.000001 +1 0.000001 0.000001 0.074563 0.116982 0.000001 +2 0.074563 0.074563 0.000001 0.148634 0.074563 +3 0.116982 0.116982 0.148634 0.000001 0.116982 +4 0.000001 0.000001 0.074563 0.116982 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a4de89ee08cbc9ddc4208e9a6e1ddfeb126c6f44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005704 0.074951 0.131963 0.005704 +1 0.005704 0.000001 0.072411 0.129423 0.000001 +2 0.074951 0.072411 0.000001 0.121732 0.072411 +3 0.131963 0.129423 0.121732 0.000001 0.129423 +4 0.005704 0.000001 0.072411 0.129423 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e07373b2e5f8588227c5bce4baac94cd9083ab44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000178_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16590550 Before NNI: tree length is 0.16590550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f4053d03a1b46cf28b27deb9cf29476818490f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002371 0.156832 0.380341 0.002371 +1 0.002371 0.000001 0.159203 0.382712 0.000001 +2 0.156832 0.159203 0.000001 0.353251 0.159203 +3 0.380341 0.382712 0.353251 0.000001 0.382712 +4 0.002371 0.000001 0.159203 0.382712 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85ada228fc9fe651b32d8e598bc9b19b4f049b61 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.20298250 Before NNI: tree length is 1.20298250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb16c858f884e3fb4ae89996b05fd5223d582fe0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08104050 Before NNI: tree length is 0.08104050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e87a1f4103d53c33350085f4736034fc8529a9a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69583613 Before NNI: tree length is 0.69583613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6169aa19cbd78f1d18896c1bd30e32b19d685401 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21393914 Before NNI: tree length is 0.21393913 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2c4ec7878eabc2d612d2f4614664f01be5c2e2ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.102124 0.552350 0.809117 0.074584 +1 0.102124 0.000001 0.550537 0.807304 0.104117 +2 0.552350 0.550537 0.000001 0.893928 0.554343 +3 0.809117 0.807304 0.893928 0.000001 0.811110 +4 0.074584 0.104117 0.554343 0.811110 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9c1d845064d1200893468e219c6ab6c525af67a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002813 0.026996 0.173552 0.005622 +1 0.002813 0.000001 0.025325 0.171881 0.003952 +2 0.026996 0.025325 0.000001 0.178823 0.024498 +3 0.173552 0.171881 0.178823 0.000001 0.171053 +4 0.005622 0.003952 0.024498 0.171053 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3e20e311a7c1a7476ff0c4b6bb1dae1a760dd06 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000191_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19181857 Before NNI: tree length is 0.19181850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000194_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000194_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c967d145577aa14aeedd8735cd42a5b272005496 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000194_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17308882 Before NNI: tree length is 0.17308875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e04cacfc7ae9fead2195ba39d32c3327d234244c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007004 0.122437 0.122348 0.015226 +1 0.007004 0.000001 0.118700 0.118611 0.011488 +2 0.122437 0.118700 0.000001 0.139603 0.115409 +3 0.122348 0.118611 0.139603 0.000001 0.115321 +4 0.015226 0.011488 0.115409 0.115321 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94e9afa3471525a6847b8301bc8a5553df48633a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18768963 Before NNI: tree length is 0.18768962 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a40894b2eb3815eee999c3abbe9129bbb9a60c7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055986 0.344869 0.451354 0.022054 +1 0.055986 0.000001 0.382348 0.488833 0.059533 +2 0.344869 0.382348 0.000001 0.403809 0.325933 +3 0.451354 0.488833 0.403809 0.000001 0.432419 +4 0.022054 0.059533 0.325933 0.432419 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72c43d287f2291f245b3dbc91775ad4a31afcf80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000199_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64830773 Before NNI: tree length is 0.64830775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d9867e8c25476053a70d5f9127c60438cadfc82f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.157554 0.231592 0.000001 +1 0.000001 0.000001 0.157554 0.231592 0.000001 +2 0.157554 0.157554 0.000001 0.225672 0.157554 +3 0.231592 0.231592 0.225672 0.000001 0.231592 +4 0.000001 0.000001 0.157554 0.231592 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5831174c2910ed91852d1ef4f9cf29eed9f2a8ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000201_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30741000 Before NNI: tree length is 0.30741000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..54eeab3826b0903735ec5f9cba9d9aea0eada90f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060007 0.161115 0.223765 0.060942 +1 0.060007 0.000001 0.158674 0.221324 0.009163 +2 0.161115 0.158674 0.000001 0.243290 0.159608 +3 0.223765 0.221324 0.243290 0.000001 0.222259 +4 0.060942 0.009163 0.159608 0.222259 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000205_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000205_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3b7f1eba47c76c9f92e0fa37fc8fa2cf85ddbd16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000205_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026212 0.390889 0.745114 0.062505 +1 0.026212 0.000001 0.402155 0.756379 0.042575 +2 0.390889 0.402155 0.000001 0.709641 0.438447 +3 0.745114 0.756379 0.709641 0.000001 0.792671 +4 0.062505 0.042575 0.438447 0.792671 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7b12259f03cda12c1bfbcd6e676f440bdbe15fb8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008117 0.072335 0.136494 0.008006 +1 0.008117 0.000001 0.071867 0.136026 0.003479 +2 0.072335 0.071867 0.000001 0.120796 0.071757 +3 0.136494 0.136026 0.120796 0.000001 0.135916 +4 0.008006 0.003479 0.071757 0.135916 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..108b859604e39f1ea1a451fa91a88143ed86a9e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010315 0.211349 0.454714 0.006435 +1 0.010315 0.000001 0.212955 0.456320 0.009776 +2 0.211349 0.212955 0.000001 0.511514 0.210810 +3 0.454714 0.456320 0.511514 0.000001 0.454175 +4 0.006435 0.009776 0.210810 0.454175 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000211_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000211_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c400b0d49bc147822285700205a64c013d7b78d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000211_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58385500 Before NNI: tree length is 0.58385500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..89fc5055abfb85160fd416608fa87f6b4a0bb563 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.197127 0.201354 0.006431 +1 0.000001 0.000001 0.197127 0.201354 0.006431 +2 0.197127 0.197127 0.000001 0.300282 0.195535 +3 0.201354 0.201354 0.300282 0.000001 0.199762 +4 0.006431 0.006431 0.195535 0.199762 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..5dd411ba691e488bef022cf52514105f93550f45 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044293 0.593562 0.512844 0.036852 +1 0.044293 0.000001 0.584096 0.503377 0.040524 +2 0.593562 0.584096 0.000001 0.668476 0.589794 +3 0.512844 0.503377 0.668476 0.000001 0.509075 +4 0.036852 0.040524 0.589794 0.509075 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a76b01e1aa2456ea34492b74f98e8ef3eeda2c74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001123 0.054140 0.164269 0.003842 +1 0.001123 0.000001 0.054695 0.164824 0.004396 +2 0.054140 0.054695 0.000001 0.144644 0.055785 +3 0.164269 0.164824 0.144644 0.000001 0.165913 +4 0.003842 0.004396 0.055785 0.165913 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9ddfdcc7fc4bee481ea6843f8b2187812a2ce60 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25128600 Before NNI: tree length is 0.25128600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1cab9a21e7f99bee103f6d076582d930a35f043e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43122531 Before NNI: tree length is 0.43122525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..20663ca6644558e14afe7c151f26d9c8612d3c6f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015954 0.397858 0.620109 0.000925 +1 0.015954 0.000001 0.398463 0.620714 0.016576 +2 0.397858 0.398463 0.000001 0.665400 0.398479 +3 0.620109 0.620714 0.665400 0.000001 0.620730 +4 0.000925 0.016576 0.398479 0.620730 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..012cc409403e41f6efb8cfd2a5a173d32ebcb2ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029488 0.032685 0.024773 0.000001 +1 0.029488 0.000001 0.031091 0.015409 0.029488 +2 0.032685 0.031091 0.000001 0.026377 0.032685 +3 0.024773 0.015409 0.026377 0.000001 0.024773 +4 0.000001 0.029488 0.032685 0.024773 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f61e71028f1e3059c7911ffbc03fcfe1c9e07236 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000237_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05197975 Before NNI: tree length is 0.05197975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fef7df752494f8d7e2f31ad141e1023d35199a06 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43097088 Before NNI: tree length is 0.43097088 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d52453975022df10aa3d3c17d46e944ac490a62 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14544375 Before NNI: tree length is 0.14544375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..60568623cc7b63365c02ccc49e56b4170f4c2789 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016967 0.342916 0.343314 0.000001 +1 0.016967 0.000001 0.358488 0.358887 0.016967 +2 0.342916 0.358488 0.000001 0.343206 0.342916 +3 0.343314 0.358887 0.343206 0.000001 0.343314 +4 0.000001 0.016967 0.342916 0.343314 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c322a4170256af18074fb4ed2bc97028e5d74ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000243_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53098825 Before NNI: tree length is 0.53098825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f8180f694f1f5ec15f3df822dcf95f7ec3ed5869 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.209431 0.531447 0.164891 +1 0.000001 0.000001 0.209431 0.531447 0.164891 +2 0.209431 0.209431 0.000001 0.673379 0.166443 +3 0.531447 0.531447 0.673379 0.000001 0.628838 +4 0.164891 0.164891 0.166443 0.628838 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d463383009d35249115897b0c3a2e97d76667f1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016984 0.149647 0.285295 0.030097 +1 0.016984 0.000001 0.143558 0.279206 0.018938 +2 0.149647 0.143558 0.000001 0.232679 0.156672 +3 0.285295 0.279206 0.232679 0.000001 0.292319 +4 0.030097 0.018938 0.156672 0.292319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..102d24f4fd4d9812d9dae34b2c0282f322d91750 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000247_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35528360 Before NNI: tree length is 0.35528362 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d5b073e766881627d5dac934fcca54a3e1f3aa6a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.11757050 Before NNI: tree length is 1.11757050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a305ab15042da53fbe9e3c91fa6753f156f2c806 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003343 0.180976 0.707892 0.003348 +1 0.003343 0.000001 0.184319 0.711234 0.006690 +2 0.180976 0.184319 0.000001 0.676825 0.182710 +3 0.707892 0.711234 0.676825 0.000001 0.709625 +4 0.003348 0.006690 0.182710 0.709625 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..fda9bf1fa7359adc8379e55be70965a522c81152 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.159936 0.219219 0.008155 +1 0.000001 0.000001 0.159936 0.219219 0.008155 +2 0.159936 0.159936 0.000001 0.225133 0.162171 +3 0.219219 0.219219 0.225133 0.000001 0.221455 +4 0.008155 0.008155 0.162171 0.221455 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd0f7a3da51be115e29adf57f77bb33a3c83b9e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097946 0.095248 0.128532 0.092729 +1 0.097946 0.000001 0.106620 0.134768 0.020192 +2 0.095248 0.106620 0.000001 0.137205 0.101403 +3 0.128532 0.134768 0.137205 0.000001 0.129551 +4 0.092729 0.020192 0.101403 0.129551 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1563f2cdd033ca13b05b500b1e5774857105b53d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000260_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24007125 Before NNI: tree length is 0.24007125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5f8361fae7b0c58458f71813d128ac7361ca9129 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.312036 0.375753 0.913568 0.329546 +1 0.312036 0.000001 0.461589 0.962612 0.036065 +2 0.375753 0.461589 0.000001 1.063122 0.479099 +3 0.913568 0.962612 1.063122 0.000001 0.980122 +4 0.329546 0.036065 0.479099 0.980122 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b9bbe81e8dd9976f953a7466fdb3c66e8856595 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000262_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.38354875 Before NNI: tree length is 1.38354875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000263_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000263_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..503be4a5c98dfb8d78ff4288e09e41c223cccce4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000263_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77461240 Before NNI: tree length is 0.77461238 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6192ea4a9dbc088c7a22150432401efb05d68a22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026108 0.167295 0.268787 0.023277 +1 0.026108 0.000001 0.178806 0.280297 0.002830 +2 0.167295 0.178806 0.000001 0.314872 0.175975 +3 0.268787 0.280297 0.314872 0.000001 0.277466 +4 0.023277 0.002830 0.175975 0.277466 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d5d2126fc762ba6d55995ad2de2f1652f45a78a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000264_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39428572 Before NNI: tree length is 0.39428575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8b86024ea0bb98be0fc8f16faec3df32efdd441c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011141 0.116825 0.176495 0.005598 +1 0.011141 0.000001 0.127966 0.187635 0.016739 +2 0.116825 0.127966 0.000001 0.152698 0.114201 +3 0.176495 0.187635 0.152698 0.000001 0.173871 +4 0.005598 0.016739 0.114201 0.173871 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..824fdce9909b3c3ab505cdfd295ca3254292761b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.32631025 Before NNI: tree length is 2.32631025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f949fbf0186abbd4b25dc99ce81b26e6eb3ed2a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009707 0.190169 0.227938 0.042017 +1 0.009707 0.000001 0.188968 0.226736 0.040815 +2 0.190169 0.188968 0.000001 0.204597 0.187640 +3 0.227938 0.226736 0.204597 0.000001 0.225409 +4 0.042017 0.040815 0.187640 0.225409 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f13102bc233ec35833316bb5bceb90c2bdef86a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030259 0.210985 0.426271 0.020764 +1 0.030259 0.000001 0.225969 0.441256 0.009495 +2 0.210985 0.225969 0.000001 0.455048 0.216474 +3 0.426271 0.441256 0.455048 0.000001 0.431760 +4 0.020764 0.009495 0.216474 0.431760 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..15dfddc37e656940b7e167d8bc6983ed822e35c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000269_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56877364 Before NNI: tree length is 0.56877363 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000271_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000271_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..59071a1746cc72bc182395cea4d1bc3fd01182f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000271_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39715213 Before NNI: tree length is 0.39715213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7b44c4edb871a4515f91ca43bd7d8e0cc16445d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004270 0.472468 0.387763 0.004270 +1 0.004270 0.000001 0.471174 0.386469 0.000001 +2 0.472468 0.471174 0.000001 0.732248 0.471174 +3 0.387763 0.386469 0.732248 0.000001 0.386469 +4 0.004270 0.000001 0.471174 0.386469 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..428a8ea78964778699e7a9ea1ea12fdc2bcacfb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000274_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79772800 Before NNI: tree length is 0.79772800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c0f46d80cd56593936cf09a7ad3fa7324000e8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35381450 Before NNI: tree length is 0.35381450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a89cfe6223c6cdc2d9d78ce09d89715a9fadeb99 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013534 0.066514 0.070663 0.017049 +1 0.013534 0.000001 0.061092 0.065241 0.006084 +2 0.066514 0.061092 0.000001 0.058406 0.064607 +3 0.070663 0.065241 0.058406 0.000001 0.068756 +4 0.017049 0.006084 0.064607 0.068756 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a4127fd2e496ec8b1f7b550d025720835417194 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58948732 Before NNI: tree length is 0.58948725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..08c853ac8b8741ef10ad77fa721b0ff3d722a214 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.016334 0.116870 0.000001 +1 0.000001 0.000001 0.016334 0.116870 0.000001 +2 0.016334 0.016334 0.000001 0.126571 0.016334 +3 0.116870 0.116870 0.126571 0.000001 0.116870 +4 0.000001 0.000001 0.016334 0.116870 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..3df76207bfe772c01c932fb7d97632f6aead8799 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005089 0.043075 0.116786 0.006365 +1 0.005089 0.000001 0.044281 0.117992 0.007570 +2 0.043075 0.044281 0.000001 0.127818 0.044503 +3 0.116786 0.117992 0.127818 0.000001 0.118215 +4 0.006365 0.007570 0.044503 0.118215 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d138925f902779d3202402ebb00e86f1229d4562 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38630475 Before NNI: tree length is 0.38630475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b995a60472a75c9373feb90b5824267a7f560973 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014245 0.019762 0.461842 0.009029 +1 0.014245 0.000001 0.012515 0.454596 0.008526 +2 0.019762 0.012515 0.000001 0.455546 0.014042 +3 0.461842 0.454596 0.455546 0.000001 0.456123 +4 0.009029 0.008526 0.014042 0.456123 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23c3a9208de274dd8f114a32ddc57a06fee180cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000292_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47372916 Before NNI: tree length is 0.47372912 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e03705d08cb16ce5fa07eb3d02e2e6cf2d193db --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17164925 Before NNI: tree length is 0.17164925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000295_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000295_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df88401656fe958575b8c31c867d7500d371b182 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000295_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004541 0.022221 0.067601 0.027668 +1 0.004541 0.000001 0.022930 0.068310 0.028378 +2 0.022221 0.022930 0.000001 0.063607 0.018287 +3 0.067601 0.068310 0.063607 0.000001 0.069054 +4 0.027668 0.028378 0.018287 0.069054 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c08503a12e457e1262121fd458fdf561770091c7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16962825 Before NNI: tree length is 0.16962825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ed57abb351d77ec9a7b9146e7ef1ed7decc64793 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007402 0.031412 0.008948 0.007402 +1 0.007402 0.000001 0.025477 0.003013 0.000001 +2 0.031412 0.025477 0.000001 0.022464 0.025477 +3 0.008948 0.003013 0.022464 0.000001 0.003013 +4 0.007402 0.000001 0.025477 0.003013 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75bf363c2b994ab13daefd3b5665a1cd8655f5e2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24646500 Before NNI: tree length is 0.24646500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..578d5b6202ea846de52645055b63c459c8ca3328 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002500 0.281362 0.026642 0.006266 +1 0.002500 0.000001 0.283859 0.029139 0.008763 +2 0.281362 0.283859 0.000001 0.277604 0.279122 +3 0.026642 0.029139 0.277604 0.000001 0.024402 +4 0.006266 0.008763 0.279122 0.024402 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4de0fc0dd26169d28514ff1765bbd326455a1dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91342825 Before NNI: tree length is 0.91342825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..67dddd682baeaf25d1255f345bacb7e1acde64cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032787 0.310860 0.910910 0.037281 +1 0.032787 0.000001 0.307507 0.907557 0.010661 +2 0.310860 0.307507 0.000001 0.937815 0.312002 +3 0.910910 0.907557 0.937815 0.000001 0.912052 +4 0.037281 0.010661 0.312002 0.912052 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d3fafd4ab324df4686c27a9f7ac8c4584a7de1da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.234366 0.729033 0.005864 +1 0.000001 0.000001 0.234366 0.729033 0.005864 +2 0.234366 0.234366 0.000001 0.713873 0.228502 +3 0.729033 0.729033 0.713873 0.000001 0.723169 +4 0.005864 0.005864 0.228502 0.723169 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ead62a91624819c39c4a179c7073d93c8639af5f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010553 0.053004 0.070026 0.000625 +1 0.010553 0.000001 0.061369 0.080579 0.009928 +2 0.053004 0.061369 0.000001 0.123030 0.052379 +3 0.070026 0.080579 0.123030 0.000001 0.070651 +4 0.000625 0.009928 0.052379 0.070651 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02f0dcabd1c851ead92e00bdc6a771d57a9b3cbd --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.85800550 Before NNI: tree length is 0.85800550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1240c612a6b69b7cff320476fc71f05e1e2e8420 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008346 0.399601 1.017626 0.040883 +1 0.008346 0.000001 0.407947 1.025972 0.032537 +2 0.399601 0.407947 0.000001 1.075431 0.440484 +3 1.017626 1.025972 1.075431 0.000001 1.058509 +4 0.040883 0.032537 0.440484 1.058509 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba9977d998ea0ae758f5b8ef55c9e033b6ae62b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000313_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.28721200 Before NNI: tree length is 1.28721200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..236b88100d61e18c593b49255b5c23e8e6d900a5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.69423220 Before NNI: tree length is 1.69423225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e3fe2ef6a9007df00f4df36215615d5106ec8f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.007722 0.045910 0.000001 +1 0.000001 0.000001 0.007722 0.045910 0.000001 +2 0.007722 0.007722 0.000001 0.041891 0.007722 +3 0.045910 0.045910 0.041891 0.000001 0.045910 +4 0.000001 0.000001 0.007722 0.045910 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e880d9426485718c57683d7e30169c2d95f26738 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000318_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04776250 Before NNI: tree length is 0.04776250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000319_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000319_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..150c857f8d4e2d95ba7fca0ce169df2590ad28bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000319_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.93241650 Before NNI: tree length is 0.93241650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d47af9ed6c5d4b063ba3d9770952e019cee8a4c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18473700 Before NNI: tree length is 0.18473700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e53a01247e4b0e6b5e7ca4e8aa1a28329cb0116 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009278 0.246052 0.241451 0.024483 +1 0.009278 0.000001 0.252298 0.247697 0.030728 +2 0.246052 0.252298 0.000001 0.193429 0.236765 +3 0.241451 0.247697 0.193429 0.000001 0.232164 +4 0.024483 0.030728 0.236765 0.232164 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f496b59bdc5df74f3de8f9f8de9b3e0aa01ce6fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009695 0.245359 0.718454 0.022894 +1 0.009695 0.000001 0.238533 0.711627 0.016068 +2 0.245359 0.238533 0.000001 0.705950 0.233189 +3 0.718454 0.711627 0.705950 0.000001 0.706284 +4 0.022894 0.016068 0.233189 0.706284 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0447c1f9f640351c9332aacd6e9230a71ff925d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000332_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.84167785 Before NNI: tree length is 0.84167788 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9b82ca165fbff06be2250120de23d6009333005f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002626 0.426257 0.382041 0.008192 +1 0.002626 0.000001 0.424163 0.379947 0.006098 +2 0.426257 0.424163 0.000001 0.748346 0.421007 +3 0.382041 0.379947 0.748346 0.000001 0.376790 +4 0.008192 0.006098 0.421007 0.376790 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c425eca71d954718535d112d69e66d675a7b2c8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022109 0.158345 0.307073 0.022835 +1 0.022109 0.000001 0.136236 0.284964 0.000727 +2 0.158345 0.136236 0.000001 0.247877 0.135509 +3 0.307073 0.284964 0.247877 0.000001 0.284237 +4 0.022835 0.000727 0.135509 0.284237 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aac9e7b954669f85bfa36bada6c5817a616905f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000335_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35664725 Before NNI: tree length is 0.35664725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c335bff72957888a5cb64f9240dd0286d3dc0b3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53705725 Before NNI: tree length is 0.53705725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..b0870dcbecee76a7639618c7b7b75284341e5a40 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002891 0.008436 0.171063 0.004208 +1 0.002891 0.000001 0.005802 0.168429 0.003802 +2 0.008436 0.005802 0.000001 0.166602 0.009348 +3 0.171063 0.168429 0.166602 0.000001 0.171975 +4 0.004208 0.003802 0.009348 0.171975 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ec328b7cdcef2b005d09c8b12b1bfea18554db4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21994005 Before NNI: tree length is 0.21994000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f5915be614a50e515d5bf220eaea1abec8b097b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42651650 Before NNI: tree length is 0.42651650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..2216adae1b5d463e13f481223bd659d2dfa34d9d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002783 0.113427 0.211764 0.005789 +1 0.002783 0.000001 0.115806 0.214144 0.008168 +2 0.113427 0.115806 0.000001 0.227289 0.116803 +3 0.211764 0.214144 0.227289 0.000001 0.215141 +4 0.005789 0.008168 0.116803 0.215141 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d55a13708b3f8ee175c2943c0d8de851761593e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86287900 Before NNI: tree length is 0.86287900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4358b8472dc08df08660536a55069b57cff7288e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44387100 Before NNI: tree length is 0.44387100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5daa72ebaf2c522f78ba2c6c5daeaa3f8c63a39e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002564 0.045962 0.304999 0.002564 +1 0.002564 0.000001 0.047222 0.306259 0.000001 +2 0.045962 0.047222 0.000001 0.295873 0.047222 +3 0.304999 0.306259 0.295873 0.000001 0.306259 +4 0.002564 0.000001 0.047222 0.306259 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b69000a9c982c09439f4f40d8565e9bb57c5f5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000347_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32532950 Before NNI: tree length is 0.32532950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000348_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000348_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c14edd552ae4f2e13feeb44e5989d6cb43bdc4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000348_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.98682100 Before NNI: tree length is 1.98682100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c347503242d5581e9261a40aecb6d8f000671ad4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21298765 Before NNI: tree length is 0.21298762 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b95c64595f4df45288f27c127172fcb2e440136 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000214 0.003180 0.077610 0.000214 +1 0.000214 0.000001 0.003394 0.077395 0.000429 +2 0.003180 0.003394 0.000001 0.080790 0.002965 +3 0.077610 0.077395 0.080790 0.000001 0.077824 +4 0.000214 0.000429 0.002965 0.077824 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12c0e8e653132d3224329ae131197aadcbfb62d2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48817047 Before NNI: tree length is 1.48817050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a213e0360ddb3ba92d21d64afe3415bf86d5a765 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.076336 0.741966 0.321449 0.076295 +1 0.076336 0.000001 0.731899 0.311382 0.005588 +2 0.741966 0.731899 0.000001 0.685263 0.731858 +3 0.321449 0.311382 0.685263 0.000001 0.311341 +4 0.076295 0.005588 0.731858 0.311341 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f995cf7cd0a68b98f7d99757329bd11cac56ce4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000356_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91024700 Before NNI: tree length is 0.91024700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..75dbea0b2885ebef445bec57df9c46ab35c570bb --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003413 0.100954 0.186396 0.018431 +1 0.003413 0.000001 0.103708 0.189151 0.021186 +2 0.100954 0.103708 0.000001 0.134896 0.103399 +3 0.186396 0.189151 0.134896 0.000001 0.188842 +4 0.018431 0.021186 0.103399 0.188842 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5251bcca80d3265fd1db05074367004cf925534 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24612800 Before NNI: tree length is 0.24612800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000363_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000363_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..08f66f71995f8331537ec7fa4358fe3526f3b972 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000363_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011597 0.055029 0.040876 0.009661 +1 0.011597 0.000001 0.055070 0.040917 0.001996 +2 0.055029 0.055070 0.000001 0.072121 0.053134 +3 0.040876 0.040917 0.072121 0.000001 0.038980 +4 0.009661 0.001996 0.053134 0.038980 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3364a23bb225cc2428e26ca396a82172f865339f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.326808 0.373668 0.474928 0.312801 +1 0.326808 0.000001 0.251582 0.471477 0.042485 +2 0.373668 0.251582 0.000001 0.518338 0.237576 +3 0.474928 0.471477 0.518338 0.000001 0.457471 +4 0.312801 0.042485 0.237576 0.457471 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b0d3a3dbbb61d2fb9163060f2ff5dc1701ee0cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000364_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.80006713 Before NNI: tree length is 0.80006712 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..248c97905c059f3a6b4876248288cbc390d2fcae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22936900 Before NNI: tree length is 0.22936900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a3336980c65699d301047c94aa20622c1bb2357 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019272 0.088845 0.452562 0.015364 +1 0.019272 0.000001 0.086618 0.450335 0.004699 +2 0.088845 0.086618 0.000001 0.459485 0.082710 +3 0.452562 0.450335 0.459485 0.000001 0.446427 +4 0.015364 0.004699 0.082710 0.446427 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000371_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000371_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d60070d54f878aa1dc0d1933752940a201110e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000371_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022263 0.242294 0.336739 0.022944 +1 0.022263 0.000001 0.242809 0.337254 0.001182 +2 0.242294 0.242809 0.000001 0.343450 0.243490 +3 0.336739 0.337254 0.343450 0.000001 0.337935 +4 0.022944 0.001182 0.243490 0.337935 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..658dc49f8d5630dd3e336c2aba7f8d4c01fe0fb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52941362 Before NNI: tree length is 0.52941362 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9d5da08fab25a86d2eb5ad6e664d6ec8ca094547 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018721 0.160593 0.386039 0.020527 +1 0.018721 0.000001 0.157018 0.382464 0.016953 +2 0.160593 0.157018 0.000001 0.371647 0.149341 +3 0.386039 0.382464 0.371647 0.000001 0.374787 +4 0.020527 0.016953 0.149341 0.374787 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..917b81bb75c5480a2b6899984d442738c9889c1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022740 0.114087 0.264934 0.019961 +1 0.022740 0.000001 0.128975 0.279821 0.002779 +2 0.114087 0.128975 0.000001 0.284804 0.126196 +3 0.264934 0.279821 0.284804 0.000001 0.277042 +4 0.019961 0.002779 0.126196 0.277042 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc8ce1a7d7039f4eb4ae87e4b7329c01a598cc6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25562861 Before NNI: tree length is 0.25562850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000381_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000381_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..381c9cf210e5ecefe635879ec5bb898b09ae8e0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000381_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10624850 Before NNI: tree length is 0.10624850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..87d4559ccdc2b35ea36c1b67e247cfd8b000b2a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.054826 0.127252 0.003410 +1 0.000001 0.000001 0.054826 0.127252 0.003410 +2 0.054826 0.054826 0.000001 0.132881 0.051415 +3 0.127252 0.127252 0.132881 0.000001 0.123842 +4 0.003410 0.003410 0.051415 0.123842 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc610f89ab7aba112ef5554d3c1c3c703e41b75a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000383_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15747970 Before NNI: tree length is 0.15747975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f2cfba343a524125935182fb38cbfd49219ed8b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018996 0.138320 0.197570 0.018429 +1 0.018996 0.000001 0.134362 0.193613 0.012039 +2 0.138320 0.134362 0.000001 0.248935 0.133795 +3 0.197570 0.193613 0.248935 0.000001 0.193046 +4 0.018429 0.012039 0.133795 0.193046 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7652951eb25f6266bfea182fff378159a1a4380 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000388_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30566777 Before NNI: tree length is 0.30566775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0507306f78fd600a423e6b844a10550c377251b6 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21937125 Before NNI: tree length is 0.21937125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc0408dbe2a0f9f59aa0c962df9b47e0730406d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.63369880 Before NNI: tree length is 0.63369875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..87036947ebdb1f02a7c2c26c72f1ff3fb6d16ba8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026396 0.209630 0.782250 0.015381 +1 0.026396 0.000001 0.235417 0.808036 0.026439 +2 0.209630 0.235417 0.000001 0.761165 0.224402 +3 0.782250 0.808036 0.761165 0.000001 0.797022 +4 0.015381 0.026439 0.224402 0.797022 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e01021ded15faebac88907c98078336002d6faa9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000396_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91032584 Before NNI: tree length is 0.91032588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..28321eec8bf2ffb00354d6681d4c235ed848c6a1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014008 0.157032 0.354430 0.029485 +1 0.014008 0.000001 0.157126 0.354524 0.029579 +2 0.157032 0.157126 0.000001 0.350459 0.158195 +3 0.354430 0.354524 0.350459 0.000001 0.355593 +4 0.029485 0.029579 0.158195 0.355593 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b37bcbd4d2242e14c076e54bf8159e8944bda54 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23388728 Before NNI: tree length is 0.23388725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c66135722897ebaa9774dbdf1dbe6844afade8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.067614 0.203489 0.617448 0.071317 +1 0.067614 0.000001 0.210093 0.624051 0.003703 +2 0.203489 0.210093 0.000001 0.637019 0.213796 +3 0.617448 0.624051 0.637019 0.000001 0.627755 +4 0.071317 0.003703 0.213796 0.627755 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..006fb113c74e76531674cf629d5d2c9643bc4b93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000399_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76978985 Before NNI: tree length is 0.76978987 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..370b77ef9d41e279d3d0b846879e25ec08f91608 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.223524 0.305363 0.480777 0.222015 +1 0.223524 0.000001 0.326738 0.502151 0.046750 +2 0.305363 0.326738 0.000001 0.470300 0.325229 +3 0.480777 0.502151 0.470300 0.000001 0.500642 +4 0.222015 0.046750 0.325229 0.500642 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38814ee86a556578441e9d90cb7aad6bf31ecb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000400_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77328975 Before NNI: tree length is 0.77328975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a608e3bdab3c199a5e46e821317c074eee28e1b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72083432 Before NNI: tree length is 0.72083425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000402_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000402_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..461e8b74695d16a8750c88c8e2936164223568e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000402_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23974836 Before NNI: tree length is 0.23974838 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b225c5dec456adac40fc0712fa12fb94771a1d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72445900 Before NNI: tree length is 0.72445900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e1c8604d2e124ae0bdb66052e7fcefee2788289 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.237324 0.595920 0.965952 0.130688 +1 0.237324 0.000001 0.598491 0.968523 0.189657 +2 0.595920 0.598491 0.000001 1.142582 0.548253 +3 0.965952 0.968523 1.142582 0.000001 0.918285 +4 0.130688 0.189657 0.548253 0.918285 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000407_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000407_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..37d846b8404f3000fefbe24836a988352f102d09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000407_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55323786 Before NNI: tree length is 0.55323787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000409_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000409_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ade5a09287a5df93246014c3e9d081d794089537 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000409_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36019150 Before NNI: tree length is 0.36019150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..29ab2a49009254462393eefee1d424ed8d799903 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015114 0.078477 0.148219 0.016661 +1 0.015114 0.000001 0.078694 0.148435 0.013817 +2 0.078477 0.078694 0.000001 0.140623 0.080242 +3 0.148219 0.148435 0.140623 0.000001 0.149983 +4 0.016661 0.013817 0.080242 0.149983 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b243481645d66db964d5884132e3774fd38dff4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16895450 Before NNI: tree length is 0.16895450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81bd115d88be15ff64999a544a36f9a23bca321e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04999800 Before NNI: tree length is 0.04999800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed5e66ed57f4aa6d9925b3913ffc96ae90452838 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012113 0.056522 0.039429 0.000001 +1 0.012113 0.000001 0.044409 0.027316 0.012113 +2 0.056522 0.044409 0.000001 0.017093 0.056522 +3 0.039429 0.027316 0.017093 0.000001 0.039429 +4 0.000001 0.012113 0.056522 0.039429 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..08b38b181d68d09cbea12b8ec7d9d818bb72e670 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000422_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05652250 Before NNI: tree length is 0.05652250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..f216950111083c9ff19e9b7186424ea0f2cb2b80 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017677 0.056340 0.033610 0.014729 +1 0.017677 0.000001 0.055935 0.033204 0.014324 +2 0.056340 0.055935 0.000001 0.029084 0.050688 +3 0.033610 0.033204 0.029084 0.000001 0.027957 +4 0.014729 0.014324 0.050688 0.027957 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7715181e13e89ee8aaf7fbb48c87f3a62b03f28a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017729 0.047246 0.389794 0.000001 +1 0.017729 0.000001 0.029517 0.372065 0.017729 +2 0.047246 0.029517 0.000001 0.356413 0.047246 +3 0.389794 0.372065 0.356413 0.000001 0.389794 +4 0.000001 0.017729 0.047246 0.389794 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000430_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000430_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d689f478f9af610a9af4d2552351aa35fe88d69b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000430_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33347775 Before NNI: tree length is 0.33347775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..463e15b938158376dd3ad61625ff1266d3c16f91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000433_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.056357 0.058257 0.000001 +1 0.000001 0.000001 0.056357 0.058257 0.000001 +2 0.056357 0.056357 0.000001 0.056328 0.056357 +3 0.058257 0.058257 0.056328 0.000001 0.058257 +4 0.000001 0.000001 0.056357 0.058257 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d45c83ebf38e7d854c3c9a87afee0534e314451a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001245 0.098171 0.132037 0.003114 +1 0.001245 0.000001 0.098796 0.132662 0.003738 +2 0.098171 0.098796 0.000001 0.164756 0.095374 +3 0.132037 0.132662 0.164756 0.000001 0.129240 +4 0.003114 0.003738 0.095374 0.129240 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e410ec946edce5b868a2ea71c737d574e9f7972b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000434_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19857525 Before NNI: tree length is 0.19857525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f209a6b6132b1d87ea8177df5ae918e6c8b6e949 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000435_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69758875 Before NNI: tree length is 0.69758875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b901b416fdbf4117e2ee1405d445a270e80076c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.92821921 Before NNI: tree length is 0.92821925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000437_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000437_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5b4be4254369118efdb6b4f50ca70a781bf4970 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000437_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.046446 0.211564 0.006957 +1 0.000001 0.000001 0.046446 0.211564 0.006957 +2 0.046446 0.046446 0.000001 0.210750 0.040085 +3 0.211564 0.211564 0.210750 0.000001 0.205203 +4 0.006957 0.006957 0.040085 0.205203 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bddb7efa3be3230146a10917069fa7392f62529c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017342 0.043452 0.122290 0.011997 +1 0.017342 0.000001 0.041994 0.120832 0.025204 +2 0.043452 0.041994 0.000001 0.127512 0.051314 +3 0.122290 0.120832 0.127512 0.000001 0.130152 +4 0.011997 0.025204 0.051314 0.130152 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..77bd3e64b74b6169fba0747dd791e507f1c4d69f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000440_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16449850 Before NNI: tree length is 0.16449850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000444_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000444_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3b43d1aba490700bebffd1399cd59abca8bfceb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000444_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.062588 0.106299 0.161751 0.061821 +1 0.062588 0.000001 0.107078 0.162529 0.036935 +2 0.106299 0.107078 0.000001 0.156988 0.106311 +3 0.161751 0.162529 0.156988 0.000001 0.161762 +4 0.061821 0.036935 0.106311 0.161762 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000445_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000445_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d86cafc1fc044bcb9585f047719f3a1cfceb3f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000445_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05864626 Before NNI: tree length is 0.05864625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c550086f56c9cdcbe0eeab3ee593f442df6256d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005410 0.041879 0.130571 0.005410 +1 0.005410 0.000001 0.047237 0.135929 0.000001 +2 0.041879 0.047237 0.000001 0.124782 0.047237 +3 0.130571 0.135929 0.124782 0.000001 0.135929 +4 0.005410 0.000001 0.047237 0.135929 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000449_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000449_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63faff994b79258f96d6f25f6b21558d82243330 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000449_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32555850 Before NNI: tree length is 0.32555850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000450_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000450_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be6d96d2f29fe6881546262301557893fb0ea421 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000450_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08684650 Before NNI: tree length is 0.08684650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..0ce2952fa2c1fefcb4912aa42fce00a2f82e12c9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005960 0.127751 0.360638 0.043342 +1 0.005960 0.000001 0.125049 0.357936 0.040641 +2 0.127751 0.125049 0.000001 0.397084 0.135889 +3 0.360638 0.357936 0.397084 0.000001 0.368775 +4 0.043342 0.040641 0.135889 0.368775 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0362d770e42d9792c5de2e55491c28fe106afb48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004072 0.078672 0.209128 0.003273 +1 0.004072 0.000001 0.082206 0.212661 0.007344 +2 0.078672 0.082206 0.000001 0.202616 0.081945 +3 0.209128 0.212661 0.202616 0.000001 0.212400 +4 0.003273 0.007344 0.081945 0.212400 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..14730350a8db57bb843d49d309cb53ba78ca3bbd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000456_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25228340 Before NNI: tree length is 0.25228337 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000458_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000458_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0316d1c09d6b0f02ca82a81ecaa004e331f42312 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000458_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007271 0.216375 0.242364 0.014731 +1 0.007271 0.000001 0.217975 0.243964 0.011500 +2 0.216375 0.217975 0.000001 0.266099 0.225436 +3 0.242364 0.243964 0.266099 0.000001 0.251425 +4 0.014731 0.011500 0.225436 0.251425 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000459_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000459_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..baaa130e77bbe60dde90db0c82554deb352a6755 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000459_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59970775 Before NNI: tree length is 0.59970775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000461_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000461_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..64c5d85cd5b88b0d0e13406ac15860517ab1bab3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000461_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.099036 0.531561 0.957560 0.102111 +1 0.099036 0.000001 0.570257 0.996255 0.089570 +2 0.531561 0.570257 0.000001 0.793427 0.573332 +3 0.957560 0.996255 0.793427 0.000001 0.999331 +4 0.102111 0.089570 0.573332 0.999331 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6800526c94e895fe9bc4b45be00be109751c693 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10668870 Before NNI: tree length is 0.10668875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c4b99a989489cba99372d9745cca1e85fb078ca --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04353200 Before NNI: tree length is 0.04353200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..057845623211124494894a418436288231c3c267 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.077212 0.205353 0.000001 +1 0.000001 0.000001 0.077212 0.205353 0.000001 +2 0.077212 0.077212 0.000001 0.188823 0.077212 +3 0.205353 0.205353 0.188823 0.000001 0.205353 +4 0.000001 0.000001 0.077212 0.205353 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..71b0751d4d7d22b7c43c1fecfa94127b35409664 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000464_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23569500 Before NNI: tree length is 0.23569500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1458cc7f133a044e44d6ca369cb0c1a34937ceb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11054950 Before NNI: tree length is 0.11054950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000467_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000467_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd1f3785eb20d5b549917c2d21fe747f9e6d775a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000467_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22403072 Before NNI: tree length is 0.22403075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38bea39e65b01edd3c6f29985aadd53bb32aa71 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54077220 Before NNI: tree length is 0.54077225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d1673dcac42068eb2261d6598c7b582be5adf1cc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011614 0.100095 0.197100 0.008680 +1 0.011614 0.000001 0.102935 0.199939 0.014405 +2 0.100095 0.102935 0.000001 0.153109 0.102886 +3 0.197100 0.199939 0.153109 0.000001 0.199891 +4 0.008680 0.014405 0.102886 0.199891 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..43017aed155a3ffd8950f2102cb21ab8b078ef0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004409 0.193307 0.445669 0.014920 +1 0.004409 0.000001 0.188897 0.441259 0.010511 +2 0.193307 0.188897 0.000001 0.460794 0.179338 +3 0.445669 0.441259 0.460794 0.000001 0.431700 +4 0.014920 0.010511 0.179338 0.431700 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf499d49ac17a56dc14e4fe47997ce1ed8466e95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000474_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55036025 Before NNI: tree length is 0.55036025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..877bd1917353bb9366f1b278c16ef5a849069638 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022541 0.313160 0.409868 0.027022 +1 0.022541 0.000001 0.313107 0.409815 0.034896 +2 0.313160 0.313107 0.000001 0.472166 0.325516 +3 0.409868 0.409815 0.472166 0.000001 0.422224 +4 0.027022 0.034896 0.325516 0.422224 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a345972b540aa5777e9d1954405b94b3c8c7ebe8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.184278 0.065653 0.198512 0.186001 +1 0.184278 0.000001 0.195346 0.204755 0.003252 +2 0.065653 0.195346 0.000001 0.209579 0.197068 +3 0.198512 0.204755 0.209579 0.000001 0.206477 +4 0.186001 0.003252 0.197068 0.206477 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..06b37deabac681ad03d7d8741d88f48fed55e710 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000479_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33461989 Before NNI: tree length is 0.33461988 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ce87bbb33decc8878e8d4696fde7333dd548613 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44387975 Before NNI: tree length is 0.44387975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f43523388ef5e8a22b569ec7147a20cc7f619bf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73838500 Before NNI: tree length is 0.73838500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c36276ee2b7c4a37a4e6764fec2004d325eab33c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014423 0.188480 0.334791 0.019244 +1 0.014423 0.000001 0.197374 0.343685 0.028138 +2 0.188480 0.197374 0.000001 0.443645 0.192425 +3 0.334791 0.343685 0.443645 0.000001 0.338737 +4 0.019244 0.028138 0.192425 0.338737 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3803cd37686fdc98ae45fb9ef3c4131524862765 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.184533 0.248241 0.000001 +1 0.000001 0.000001 0.184533 0.248241 0.000001 +2 0.184533 0.184533 0.000001 0.225356 0.184533 +3 0.248241 0.248241 0.225356 0.000001 0.248241 +4 0.000001 0.000001 0.184533 0.248241 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a9aac792bd027125d6f8d192c289f8c7133740a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000489_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32906600 Before NNI: tree length is 0.32906600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc663060924a16dd641bfff5b9865a474e65cc68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59026627 Before NNI: tree length is 0.59026625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000492_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000492_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0ab469720bc0a89ec8275af22f6ff8744cfb596 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000492_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.70618550 Before NNI: tree length is 0.70618550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..22531b5336fc32bfbe45e72827917b9835487c6f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000172 0.267546 0.222503 0.002645 +1 0.000172 0.000001 0.267718 0.222675 0.002473 +2 0.267546 0.267718 0.000001 0.216452 0.270191 +3 0.222503 0.222675 0.216452 0.000001 0.225148 +4 0.002645 0.002473 0.270191 0.225148 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..93551b79107b5c6ae8a22958beeb5d04bbb3ad70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000494_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35589550 Before NNI: tree length is 0.35589550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36c3ad4ae9196222a07e5593040d3688bd662db7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.254755 0.541293 0.016478 +1 0.000001 0.000001 0.254755 0.541293 0.016478 +2 0.254755 0.254755 0.000001 0.622051 0.252235 +3 0.541293 0.541293 0.622051 0.000001 0.538773 +4 0.016478 0.016478 0.252235 0.538773 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b1f8c705fb0853e2f7da77a707c5be69246253f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000495_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71602900 Before NNI: tree length is 0.71602900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000496_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000496_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a691a54c3ba0ca37fa6072ed405a4f123f550d7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000496_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11810800 Before NNI: tree length is 0.11810800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000500_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000500_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..226f8cc7bec4494fcd1fff4fac7f26c83cdff8e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000500_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35297272 Before NNI: tree length is 0.35297275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..b9d65e43e74cb6d4181c73fbe6e517a47bc25511 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015521 0.363110 0.517409 0.004279 +1 0.015521 0.000001 0.361439 0.515738 0.011506 +2 0.363110 0.361439 0.000001 0.474846 0.359096 +3 0.517409 0.515738 0.474846 0.000001 0.513395 +4 0.004279 0.011506 0.359096 0.513395 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b8746cfa85ffe14d4cd48aa41ab8060633017348 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.330493 0.530429 0.000001 +1 0.000001 0.000001 0.330493 0.530429 0.000001 +2 0.330493 0.330493 0.000001 0.643776 0.330493 +3 0.530429 0.530429 0.643776 0.000001 0.530429 +4 0.000001 0.000001 0.330493 0.530429 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000505_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000505_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4fa9a9a17994745391a1bb4c6b0f8b59f2d87b1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000505_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003813 0.034942 0.078581 0.002436 +1 0.003813 0.000001 0.033532 0.077171 0.001548 +2 0.034942 0.033532 0.000001 0.068714 0.032676 +3 0.078581 0.077171 0.068714 0.000001 0.076316 +4 0.002436 0.001548 0.032676 0.076316 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000507_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000507_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b323e5eeedb066311e0a534942167835e09af2a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000507_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71888712 Before NNI: tree length is 0.71888713 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..036a73e5821acf690ec3b8bb70281b13911bdd68 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21512159 Before NNI: tree length is 0.21512163 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6144ea8b93a3a2b1407f37c2833ae6753f91d47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20845755 Before NNI: tree length is 0.20845750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ba166b1f68883f08c2ab280bcdac37c8e69a4d4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35154986 Before NNI: tree length is 0.35154988 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..edafc97b2d27ae096305623bc51ab98056c337d7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016595 0.054294 0.176139 0.014929 +1 0.016595 0.000001 0.053676 0.175521 0.012354 +2 0.054294 0.053676 0.000001 0.171492 0.052010 +3 0.176139 0.175521 0.171492 0.000001 0.173855 +4 0.014929 0.012354 0.052010 0.173855 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ffc8573228ee1a594ddbe83642b6691199ddc444 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016388 0.097354 0.145053 0.003715 +1 0.016388 0.000001 0.102202 0.149901 0.013498 +2 0.097354 0.102202 0.000001 0.130160 0.094463 +3 0.145053 0.149901 0.130160 0.000001 0.142163 +4 0.003715 0.013498 0.094463 0.142163 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5eb7b2b8bad2d80257c87d059d3d773d23430381 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000515_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19731389 Before NNI: tree length is 0.19731388 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d34d024a53503377fdeb6d83db02ad252412c7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08978700 Before NNI: tree length is 0.08978700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000518_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000518_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d3005a87588ebc208c274539ec7bf3a511cfdea5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000518_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048679 0.452260 0.648066 0.059215 +1 0.048679 0.000001 0.437947 0.633753 0.059469 +2 0.452260 0.437947 0.000001 0.665541 0.463050 +3 0.648066 0.633753 0.665541 0.000001 0.658856 +4 0.059215 0.059469 0.463050 0.658856 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000519_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000519_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc7bbafef7d4ec736d4972c43c7804f58062000b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000519_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29383075 Before NNI: tree length is 0.29383075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6165ce9ef19844d074ba71210060d152d629d1f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32269075 Before NNI: tree length is 0.32269075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..058af786481fdbb685f52e8fb1f3ca933fc3f0d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.131198 0.203741 0.250753 0.179362 +1 0.131198 0.000001 0.205950 0.252962 0.181572 +2 0.203741 0.205950 0.000001 0.201622 0.165495 +3 0.250753 0.252962 0.201622 0.000001 0.212507 +4 0.179362 0.181572 0.165495 0.212507 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1332d3f84e4d82e2f230164de35ef96caf575355 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000526_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46531975 Before NNI: tree length is 0.46531975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..888d75391cbcbba32fee44de704c5959a9e304cf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24544100 Before NNI: tree length is 0.24544100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..59140259f31f3c6bc94dc17e16dc39b2854dbb4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036688 0.055894 0.033191 0.022544 +1 0.036688 0.000001 0.056690 0.033987 0.041777 +2 0.055894 0.056690 0.000001 0.047855 0.060983 +3 0.033191 0.033987 0.047855 0.000001 0.038280 +4 0.022544 0.041777 0.060983 0.038280 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1bd1ca1f0666a85b2d80aaa595860686449b9ca5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32752650 Before NNI: tree length is 0.32752650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf53f8f0372b3c78e79a8fd6a6e1114c83b988f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.091037 0.238088 0.485565 0.087572 +1 0.091037 0.000001 0.238545 0.486023 0.061938 +2 0.238088 0.238545 0.000001 0.538403 0.235081 +3 0.485565 0.486023 0.538403 0.000001 0.482558 +4 0.087572 0.061938 0.235081 0.482558 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f14d4a4da844d9b8c4130dabe1b5457d6dbaeccf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000532_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.70601189 Before NNI: tree length is 0.70601188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f451d3451ef5a3602925245606d15ca54269e5da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48612879 Before NNI: tree length is 1.48612875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..732df38b65d76571ea609c3e2985fa3a45d2c062 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017003 0.159511 0.437294 0.025024 +1 0.017003 0.000001 0.176513 0.454296 0.042027 +2 0.159511 0.176513 0.000001 0.380849 0.158581 +3 0.437294 0.454296 0.380849 0.000001 0.436364 +4 0.025024 0.042027 0.158581 0.436364 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1df36f2022514649149ded6a3562ddc6a1ce3ee1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39448103 Before NNI: tree length is 0.39448100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..017e440b7e27e68645c9ce3ffa7f223d4f1258f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22204021 Before NNI: tree length is 0.22204025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000542_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000542_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1ccd7ad72309a803eeed3211badc373577c2a1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000542_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29132000 Before NNI: tree length is 0.29132000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000544_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000544_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b717a4b4a9fe1e57b355a84d2f7ed6c0adf5427f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000544_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19537135 Before NNI: tree length is 0.19537138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ef486eca371515f80bf5e502d111c9e1572ea0a1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040601 0.466107 1.006724 0.000001 +1 0.040601 0.000001 0.450976 0.991594 0.040601 +2 0.466107 0.450976 0.000001 0.840810 0.466107 +3 1.006724 0.991594 0.840810 0.000001 1.006724 +4 0.000001 0.040601 0.466107 1.006724 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..188f22926204c5c0b553a6807effef23122f5af1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002460 0.023876 0.083423 0.000001 +1 0.002460 0.000001 0.025921 0.085468 0.002460 +2 0.023876 0.025921 0.000001 0.073839 0.023876 +3 0.083423 0.085468 0.073839 0.000001 0.083423 +4 0.000001 0.002460 0.023876 0.083423 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f64105f09dd5f636e76ce47e4b16a4df146c7230 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81702425 Before NNI: tree length is 0.81702425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f9cd1218d63f350e1e10d3f0c445698949bcb69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25761276 Before NNI: tree length is 0.25761275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..19a0944a1fa69f7c88518e64f5d5faeb75f62dd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022489 0.199316 0.222665 0.016437 +1 0.022489 0.000001 0.217080 0.240429 0.034202 +2 0.199316 0.217080 0.000001 0.241168 0.205272 +3 0.222665 0.240429 0.241168 0.000001 0.228621 +4 0.016437 0.034202 0.205272 0.228621 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc84665db28841911e9252dca48b21eb828683e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000556_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36289775 Before NNI: tree length is 0.36289775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3512c56531c6fd14cfc98f0eb239b75b40dd7b02 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48640589 Before NNI: tree length is 0.48640587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e211eddb3f8d83f44d64c0ec9e0ae6d29ffffe0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060724 0.213862 0.240725 0.000001 +1 0.060724 0.000001 0.168090 0.194954 0.060724 +2 0.213862 0.168090 0.000001 0.276046 0.213862 +3 0.240725 0.194954 0.276046 0.000001 0.240725 +4 0.000001 0.060724 0.213862 0.240725 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..891e393bfdbe0cddf63900befe97f4701a433c4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000562_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37279325 Before NNI: tree length is 0.37279325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85d38dec9a594b5f806284a7fbf2c2e5349c7015 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71290550 Before NNI: tree length is 0.71290550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc96f82b8aaac11c16ea34c12fcedaa014cc1864 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19057863 Before NNI: tree length is 0.19057862 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000572_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000572_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..275227c32b6b6c31364a3c0b13d6343feaf24220 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000572_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.178927 1.015280 0.189530 0.128324 +1 0.178927 0.000001 0.952754 0.158588 0.204891 +2 1.015280 0.952754 0.000001 0.994941 1.041244 +3 0.189530 0.158588 0.994941 0.000001 0.215494 +4 0.128324 0.204891 1.041244 0.215494 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..24f419c6bd6c94cd0351f0b08baf4f883010da8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008203 0.148480 0.021204 0.021491 +1 0.008203 0.000001 0.144546 0.017270 0.017558 +2 0.148480 0.144546 0.000001 0.150124 0.150412 +3 0.021204 0.017270 0.150124 0.000001 0.012323 +4 0.021491 0.017558 0.150412 0.012323 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..492507f374086fbc3c2bad28df519c19a49fff71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000579_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16834387 Before NNI: tree length is 0.16834388 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7b925e8395303b71f91ebe2483497f0f7d0cb59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.050340 0.149568 0.577426 0.037463 +1 0.050340 0.000001 0.125330 0.553188 0.042578 +2 0.149568 0.125330 0.000001 0.567598 0.141807 +3 0.577426 0.553188 0.567598 0.000001 0.569665 +4 0.037463 0.042578 0.141807 0.569665 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbfc02e02db0b4e95b34ca2d80d465712b2d371e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000583_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67519775 Before NNI: tree length is 0.67519775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000585_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000585_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9dd7c5c754f5bce3d0c5b9469ed367c4748a9dd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000585_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014270 0.029585 0.075215 0.000001 +1 0.014270 0.000001 0.035367 0.080997 0.014270 +2 0.029585 0.035367 0.000001 0.083874 0.029585 +3 0.075215 0.080997 0.083874 0.000001 0.075215 +4 0.000001 0.014270 0.029585 0.075215 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8d3b5555cec276614e75b42469b49130fc698423 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.031369 0.097671 0.000001 +1 0.000001 0.000001 0.031369 0.097671 0.000001 +2 0.031369 0.031369 0.000001 0.086328 0.031369 +3 0.097671 0.097671 0.086328 0.000001 0.097671 +4 0.000001 0.000001 0.031369 0.097671 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..58d37f9db3480b4b7a7301a601330bb0acacf89d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007977 0.066803 0.409598 0.006250 +1 0.007977 0.000001 0.067668 0.410462 0.007114 +2 0.066803 0.067668 0.000001 0.407789 0.060553 +3 0.409598 0.410462 0.407789 0.000001 0.403347 +4 0.006250 0.007114 0.060553 0.403347 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4bd900fe2ed9bd858066aeacd43c3b615b9a646a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18017475 Before NNI: tree length is 0.18017475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a6ab85336993aa578c6056ac2881033871bf5f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006375 0.158134 0.468545 0.050655 +1 0.006375 0.000001 0.160747 0.471158 0.053268 +2 0.158134 0.160747 0.000001 0.487601 0.153572 +3 0.468545 0.471158 0.487601 0.000001 0.463983 +4 0.050655 0.053268 0.153572 0.463983 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e719a35238138144668dd4936898bc87dfe4b96b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000592_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58468050 Before NNI: tree length is 0.58468050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1cc90f35452b2c7e2bafa776729b816c83112cd1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36835375 Before NNI: tree length is 0.36835375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a2c0e63bbb4a04d58912765270dde7dd435f36f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.131971 0.295246 0.000001 +1 0.000001 0.000001 0.131971 0.295246 0.000001 +2 0.131971 0.131971 0.000001 0.279944 0.131971 +3 0.295246 0.295246 0.279944 0.000001 0.295246 +4 0.000001 0.000001 0.131971 0.295246 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f976b5a24a3f39ac63da0eaf19896b6975973ff0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000599_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35358150 Before NNI: tree length is 0.35358150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..356ef75c3e29cf95283938833f514578de8e1f92 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001714 0.039125 0.069675 0.001520 +1 0.001714 0.000001 0.037412 0.067961 0.000193 +2 0.039125 0.037412 0.000001 0.059410 0.037605 +3 0.069675 0.067961 0.059410 0.000001 0.068155 +4 0.001520 0.000193 0.037605 0.068155 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..77345d2ca7a46cfb577e6007d14378b5c296f62c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27128060 Before NNI: tree length is 0.27128063 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000603_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000603_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..69713f5254db64ee8c675a06c91d4c8e53e41816 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000603_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38353350 Before NNI: tree length is 0.38353350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8873bb43fefab4bd2f7f0c54c1693794835b3d57 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.243701 0.547674 0.006888 +1 0.000001 0.000001 0.243701 0.547674 0.006888 +2 0.243701 0.243701 0.000001 0.523719 0.237579 +3 0.547674 0.547674 0.523719 0.000001 0.541551 +4 0.006888 0.006888 0.237579 0.541551 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000605_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000605_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5b57fe7c32061a3803104e9eb418288f839866de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000605_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22603200 Before NNI: tree length is 0.22603200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000607_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000607_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c0db3a46cb2d9ef79d49e3e0988d102898436b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000607_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15804400 Before NNI: tree length is 0.15804400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..abe265bbec84ac06c6f6e595c2b42009c35308eb --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003897 0.065661 0.243551 0.003135 +1 0.003897 0.000001 0.069558 0.247448 0.007033 +2 0.065661 0.069558 0.000001 0.266791 0.067256 +3 0.243551 0.247448 0.266791 0.000001 0.245145 +4 0.003135 0.007033 0.067256 0.245145 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..793f9ce4d60030aea5cdac3c659c7b745b05d5c7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.095080 0.166291 0.000001 +1 0.000001 0.000001 0.095080 0.166291 0.000001 +2 0.095080 0.095080 0.000001 0.141201 0.095080 +3 0.166291 0.166291 0.141201 0.000001 0.166291 +4 0.000001 0.000001 0.095080 0.166291 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ac37aff7dd3d108128c41394f542f929a4132c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.221279 0.362110 0.000001 +1 0.000001 0.000001 0.221279 0.362110 0.000001 +2 0.221279 0.221279 0.000001 0.390720 0.221279 +3 0.362110 0.362110 0.390720 0.000001 0.362110 +4 0.000001 0.000001 0.221279 0.362110 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b38264913fb584fca0d3c72dcd2b0cd32977ee70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000610_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48705550 Before NNI: tree length is 0.48705550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6df89bf655d2d919523cefa86b3ac691ec63d134 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011336 0.391684 0.426566 0.000001 +1 0.011336 0.000001 0.385698 0.420580 0.011336 +2 0.391684 0.385698 0.000001 0.403792 0.391684 +3 0.426566 0.420580 0.403792 0.000001 0.426566 +4 0.000001 0.011336 0.391684 0.426566 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4e48405c0dd5a2d1e7c76a5b2a1050d94c82652f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.000001 0.000001 +1 0.000001 0.000001 0.000001 0.000001 0.000001 +2 0.000001 0.000001 0.000001 0.000001 0.000001 +3 0.000001 0.000001 0.000001 0.000001 0.000001 +4 0.000001 0.000001 0.000001 0.000001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..599985b3e3ea3a1afb38757b1a759122baffb83f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000614_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00000250 Before NNI: tree length is 0.00000250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : -4460149039706124200828622340096.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000616_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000616_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2033109a17bc2fcbcf5145e9f8790f2f6c2278d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000616_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.063593 0.147769 0.003542 +1 0.000001 0.000001 0.063593 0.147769 0.003542 +2 0.063593 0.063593 0.000001 0.140843 0.061085 +3 0.147769 0.147769 0.140843 0.000001 0.145261 +4 0.003542 0.003542 0.061085 0.145261 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5d7c0a85e8cf89741dcf27d3b17ef5c409cb586d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.077919 0.290120 0.746057 0.075362 +1 0.077919 0.000001 0.228925 0.684862 0.004733 +2 0.290120 0.228925 0.000001 0.663666 0.226368 +3 0.746057 0.684862 0.663666 0.000001 0.682305 +4 0.075362 0.004733 0.226368 0.682305 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8ff013c108e970581383889f378a16e52623d16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54384050 Before NNI: tree length is 0.54384050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4069563f50fb8e91e08773220497454d7a4ac890 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007068 0.070513 0.212265 0.021332 +1 0.007068 0.000001 0.071657 0.213409 0.014779 +2 0.070513 0.071657 0.000001 0.187804 0.085920 +3 0.212265 0.213409 0.187804 0.000001 0.227672 +4 0.021332 0.014779 0.085920 0.227672 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f774321bf18e7ca725217326bcd72df6100a9da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000622_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25391825 Before NNI: tree length is 0.25391825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000626_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000626_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..57bf6d10dbbce521f927a5f58f615cf010c39fcf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000626_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10071040 Before NNI: tree length is 0.10071037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c4f02651803a096bc1b234663073c5b9c6a9784b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045904 0.217398 0.045784 0.041763 +1 0.045904 0.000001 0.219626 0.048012 0.027876 +2 0.217398 0.219626 0.000001 0.202984 0.215485 +3 0.045784 0.048012 0.202984 0.000001 0.043871 +4 0.041763 0.027876 0.215485 0.043871 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c34c9358233b804dffc2be91a333c15ec61bd15b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000629_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26901650 Before NNI: tree length is 0.26901650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d18f4aff3ff9507ed74026438617f5ccabb43dd0 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021153 0.261366 0.269195 0.027223 +1 0.021153 0.000001 0.267568 0.275398 0.006069 +2 0.261366 0.267568 0.000001 0.030211 0.273637 +3 0.269195 0.275398 0.030211 0.000001 0.281467 +4 0.027223 0.006069 0.273637 0.281467 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fe88140f7f52775b260a5352208de364a763cea8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014804 0.126152 0.152746 0.006406 +1 0.014804 0.000001 0.120557 0.147151 0.008461 +2 0.126152 0.120557 0.000001 0.129868 0.119809 +3 0.152746 0.147151 0.129868 0.000001 0.146403 +4 0.006406 0.008461 0.119809 0.146403 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e20f2472b14dd89643918642b61aa2e67034c47b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.131534 0.610145 0.000001 +1 0.000001 0.000001 0.131534 0.610145 0.000001 +2 0.131534 0.131534 0.000001 0.600606 0.131534 +3 0.610145 0.610145 0.600606 0.000001 0.610145 +4 0.000001 0.000001 0.131534 0.610145 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b9172dea0af9220e8d0d43d5f50fc0d19ef0120 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000636_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67114350 Before NNI: tree length is 0.67114350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..22c53fc2e989a6e6fe49c795b491cb2b1a8e8850 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06317045 Before NNI: tree length is 0.06317050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c8e9bb877bad371766471870db0c18cd3aa65c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003186 0.044931 0.128107 0.003186 +1 0.003186 0.000001 0.048117 0.131293 0.000001 +2 0.044931 0.048117 0.000001 0.130820 0.048117 +3 0.128107 0.131293 0.130820 0.000001 0.131293 +4 0.003186 0.000001 0.048117 0.131293 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c38449c833170460d68bddbb8336f415e3c92b7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030208 0.116927 0.254687 0.009186 +1 0.030208 0.000001 0.120986 0.258746 0.029551 +2 0.116927 0.120986 0.000001 0.238212 0.116271 +3 0.254687 0.258746 0.238212 0.000001 0.254031 +4 0.009186 0.029551 0.116271 0.254031 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f70e54b1bac8d9512ec35c6a07196437106f6a53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000642_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32631125 Before NNI: tree length is 0.32631125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..798ae959b3ee947dfd9bdcf2e5063b3c6c6f877b --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.227188 0.703158 0.000001 +1 0.000001 0.000001 0.227188 0.703158 0.000001 +2 0.227188 0.227188 0.000001 0.682079 0.227188 +3 0.703158 0.703158 0.682079 0.000001 0.703158 +4 0.000001 0.000001 0.227188 0.703158 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85d50f3d1b41efe2f8e0945e65d82da3c5b46f53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16056850 Before NNI: tree length is 0.16056850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e4776dd5e806a5b609b665d9d0ac9ac36a60ca30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014482 0.172941 0.409435 0.000001 +1 0.014482 0.000001 0.170156 0.406650 0.014482 +2 0.172941 0.170156 0.000001 0.366573 0.172941 +3 0.409435 0.406650 0.366573 0.000001 0.409435 +4 0.000001 0.014482 0.172941 0.409435 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000651_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000651_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..299e2bd5991006ccd30be8afc332c15d0c77851b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000651_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009282 0.083362 0.233531 0.018702 +1 0.009282 0.000001 0.087865 0.238035 0.023206 +2 0.083362 0.087865 0.000001 0.207782 0.088333 +3 0.233531 0.238035 0.207782 0.000001 0.238503 +4 0.018702 0.023206 0.088333 0.238503 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..66a62f5bfbbc14f774626f1fcd7a4934cd5ef253 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59330440 Before NNI: tree length is 0.59330438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7a749fa1fa3aaffcdd23336b261e631efafddd61 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002583 0.041675 0.069458 0.000001 +1 0.002583 0.000001 0.039092 0.066875 0.002583 +2 0.041675 0.039092 0.000001 0.063780 0.041675 +3 0.069458 0.066875 0.063780 0.000001 0.069458 +4 0.000001 0.002583 0.041675 0.069458 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..485c74aa8a14b367652f7d6667de4b6bc6596878 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02121125 Before NNI: tree length is 0.02121125 + 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/OG0000661_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000661_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..997dd700a2f2a003f637678cfc3b44aaf9e831f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000661_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025151 0.063358 0.013986 0.022095 +1 0.025151 0.000001 0.044081 0.013567 0.010594 +2 0.063358 0.044081 0.000001 0.051775 0.048801 +3 0.013986 0.013567 0.051775 0.000001 0.010511 +4 0.022095 0.010594 0.048801 0.010511 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7be3f683497d81b75912e794961d1a6b9ee69347 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009132 0.012209 0.000001 0.000001 +1 0.009132 0.000001 0.018373 0.009132 0.009132 +2 0.012209 0.018373 0.000001 0.012209 0.012209 +3 0.000001 0.009132 0.012209 0.000001 0.000001 +4 0.000001 0.009132 0.012209 0.000001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000664_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000664_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..406ec1b5dddac0cb29413ca73020f1d2376f1b41 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000664_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22182000 Before NNI: tree length is 0.22182000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef7c82c54812eccbf726e98465f2029a1a67ecd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.074539 0.234438 0.400765 0.064890 +1 0.074539 0.000001 0.269376 0.435704 0.010753 +2 0.234438 0.269376 0.000001 0.420854 0.259728 +3 0.400765 0.435704 0.420854 0.000001 0.426055 +4 0.064890 0.010753 0.259728 0.426055 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3d9ab10cf2ad565faf51efe59305049f7b7c3697 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005311 0.105536 0.273340 0.011980 +1 0.005311 0.000001 0.105031 0.272834 0.011475 +2 0.105536 0.105031 0.000001 0.264952 0.108348 +3 0.273340 0.272834 0.264952 0.000001 0.276151 +4 0.011980 0.011475 0.108348 0.276151 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2845f7ad582ca3935450bf8c5e539dfbbb1f53bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000670_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33171266 Before NNI: tree length is 0.33171263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c9e749cd25536d008ad0b4a6df68bb6e81a3284 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22366170 Before NNI: tree length is 0.22366175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..044557977ff8b33f8a3db5d7543353a6b56c5c9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43639500 Before NNI: tree length is 0.43639500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000675_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000675_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64100dd854dab723e608677b44be6309337205f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000675_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46829298 Before NNI: tree length is 0.46829300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8747579c9ad735b3d15bcfa181acc28d2166535 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65257638 Before NNI: tree length is 0.65257637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a27edb2f3614b34837184c7716f2955f27c84ad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011352 0.153883 0.172350 0.004391 +1 0.011352 0.000001 0.156065 0.174532 0.010699 +2 0.153883 0.156065 0.000001 0.184731 0.153229 +3 0.172350 0.174532 0.184731 0.000001 0.171696 +4 0.004391 0.010699 0.153229 0.171696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000681_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000681_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f9d1a1e3a097378c89f928787d9d4cdcb1d68de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000681_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007392 0.021137 0.040009 0.019819 +1 0.007392 0.000001 0.026157 0.045030 0.024839 +2 0.021137 0.026157 0.000001 0.055442 0.016702 +3 0.040009 0.045030 0.055442 0.000001 0.054125 +4 0.019819 0.024839 0.016702 0.054125 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000682_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000682_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d4109eb5ade52534e9e34657a996e810bda1a37a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000682_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019782 0.125023 0.272789 0.007942 +1 0.019782 0.000001 0.117580 0.265347 0.011841 +2 0.125023 0.117580 0.000001 0.231109 0.117081 +3 0.272789 0.265347 0.231109 0.000001 0.264847 +4 0.007942 0.011841 0.117081 0.264847 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..efeea2f376d7ebb257ed84cbb7c7953b653ff370 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.065227 0.081345 0.043697 +1 0.000001 0.000001 0.065227 0.081345 0.043697 +2 0.065227 0.065227 0.000001 0.103709 0.066061 +3 0.081345 0.081345 0.103709 0.000001 0.077287 +4 0.043697 0.043697 0.066061 0.077287 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..195fc331d50bc5698e387f4255173bf404347556 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024380 0.048961 0.261529 0.041701 +1 0.024380 0.000001 0.052759 0.237148 0.017320 +2 0.048961 0.052759 0.000001 0.289908 0.070080 +3 0.261529 0.237148 0.289908 0.000001 0.223921 +4 0.041701 0.017320 0.070080 0.223921 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..39dc769af1baaafce0cd7b4e99193263c3d69cbe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16798150 Before NNI: tree length is 0.16798150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000688_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000688_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8942eb0218a20005c26baacee4a8dbb08b59ee05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000688_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022616 0.049173 0.260739 0.020321 +1 0.022616 0.000001 0.052799 0.264364 0.034518 +2 0.049173 0.052799 0.000001 0.254728 0.061075 +3 0.260739 0.264364 0.254728 0.000001 0.272641 +4 0.020321 0.034518 0.061075 0.272641 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d2608304615a0aadc94f258fd6b8779fe6788bff --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004757 0.016930 0.150986 0.006904 +1 0.004757 0.000001 0.015889 0.149946 0.009651 +2 0.016930 0.015889 0.000001 0.146967 0.021823 +3 0.150986 0.149946 0.146967 0.000001 0.155880 +4 0.006904 0.009651 0.021823 0.155880 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c06f8d5072dbbb08f589f3c6e65171f5d71ea73 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50362411 Before NNI: tree length is 0.50362413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb01fd50721cb845d68fb8579f3999be21659f7a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.63528650 Before NNI: tree length is 0.63528650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a118e8e0546913d93a5c0c76b5fbfc128db75c5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45758150 Before NNI: tree length is 0.45758150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..86cdfc2646835b657610880a7402899a1551858c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27538450 Before NNI: tree length is 0.27538450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d5d4858d2871b5a145307487c63f8d9e20f652c9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004957 0.065136 0.246272 0.020926 +1 0.004957 0.000001 0.060179 0.241315 0.015970 +2 0.065136 0.060179 0.000001 0.226863 0.046845 +3 0.246272 0.241315 0.226863 0.000001 0.227980 +4 0.020926 0.015970 0.046845 0.227980 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d427367e18c80430d84ed3d052cd5407385894d6 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09881165 Before NNI: tree length is 0.09881162 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..762be894445fff8cb768c3c0991c7dd9416879a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13279950 Before NNI: tree length is 0.13279950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed127a19c690b1e9813d0a8d15da270d355a1076 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034584 0.211471 0.155424 0.028590 +1 0.034584 0.000001 0.210980 0.154933 0.028099 +2 0.211471 0.210980 0.000001 0.206232 0.199454 +3 0.155424 0.154933 0.206232 0.000001 0.143407 +4 0.028590 0.028099 0.199454 0.143407 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7ff7346e98832b46e35969567a6de9f7673727c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025757 0.221408 0.359973 0.020759 +1 0.025757 0.000001 0.220432 0.358998 0.010274 +2 0.221408 0.220432 0.000001 0.335335 0.215434 +3 0.359973 0.358998 0.335335 0.000001 0.354000 +4 0.020759 0.010274 0.215434 0.354000 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c46108f4692ae8731dd2165576318c488330f4d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024578 0.160984 0.158141 0.030378 +1 0.024578 0.000001 0.155930 0.153086 0.017915 +2 0.160984 0.155930 0.000001 0.147338 0.161730 +3 0.158141 0.153086 0.147338 0.000001 0.158886 +4 0.030378 0.017915 0.161730 0.158886 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6530cae977605d74cffeb3b10a8234cf44008ec3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000712_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25485075 Before NNI: tree length is 0.25485075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..fca54ba4c9feabb3ffe1039a5a846c2c94993e69 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052295 0.314234 0.449524 0.045853 +1 0.052295 0.000001 0.307405 0.442696 0.018965 +2 0.314234 0.307405 0.000001 0.505173 0.300964 +3 0.449524 0.442696 0.505173 0.000001 0.436255 +4 0.045853 0.018965 0.300964 0.436255 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000714_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000714_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58fb32c479ce10e06895f4629dcc489a8e7e5e5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000714_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.118992 0.285759 0.027975 +1 0.000001 0.000001 0.118992 0.285759 0.027975 +2 0.118992 0.118992 0.000001 0.210836 0.134042 +3 0.285759 0.285759 0.210836 0.000001 0.300809 +4 0.027975 0.027975 0.134042 0.300809 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dd626b3c14bbb0b4db8a3b485d60f17760a7488c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005695 0.038405 0.433273 0.005695 +1 0.005695 0.000001 0.040349 0.435217 0.000001 +2 0.038405 0.040349 0.000001 0.462658 0.040349 +3 0.433273 0.435217 0.462658 0.000001 0.435217 +4 0.005695 0.000001 0.040349 0.435217 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b16e66343bc219325d604e60516c82a3d91c6d91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.021215 0.194425 0.000001 +1 0.000001 0.000001 0.021215 0.194425 0.000001 +2 0.021215 0.021215 0.000001 0.203392 0.021215 +3 0.194425 0.194425 0.203392 0.000001 0.194425 +4 0.000001 0.000001 0.021215 0.194425 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a77ec565dd4bce98aa10b458034ac531e4ebb4f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71373225 Before NNI: tree length is 0.71373225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..717406d775df6c162c87bad08095ba28ccc4af51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052192 0.251534 0.473717 0.044237 +1 0.052192 0.000001 0.205987 0.428169 0.009339 +2 0.251534 0.205987 0.000001 0.473622 0.208681 +3 0.473717 0.428169 0.473622 0.000001 0.430864 +4 0.044237 0.009339 0.208681 0.430864 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..27cd75d14f1776d53fde87f20d15a7cc26cfd63b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000724_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60345079 Before NNI: tree length is 0.60345075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd1c3fe8b79d101fee1d8ac5d84952a781a6710b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.70036752 Before NNI: tree length is 0.70036750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a198254bc3b78056774d307a81a772667cbb485e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17206550 Before NNI: tree length is 0.17206550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000732_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000732_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b8fd41c59ce149c748cb7f1c62a455de2a8749c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000732_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031889 0.250134 0.491923 0.038722 +1 0.031889 0.000001 0.219805 0.461595 0.006834 +2 0.250134 0.219805 0.000001 0.448535 0.226639 +3 0.491923 0.461595 0.448535 0.000001 0.468428 +4 0.038722 0.006834 0.226639 0.468428 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000733_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000733_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eca1ded03921cedfce4932bb485d6fff54f42083 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000733_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13714050 Before NNI: tree length is 0.13714050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..46d0393d5f0f377933ce164f1b1abfc29199b8b8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011535 0.033526 0.149209 0.007437 +1 0.011535 0.000001 0.034978 0.150661 0.005237 +2 0.033526 0.034978 0.000001 0.156145 0.030879 +3 0.149209 0.150661 0.156145 0.000001 0.146563 +4 0.007437 0.005237 0.030879 0.146563 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..463ce75a00d01b46885831d8c3f78c4cc129cfc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001368 0.079244 0.196937 0.000001 +1 0.001368 0.000001 0.079809 0.197502 0.001368 +2 0.079244 0.079809 0.000001 0.192078 0.079244 +3 0.196937 0.197502 0.192078 0.000001 0.196937 +4 0.000001 0.001368 0.079244 0.196937 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000740_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000740_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6c9c1214b6a0c42b3e292391a919f398c3eb8c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000740_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23852400 Before NNI: tree length is 0.23852400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5f3e411593ee59e5b4cdc21793e87aa48293af2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09882873 Before NNI: tree length is 0.09882875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..c6d02f73c29e9fe38094ee776c319960dc2113bc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048025 0.076132 0.151185 0.048025 +1 0.048025 0.000001 0.091185 0.166239 0.000001 +2 0.076132 0.091185 0.000001 0.151948 0.091185 +3 0.151185 0.166239 0.151948 0.000001 0.166239 +4 0.048025 0.000001 0.091185 0.166239 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..809192275db1faebcfee862eefae928270053316 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012529 0.088445 0.130405 0.012529 +1 0.012529 0.000001 0.090837 0.132798 0.000001 +2 0.088445 0.090837 0.000001 0.143409 0.090837 +3 0.130405 0.132798 0.143409 0.000001 0.132798 +4 0.012529 0.000001 0.090837 0.132798 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..601adc301a444ce9b8564dd30cd6073576094401 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026869 0.260105 0.561199 0.024979 +1 0.026869 0.000001 0.258420 0.559516 0.023296 +2 0.260105 0.258420 0.000001 0.521732 0.245403 +3 0.561199 0.559516 0.521732 0.000001 0.546497 +4 0.024979 0.023296 0.245403 0.546497 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..08f312a70aacba6585fe2be0f4221e488e293a91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.043932 0.133386 0.004832 +1 0.000001 0.000001 0.043932 0.133386 0.004832 +2 0.043932 0.043932 0.000001 0.135869 0.039099 +3 0.133386 0.133386 0.135869 0.000001 0.128553 +4 0.004832 0.004832 0.039099 0.128553 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..1faaf5ae82d10306c5c4572b1a2d42b5301de0a9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024502 0.224162 0.379348 0.025594 +1 0.024502 0.000001 0.210311 0.365497 0.013212 +2 0.224162 0.210311 0.000001 0.299508 0.212871 +3 0.379348 0.365497 0.299508 0.000001 0.368057 +4 0.025594 0.013212 0.212871 0.368057 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3a317d25091a7682f93ac49102ef44e2afdea42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30537615 Before NNI: tree length is 0.30537612 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b34c0fd54e39ea6392f7e609ab3ecd39562506d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015676 0.104746 0.198227 0.013109 +1 0.015676 0.000001 0.103099 0.196580 0.017889 +2 0.104746 0.103099 0.000001 0.241749 0.106960 +3 0.198227 0.196580 0.241749 0.000001 0.200441 +4 0.013109 0.017889 0.106960 0.200441 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..436730ecbc4b137790209819b907306550705093 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000759_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28703675 Before NNI: tree length is 0.28703675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a584be89392e46510d61fc6417f856c9ad516ed0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025137 0.105455 0.279408 0.021895 +1 0.025137 0.000001 0.115648 0.289601 0.028171 +2 0.105455 0.115648 0.000001 0.251963 0.112405 +3 0.279408 0.289601 0.251963 0.000001 0.286358 +4 0.021895 0.028171 0.112405 0.286358 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7f3b970cfa488c525154d31bdbcaac7b721f8a41 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007176 0.042701 0.176393 0.007176 +1 0.007176 0.000001 0.049877 0.183569 0.000001 +2 0.042701 0.049877 0.000001 0.212925 0.049877 +3 0.176393 0.183569 0.212925 0.000001 0.183569 +4 0.007176 0.000001 0.049877 0.183569 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f504900bb97a761cea37f94798d55db5205588b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31539954 Before NNI: tree length is 0.31539950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a355b0ca61c703f0a1d179fd10b4e3b94bf4b842 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.83159300 Before NNI: tree length is 0.83159300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a9d0b10848c9d3fe663601d0971ab79855e9f36 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013986 0.191335 0.368231 0.169790 +1 0.013986 0.000001 0.191115 0.368011 0.169571 +2 0.191335 0.191115 0.000001 0.433549 0.067619 +3 0.368231 0.368011 0.433549 0.000001 0.412005 +4 0.169790 0.169571 0.067619 0.412005 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ecb6ddf4f47e78343e58bf77a1cb98846a3a666 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.67638050 Before NNI: tree length is 1.67638050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a5df86ed46aebb69b538e04a86a8934fd2e4a7d1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.125951 0.061687 0.244299 0.126211 +1 0.125951 0.000001 0.147932 0.246260 0.009829 +2 0.061687 0.147932 0.000001 0.266279 0.148191 +3 0.244299 0.246260 0.266279 0.000001 0.246520 +4 0.126211 0.009829 0.148191 0.246520 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9714d6563dd6afaf8e0f35f9b7b61cbac3efe4f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15108450 Before NNI: tree length is 0.15108450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..2c820fcab08abb841c0090380ed69285877f1a17 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.013072 0.099216 0.000001 +1 0.000001 0.000001 0.013072 0.099216 0.000001 +2 0.013072 0.013072 0.000001 0.092048 0.013072 +3 0.099216 0.099216 0.092048 0.000001 0.099216 +4 0.000001 0.000001 0.013072 0.099216 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000781_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000781_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f134ecf54f913fdef7fc7441f30c299922c46bb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000781_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26696650 Before NNI: tree length is 0.26696650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000786_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000786_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..43af09ec90c669b59481dc3d276e003ec514157f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000786_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20811300 Before NNI: tree length is 0.20811300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000787_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000787_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36732d899e41c74405645ec19ab3f1d56d912092 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000787_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012375 0.129895 0.363027 0.000001 +1 0.012375 0.000001 0.129961 0.363093 0.012375 +2 0.129895 0.129961 0.000001 0.338916 0.129895 +3 0.363027 0.363093 0.338916 0.000001 0.363027 +4 0.000001 0.012375 0.129895 0.363027 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bd4a4b8d67e067838963b545c992afc14f600b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31367250 Before NNI: tree length is 0.31367250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b716d02c7ecf5432c3e26bd9779a11e6ac836b8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05355464 Before NNI: tree length is 0.05355463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..efc51e08bda1fc06537cc3abf3db22388efff29f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001477 0.114765 0.143481 0.002218 +1 0.001477 0.000001 0.114224 0.142939 0.002219 +2 0.114765 0.114224 0.000001 0.195888 0.115507 +3 0.143481 0.142939 0.195888 0.000001 0.144222 +4 0.002218 0.002219 0.115507 0.144222 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d7dbe9126bec31065f8cca2662f3d8cb0696d3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000794_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22901463 Before NNI: tree length is 0.22901462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d79e5cbdd060ed481e4751aa5ba3c69e39bce194 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004497 0.097389 0.300944 0.011883 +1 0.004497 0.000001 0.100714 0.304269 0.015208 +2 0.097389 0.100714 0.000001 0.319127 0.103471 +3 0.300944 0.304269 0.319127 0.000001 0.307026 +4 0.011883 0.015208 0.103471 0.307026 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3b060598a9e461515e0c4fe5306b3a1836d17b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000796_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37162350 Before NNI: tree length is 0.37162350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e410fe9a2f7533374b91da20ea20d6b57e01cd0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08154404 Before NNI: tree length is 0.08154400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d70a917041bbdecc2135e3b37369685715589bb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010811 0.103293 0.287942 0.000001 +1 0.010811 0.000001 0.113043 0.297691 0.010811 +2 0.103293 0.113043 0.000001 0.316240 0.103293 +3 0.287942 0.297691 0.316240 0.000001 0.287942 +4 0.000001 0.010811 0.103293 0.287942 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..668e34d217516994139bb379bb8d313b7b0951f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000798_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36401830 Before NNI: tree length is 0.36401825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..346ec8d034fdf58e675b8a6b93d64e7168659509 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.090480 0.292340 0.544079 0.045773 +1 0.090480 0.000001 0.285645 0.537383 0.080191 +2 0.292340 0.285645 0.000001 0.439586 0.282052 +3 0.544079 0.537383 0.439586 0.000001 0.533790 +4 0.045773 0.080191 0.282052 0.533790 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ce4cd222a0fdfb928b90f5115031d64ce03f24ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000800_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69763690 Before NNI: tree length is 0.69763688 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cc7ff9108644a1829b09f14292dadf64865d05ff --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025693 0.458813 0.588615 0.070762 +1 0.025693 0.000001 0.462724 0.592526 0.074674 +2 0.458813 0.462724 0.000001 0.756399 0.474569 +3 0.588615 0.592526 0.756399 0.000001 0.604371 +4 0.070762 0.074674 0.474569 0.604371 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000803_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000803_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9fae9f48af94b71df28d3a6da67ec3adfc2923c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000803_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50987350 Before NNI: tree length is 0.50987350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..017d84cadcb714a339dc59da6f263ed86b9675b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039380 0.047741 0.606581 0.041232 +1 0.039380 0.000001 0.038619 0.597458 0.032109 +2 0.047741 0.038619 0.000001 0.597431 0.027907 +3 0.606581 0.597458 0.597431 0.000001 0.590921 +4 0.041232 0.032109 0.027907 0.590921 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..10e1232b488c7ed550cf134807921f8119951457 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000809_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65170387 Before NNI: tree length is 0.65170387 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0f1fa8d3020640959e8488502fdca4a639b1cfb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068937 0.218645 1.024139 0.036252 +1 0.068937 0.000001 0.193397 0.998891 0.040425 +2 0.218645 0.193397 0.000001 0.897718 0.190132 +3 1.024139 0.998891 0.897718 0.000001 0.995626 +4 0.036252 0.040425 0.190132 0.995626 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a4d1e52ada6d73be126825028405c01e320155f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042035 0.237608 0.343243 0.030740 +1 0.042035 0.000001 0.239630 0.345266 0.047528 +2 0.237608 0.239630 0.000001 0.330483 0.243100 +3 0.343243 0.345266 0.330483 0.000001 0.348736 +4 0.030740 0.047528 0.243100 0.348736 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5b4ccb5f197910e843bc1734765ea645480068fe --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19644645 Before NNI: tree length is 0.19644650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf084732ce5eee39bd90d8dfef1897bacb77ac0b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39440113 Before NNI: tree length is 0.39440113 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000818_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000818_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b703c6b22c0a7d3b9faa49eb1f1bde39dd3a6a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000818_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30177995 Before NNI: tree length is 0.30178000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b39a6d82a7d4893e65964761cc8a809e6fd9b38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27943500 Before NNI: tree length is 0.27943500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f19f9aa141ad6ea84587be57def06fd9c3dddd8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38995150 Before NNI: tree length is 0.38995150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32b099f4b3dac39245e78519ea6e61570d94f991 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48976271 Before NNI: tree length is 0.48976275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8cb3c6278c48f15e1d8e899f7d39d71cb196fa9c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20634350 Before NNI: tree length is 0.20634350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b60546e3ad80a54a9a44c770bfe84a1906be96be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.308293 0.040355 0.000001 +1 0.000001 0.000001 0.308293 0.040355 0.000001 +2 0.308293 0.308293 0.000001 0.319442 0.308293 +3 0.040355 0.040355 0.319442 0.000001 0.040355 +4 0.000001 0.000001 0.308293 0.040355 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000835_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000835_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b89d505ffd6c789f634e9ce1eea537c62859ec66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000835_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18802367 Before NNI: tree length is 0.18802375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0beb45cbf96747f8829be2c4b608963aa58e5bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44583700 Before NNI: tree length is 0.44583700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dfe15d78e9f09653cbc3e4012a3008c292641733 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012645 0.018988 0.008339 0.005027 +1 0.012645 0.000001 0.014170 0.004306 0.015967 +2 0.018988 0.014170 0.000001 0.010649 0.022309 +3 0.008339 0.004306 0.010649 0.000001 0.011660 +4 0.005027 0.015967 0.022309 0.011660 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f498722485a401c0f78a4dc3587cc69f402a5ded --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000838_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02707565 Before NNI: tree length is 0.02707562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000840_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000840_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b453a34c86d049d46d4be1a261bf5fd94a6cb58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000840_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01760589 Before NNI: tree length is 0.01760587 + 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/OG0000841_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000841_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b8f61d7ce5c34d9ec31bcb3dffe7f6d06d3b0ced --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000841_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003224 0.040728 0.035815 0.000001 +1 0.003224 0.000001 0.041189 0.036277 0.003224 +2 0.040728 0.041189 0.000001 0.028227 0.040728 +3 0.035815 0.036277 0.028227 0.000001 0.035815 +4 0.000001 0.003224 0.040728 0.035815 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9efdd1bc4936161be61ab32475bf8abbd68ed051 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03442450 Before NNI: tree length is 0.03442450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed47a077e0fabe18cc9d65940615839bd5b2dba6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006393 0.029570 0.111094 0.007470 +1 0.006393 0.000001 0.029745 0.111269 0.006157 +2 0.029570 0.029745 0.000001 0.113239 0.030822 +3 0.111094 0.111269 0.113239 0.000001 0.112346 +4 0.007470 0.006157 0.030822 0.112346 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3db8d51b67b7be4afc3e2b01c4c611fe7848bcbd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000844_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13385250 Before NNI: tree length is 0.13385250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..53d568815aecb7821824d1bcde0ba0cbc42af1b1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24603250 Before NNI: tree length is 0.24603250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0f3730b2d3e15c813dd285863ccbed3540c2797 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79576425 Before NNI: tree length is 0.79576425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..292a7e6ae5def13fb79cb469cf589f88d38a98ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33009435 Before NNI: tree length is 0.33009437 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000855_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000855_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ae6007401606aefc01a85346123234b47597170 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000855_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26951430 Before NNI: tree length is 0.26951425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1c4c7b4be326e895815de2bc110e6fe54de03de --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.74741350 Before NNI: tree length is 0.74741350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b14a9013aa8f01634dc3330c1cb872388785a9dc --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.81406017 Before NNI: tree length is 2.81406025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..6f7e89dafdd7341681feb0678a3ae9688e4d490e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034392 0.283833 0.604847 0.040718 +1 0.034392 0.000001 0.275131 0.596145 0.032017 +2 0.283833 0.275131 0.000001 0.621599 0.259333 +3 0.604847 0.596145 0.621599 0.000001 0.580347 +4 0.040718 0.032017 0.259333 0.580347 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..469e2cde394a94e0894451aaac238f12b6abd257 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013294 0.231232 0.380123 0.052438 +1 0.013294 0.000001 0.217938 0.366829 0.065705 +2 0.231232 0.217938 0.000001 0.344872 0.283643 +3 0.380123 0.366829 0.344872 0.000001 0.432534 +4 0.052438 0.065705 0.283643 0.432534 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dbcc12ad5fd5965784faff4946316eee7b5cf6e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.019159 0.082184 0.004191 +1 0.000001 0.000001 0.019159 0.082184 0.004191 +2 0.019159 0.019159 0.000001 0.085951 0.020341 +3 0.082184 0.082184 0.085951 0.000001 0.083366 +4 0.004191 0.004191 0.020341 0.083366 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb8965320e1137b6431caaa81d001b26751ec9f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060217 0.057987 0.030133 0.028766 +1 0.060217 0.000001 0.011816 0.035292 0.036152 +2 0.057987 0.011816 0.000001 0.033063 0.033922 +3 0.030133 0.035292 0.033063 0.000001 0.006067 +4 0.028766 0.036152 0.033922 0.006067 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5642773b512078b5f0d2bad4a30696f757425a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000872_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06996452 Before NNI: tree length is 0.06996450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cf974ee92df50b01c960922809fb0c943233a90e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014079 0.238614 0.412078 0.042664 +1 0.014079 0.000001 0.238964 0.412428 0.043014 +2 0.238614 0.238964 0.000001 0.279694 0.207592 +3 0.412078 0.412428 0.279694 0.000001 0.381055 +4 0.042664 0.043014 0.207592 0.381055 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000878_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000878_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d1bf70d6975b8545bb86029584fe268005d3295 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000878_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33411350 Before NNI: tree length is 0.33411350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..35b6b54e6fa2ba9ed5396de502a539450e712cb1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002715 0.099842 0.091658 0.001846 +1 0.002715 0.000001 0.097127 0.088943 0.002697 +2 0.099842 0.097127 0.000001 0.085799 0.099823 +3 0.091658 0.088943 0.085799 0.000001 0.091640 +4 0.001846 0.002697 0.099823 0.091640 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000882_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000882_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..256c9e677f2a75415cdc84ef0e81df5271b100a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000882_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44015286 Before NNI: tree length is 0.44015287 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000884_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000884_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9430bc42c090cdc635ff20fb80143bd41070bd10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000884_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018360 0.084039 0.162577 0.001617 +1 0.018360 0.000001 0.087981 0.166519 0.019146 +2 0.084039 0.087981 0.000001 0.166689 0.084825 +3 0.162577 0.166519 0.166689 0.000001 0.163362 +4 0.001617 0.019146 0.084825 0.163362 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31061ca10f8e5c573e2ad172670c247175277438 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21588587 Before NNI: tree length is 0.21588587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d7b8b496ba72cb1f17d0534b5d77279f309213fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003433 0.128749 0.245580 0.019387 +1 0.003433 0.000001 0.125879 0.242710 0.016517 +2 0.128749 0.125879 0.000001 0.246104 0.130005 +3 0.245580 0.242710 0.246104 0.000001 0.246837 +4 0.019387 0.016517 0.130005 0.246837 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..586ff1d1372a8acc633b27026cf282d8adfd5bc4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39870250 Before NNI: tree length is 0.39870250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..04e2a2a745b81ae6abc247a22198e1cba9368e46 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027393 0.169415 0.297202 0.016142 +1 0.027393 0.000001 0.160058 0.287845 0.023608 +2 0.169415 0.160058 0.000001 0.291490 0.165629 +3 0.297202 0.287845 0.291490 0.000001 0.293416 +4 0.016142 0.023608 0.165629 0.293416 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c09d906c7b15ffbab68763500e692b933a470bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009434 0.098868 0.201408 0.016962 +1 0.009434 0.000001 0.107808 0.210349 0.025903 +2 0.098868 0.107808 0.000001 0.232939 0.097722 +3 0.201408 0.210349 0.232939 0.000001 0.200263 +4 0.016962 0.025903 0.097722 0.200263 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000893_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000893_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3322fe81f0ea7041b6e77a584ff67806a8521f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000893_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003577 0.148136 0.238494 0.003577 +1 0.003577 0.000001 0.151713 0.242071 0.000001 +2 0.148136 0.151713 0.000001 0.233790 0.151713 +3 0.238494 0.242071 0.233790 0.000001 0.242071 +4 0.003577 0.000001 0.151713 0.242071 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9979282e51fa1cce969050dbcc52fd21ea37c0b6 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016647 0.074252 0.192138 0.016647 +1 0.016647 0.000001 0.065255 0.183141 0.000001 +2 0.074252 0.065255 0.000001 0.194121 0.065255 +3 0.192138 0.183141 0.194121 0.000001 0.183141 +4 0.016647 0.000001 0.065255 0.183141 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92f01f1bcd0ec2bab8d12cc29f348ddd3b5f1bd9 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14044225 Before NNI: tree length is 0.14044225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000903_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000903_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9266336f6c2503831efa50cef8c980410079fc6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000903_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33093750 Before NNI: tree length is 0.33093750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7d20dcdc1fc4dd52f3c5f325f67c51bcfa805eb3 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016285 0.340908 0.196611 0.016285 +1 0.016285 0.000001 0.331046 0.186750 0.000001 +2 0.340908 0.331046 0.000001 0.357853 0.331046 +3 0.196611 0.186750 0.357853 0.000001 0.186750 +4 0.016285 0.000001 0.331046 0.186750 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5df29e5e8581f89a66ee8786624e6e03b2291844 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37094225 Before NNI: tree length is 0.37094225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e91327b1321f5dd4d79fd992546883784b151b1f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17933523 Before NNI: tree length is 0.17933525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000908_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000908_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ae8eb8a443779052bb231788b70097d981d1f9ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000908_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.132532 0.256456 0.000001 +1 0.000001 0.000001 0.132532 0.256456 0.000001 +2 0.132532 0.132532 0.000001 0.269021 0.132532 +3 0.256456 0.256456 0.269021 0.000001 0.256456 +4 0.000001 0.000001 0.132532 0.256456 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000910_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000910_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..83b3b18c68aea7a7d9fb4bd8a5d6019b8e63b8d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000910_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.328900 0.543478 0.000001 +1 0.000001 0.000001 0.328900 0.543478 0.000001 +2 0.328900 0.328900 0.000001 0.528667 0.328900 +3 0.543478 0.543478 0.528667 0.000001 0.543478 +4 0.000001 0.000001 0.328900 0.543478 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..dcc92ca6e458d292bcd8b64b286558e45819f2e8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.174730 0.184323 0.000001 +1 0.000001 0.000001 0.174730 0.184323 0.000001 +2 0.174730 0.174730 0.000001 0.246805 0.174730 +3 0.184323 0.184323 0.246805 0.000001 0.184323 +4 0.000001 0.000001 0.174730 0.184323 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..17f931612f4b83bb5b74bc86f9333b2d59cadbc5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31963119 Before NNI: tree length is 0.31963125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000915_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000915_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c6205467ea3ddd05326b06d74840b5258caea2bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000915_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026664 0.215139 0.409994 0.038214 +1 0.026664 0.000001 0.223089 0.417945 0.046165 +2 0.215139 0.223089 0.000001 0.372750 0.220885 +3 0.409994 0.417945 0.372750 0.000001 0.415740 +4 0.038214 0.046165 0.220885 0.415740 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32bd28239c549374e503092fec767bddb8db97b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08940100 Before NNI: tree length is 0.08940100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88e3a0578ce43659cc839696b64e7a8ca326be29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007181 0.214595 0.365318 0.000001 +1 0.007181 0.000001 0.220154 0.370878 0.007181 +2 0.214595 0.220154 0.000001 0.392111 0.214595 +3 0.365318 0.370878 0.392111 0.000001 0.365318 +4 0.000001 0.007181 0.214595 0.365318 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3465fe58728e543bc12778658bc8fd93888cd5aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000924_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49238272 Before NNI: tree length is 0.49238275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..171d9aafedf1902768b8c79164b48b642a89162e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13609850 Before NNI: tree length is 0.13609850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000928_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000928_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..08ace73dbac2226e88380b572366247844a6d542 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000928_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20447311 Before NNI: tree length is 0.20447313 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000929_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000929_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c5e6ed7bee1cc7daf36f4c417436ef15e66dc7e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000929_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.114304 0.239705 0.000001 +1 0.000001 0.000001 0.114304 0.239705 0.000001 +2 0.114304 0.114304 0.000001 0.238251 0.114304 +3 0.239705 0.239705 0.238251 0.000001 0.239705 +4 0.000001 0.000001 0.114304 0.239705 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000930_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000930_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a4018448da4c236a9e80c2cecd02fceb0c71328 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000930_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31922035 Before NNI: tree length is 0.31922038 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000933_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000933_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..508c3f97e3a47258be8ebef44197936f858da6b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000933_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16728525 Before NNI: tree length is 0.16728525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000934_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000934_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4b9caa17ad78cc734b93f0d80ca8a36958cda15b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000934_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025069 0.094518 0.194194 0.002009 +1 0.025069 0.000001 0.073919 0.173596 0.024263 +2 0.094518 0.073919 0.000001 0.179617 0.093712 +3 0.194194 0.173596 0.179617 0.000001 0.193388 +4 0.002009 0.024263 0.093712 0.193388 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e63ef64b00572dfeb29bbc5546c7f1c347f765c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.314485 0.489867 0.009434 +1 0.000001 0.000001 0.314485 0.489867 0.009434 +2 0.314485 0.314485 0.000001 0.622566 0.320631 +3 0.489867 0.489867 0.622566 0.000001 0.496012 +4 0.009434 0.009434 0.320631 0.496012 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e77b7fa2317f734c36828fb61e1d41fad5528c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000936_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72124927 Before NNI: tree length is 0.72124925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2788634557ac059a0e2e2209d27a28fdfcd5cb62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.055168 0.222316 0.000001 +1 0.000001 0.000001 0.055168 0.222316 0.000001 +2 0.055168 0.055168 0.000001 0.219036 0.055168 +3 0.222316 0.222316 0.219036 0.000001 0.222316 +4 0.000001 0.000001 0.055168 0.222316 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..968b419c462477f86adb8444a0339bda12f4b100 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000937_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24826100 Before NNI: tree length is 0.24826100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b923140c856932aa569af732bf7e7ff0ba5ad64f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.132203 0.315659 0.003445 +1 0.000001 0.000001 0.132203 0.315659 0.003445 +2 0.132203 0.132203 0.000001 0.336368 0.129825 +3 0.315659 0.315659 0.336368 0.000001 0.313281 +4 0.003445 0.003445 0.129825 0.313281 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9abafe06dbc2b79abd62a6b92671ad61c6494256 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000939_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39264900 Before NNI: tree length is 0.39264900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7add8034e9070c16153161827cfbc57089d984f2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29435150 Before NNI: tree length is 0.29435150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0033ac5af927e70dc3e6f737c62de73343476abc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.084243 0.134092 0.002067 +1 0.000001 0.000001 0.084243 0.134092 0.002067 +2 0.084243 0.084243 0.000001 0.124740 0.082200 +3 0.134092 0.134092 0.124740 0.000001 0.132049 +4 0.002067 0.002067 0.082200 0.132049 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58277c8ab42a1d04fd235bdcc72640a60f0a3aa4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.196704 0.655969 0.014331 +1 0.000001 0.000001 0.196704 0.655969 0.014331 +2 0.196704 0.196704 0.000001 0.634826 0.195418 +3 0.655969 0.655969 0.634826 0.000001 0.654683 +4 0.014331 0.014331 0.195418 0.654683 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3bbf6692cc41c05980acb5e4187a86c9bb757230 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.099090 0.345137 0.000001 +1 0.000001 0.000001 0.099090 0.345137 0.000001 +2 0.099090 0.099090 0.000001 0.378600 0.099090 +3 0.345137 0.345137 0.378600 0.000001 0.345137 +4 0.000001 0.000001 0.099090 0.345137 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000947_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000947_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..70c6716bf71e300a268419fecc09993c983a23f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000947_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002663 0.026038 0.054251 0.001987 +1 0.002663 0.000001 0.026793 0.055005 0.001550 +2 0.026038 0.026793 0.000001 0.056302 0.026117 +3 0.054251 0.055005 0.056302 0.000001 0.054329 +4 0.001987 0.001550 0.026117 0.054329 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..07f4f59bb3db73ea7a3413f75201e5bbc58c6242 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015499 0.006819 0.041968 0.015499 +1 0.015499 0.000001 0.019814 0.054963 0.000001 +2 0.006819 0.019814 0.000001 0.040455 0.019814 +3 0.041968 0.054963 0.040455 0.000001 0.054963 +4 0.015499 0.000001 0.019814 0.054963 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..211a7ae09f0d05957de5fe01f2d31ee64707b3d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000950_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05886850 Before NNI: tree length is 0.05886850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c3ac70d80ec85b899949383e748ace98c95b487 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003953 0.026761 0.080028 0.007408 +1 0.003953 0.000001 0.022831 0.076098 0.003478 +2 0.026761 0.022831 0.000001 0.081849 0.022595 +3 0.080028 0.076098 0.081849 0.000001 0.075862 +4 0.007408 0.003478 0.022595 0.075862 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..13cc442162cc22ae8de307ffee9d76da1677417b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000952_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09595150 Before NNI: tree length is 0.09595150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..33f7a1b4f0c0c9995c4f532bce76e4121a5d1196 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42775950 Before NNI: tree length is 0.42775950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000954_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000954_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf6b859889160b6965bae7e7828355706ab019f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000954_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.85119215 Before NNI: tree length is 0.85119213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9aa2a648a4466470acee3c7f792c1407a5083d3e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36791270 Before NNI: tree length is 0.36791275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..20db56854d480c573a6d8f9d220d9ec4c5d8f97e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.017291 0.020355 0.000001 +1 0.000001 0.000001 0.017291 0.020355 0.000001 +2 0.017291 0.017291 0.000001 0.020355 0.017291 +3 0.020355 0.020355 0.020355 0.000001 0.020355 +4 0.000001 0.000001 0.017291 0.020355 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ee8e042f1b186a3528ec8756b1a37c05b844c8f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001264 0.071989 0.174542 0.000001 +1 0.001264 0.000001 0.070961 0.173514 0.001264 +2 0.071989 0.070961 0.000001 0.162854 0.071989 +3 0.174542 0.173514 0.162854 0.000001 0.174542 +4 0.000001 0.001264 0.071989 0.174542 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..624952fcc0c9dcb2a79114067f6387fe67340642 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009924 0.094850 0.158320 0.004662 +1 0.009924 0.000001 0.094853 0.158323 0.011102 +2 0.094850 0.094853 0.000001 0.142240 0.096029 +3 0.158320 0.158323 0.142240 0.000001 0.159498 +4 0.004662 0.011102 0.096029 0.159498 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6f4e742f4eb26af335bb42fd58f85bf60397cd59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023590 0.248622 0.509065 0.023765 +1 0.023590 0.000001 0.255144 0.515587 0.030288 +2 0.248622 0.255144 0.000001 0.507845 0.237552 +3 0.509065 0.515587 0.507845 0.000001 0.497995 +4 0.023765 0.030288 0.237552 0.497995 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9969b73a4172d1b7ee208cdb7457b265cb999d0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30043869 Before NNI: tree length is 0.30043875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc03c5dc67320dcf7add943c1dcccde14d0336da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28535629 Before NNI: tree length is 0.28535625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..483c6c63bc491105ed0cd372b1a5df0b22e5d784 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21902031 Before NNI: tree length is 0.21902025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6cd1c8677ee940f23aa5001a27721aa8a01e497 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33194750 Before NNI: tree length is 0.33194750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a3627d5ed663d16ed7b89407902d9747adeeaf6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53361750 Before NNI: tree length is 0.53361750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ef1cea9f977ee51fa08769a4a4d729618af5415 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024268 0.105698 0.264457 0.001615 +1 0.024268 0.000001 0.108622 0.267381 0.025883 +2 0.105698 0.108622 0.000001 0.242938 0.107313 +3 0.264457 0.267381 0.242938 0.000001 0.266071 +4 0.001615 0.025883 0.107313 0.266071 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a89018548ea8a0c9b764dd3db5868d710b611be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71874500 Before NNI: tree length is 0.71874500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fb070c1b383f7f27d2ad8a1970a04786da5254fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009677 0.209658 0.584427 0.000001 +1 0.009677 0.000001 0.210064 0.584833 0.009677 +2 0.209658 0.210064 0.000001 0.507929 0.209658 +3 0.584427 0.584833 0.507929 0.000001 0.584427 +4 0.000001 0.009677 0.209658 0.584427 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e3b73bd3af5223af1811c0222dd638b1bf888c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.202790 1.390240 1.355212 0.238648 +1 0.202790 0.000001 1.413529 1.378501 0.203557 +2 1.390240 1.413529 0.000001 1.520597 1.449387 +3 1.355212 1.378501 1.520597 0.000001 1.414358 +4 0.238648 0.203557 1.449387 1.414358 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85541ce3f72e8ed6fa0b5769e7b7b276dbf777e8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08305275 Before NNI: tree length is 1.08305275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..93a4b431746a3b612534139c187a2c04c9bd5c03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011364 0.046869 0.151059 0.023656 +1 0.011364 0.000001 0.036303 0.140492 0.013090 +2 0.046869 0.036303 0.000001 0.166304 0.038901 +3 0.151059 0.140492 0.166304 0.000001 0.133536 +4 0.023656 0.013090 0.038901 0.133536 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..634cb29341794c25aff060c28a81eaebd6587c61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000998_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18558141 Before NNI: tree length is 0.18558137 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f5c090e306daa49d18b50ef7996c9507053cb69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004508 0.119331 0.166889 0.004508 +1 0.004508 0.000001 0.115045 0.162604 0.000001 +2 0.119331 0.115045 0.000001 0.151150 0.115045 +3 0.166889 0.162604 0.151150 0.000001 0.162604 +4 0.004508 0.000001 0.115045 0.162604 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1439ce1feb2e8bd4fb133e714507d50e92711a6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000999_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21879678 Before NNI: tree length is 0.21879675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001002_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001002_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a21576738866f4e8767af038bd3301f6ae215b4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001002_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13430950 Before NNI: tree length is 0.13430950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b4b4b69a3debec8b460ad831c4396469be7879a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26689603 Before NNI: tree length is 0.26689600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..0929e66d618904acabc7fd3c6ab4bd906562eb9a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028932 0.055813 0.208070 0.023746 +1 0.028932 0.000001 0.041971 0.194228 0.015180 +2 0.055813 0.041971 0.000001 0.188132 0.042062 +3 0.208070 0.194228 0.188132 0.000001 0.194319 +4 0.023746 0.015180 0.042062 0.194319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..22947efec68ae0699a0760cbcf9cfd1d0f41f46c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.038644 0.268384 0.333309 0.000001 +1 0.038644 0.000001 0.278537 0.343462 0.038644 +2 0.268384 0.278537 0.000001 0.475402 0.268384 +3 0.333309 0.343462 0.475402 0.000001 0.333309 +4 0.000001 0.038644 0.268384 0.333309 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..965b92318ce6d124e265dc0d18032bbb965266af --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81788050 Before NNI: tree length is 0.81788050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..745f4695056beade8c0d7a158a91fca42ecf65b9 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47022900 Before NNI: tree length is 0.47022900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..aa091f735fa8add1924d5cd7830f0462d5d66fa3 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008086 0.127888 0.324020 0.000001 +1 0.008086 0.000001 0.132006 0.328139 0.008086 +2 0.127888 0.132006 0.000001 0.308067 0.127888 +3 0.324020 0.328139 0.308067 0.000001 0.324020 +4 0.000001 0.008086 0.127888 0.324020 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..604d0f7a840cc07fbbfb584590ebcbeab7dcd9f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.078436 0.125266 0.000001 +1 0.000001 0.000001 0.078436 0.125266 0.000001 +2 0.078436 0.078436 0.000001 0.141601 0.078436 +3 0.125266 0.125266 0.141601 0.000001 0.125266 +4 0.000001 0.000001 0.078436 0.125266 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5be722bfc5332279a4185e1ceb1d16ee6511eddf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001016_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17265250 Before NNI: tree length is 0.17265250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f2a56d5c02c2428b07cb91482e91313f2350724 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.083686 0.251198 0.003617 +1 0.000001 0.000001 0.083686 0.251198 0.003617 +2 0.083686 0.083686 0.000001 0.266845 0.085545 +3 0.251198 0.251198 0.266845 0.000001 0.253057 +4 0.003617 0.003617 0.085545 0.253057 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eace9a3fb0a15752b87aebe0088ae79503a36c21 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011453 0.105329 0.210747 0.006431 +1 0.011453 0.000001 0.094739 0.200157 0.007871 +2 0.105329 0.094739 0.000001 0.198298 0.101747 +3 0.210747 0.200157 0.198298 0.000001 0.207165 +4 0.006431 0.007871 0.101747 0.207165 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..38a87a880967c372cfc9b88609b7956d7f80c2ff --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010511 0.103842 0.141693 0.010447 +1 0.010511 0.000001 0.110636 0.148488 0.013983 +2 0.103842 0.110636 0.000001 0.184333 0.110573 +3 0.141693 0.148488 0.184333 0.000001 0.148424 +4 0.010447 0.013983 0.110573 0.148424 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..961897d11c365f97304912da6fefe1c410ac689f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86954611 Before NNI: tree length is 0.86954613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..f35c8feb648f1b69381beb4215134f96c9380712 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028672 0.028672 0.136673 0.028672 +1 0.028672 0.000001 0.000001 0.141290 0.000001 +2 0.028672 0.000001 0.000001 0.141290 0.000001 +3 0.136673 0.141290 0.141290 0.000001 0.141290 +4 0.028672 0.000001 0.000001 0.141290 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21aa5487801986d476de2618edf93ba58c79923b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28017450 Before NNI: tree length is 0.28017450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d8be961e9cd26bef4069187fdd18c4d453c8453 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.058174 0.446082 0.663599 0.057764 +1 0.058174 0.000001 0.442269 0.659786 0.001316 +2 0.446082 0.442269 0.000001 0.659171 0.441859 +3 0.663599 0.659786 0.659171 0.000001 0.659376 +4 0.057764 0.001316 0.441859 0.659376 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ccd47c590247608fede199bbde49149e78cbd07d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001027_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91205950 Before NNI: tree length is 0.91205950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c437b91e7a8dbf379fa6c98882c0213c0e817a3 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.45140400 Before NNI: tree length is 1.45140400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001029_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001029_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7955203b68a47e0cad020b72fbb8b64cfb3df286 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001029_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010939 0.086260 0.422910 0.010939 +1 0.010939 0.000001 0.086650 0.423300 0.000001 +2 0.086260 0.086650 0.000001 0.462286 0.086650 +3 0.422910 0.423300 0.462286 0.000001 0.423300 +4 0.010939 0.000001 0.086650 0.423300 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af4b9e5dca17fd67e1d5bdaa873452f3968e054b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16585526 Before NNI: tree length is 0.16585525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..34d39dc1cfebb5113380db36a35ed6364e40d093 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026663 0.276492 0.304958 0.011610 +1 0.026663 0.000001 0.275510 0.303975 0.026731 +2 0.276492 0.275510 0.000001 0.312240 0.276561 +3 0.304958 0.303975 0.312240 0.000001 0.305026 +4 0.011610 0.026731 0.276561 0.305026 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8d545c204e95db0d7acff148c7a19029c7c19495 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003935 0.048665 0.147092 0.006609 +1 0.003935 0.000001 0.044730 0.143157 0.002674 +2 0.048665 0.044730 0.000001 0.153100 0.046542 +3 0.147092 0.143157 0.153100 0.000001 0.144969 +4 0.006609 0.002674 0.046542 0.144969 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..78ed8d411314bc3256a0a918e4139a6d59311ed1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001034_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17667150 Before NNI: tree length is 0.17667150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..29d4b61d306e99c8e7d0b28fc44134ff485f435d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41631464 Before NNI: tree length is 0.41631463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001036_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001036_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eefdea5c32c6312a8760e9870a1032150fe9ffba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001036_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040596 0.075846 0.531318 0.040596 +1 0.040596 0.000001 0.068373 0.523844 0.000001 +2 0.075846 0.068373 0.000001 0.508986 0.068373 +3 0.531318 0.523844 0.508986 0.000001 0.523844 +4 0.040596 0.000001 0.068373 0.523844 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..359e93c5ff6b123e84508e4032c3dc4b6674acf9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25181285 Before NNI: tree length is 0.25181287 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd3bbfd969efe17fde89243f7b6fd947567c7f2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039331 0.161750 0.347447 0.000001 +1 0.039331 0.000001 0.178423 0.364120 0.039331 +2 0.161750 0.178423 0.000001 0.268881 0.161750 +3 0.347447 0.364120 0.268881 0.000001 0.347447 +4 0.000001 0.039331 0.161750 0.347447 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001039_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001039_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..abfbd10c82b648aa636f11914865a7c9a70bd82e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001039_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006762 0.206330 0.375213 0.002718 +1 0.006762 0.000001 0.202073 0.370956 0.004142 +2 0.206330 0.202073 0.000001 0.336976 0.203709 +3 0.375213 0.370956 0.336976 0.000001 0.372593 +4 0.002718 0.004142 0.203709 0.372593 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..44f0316a46b510fb713e8f34c4f7eb64d68ac677 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000947 0.038706 0.078176 0.000001 +1 0.000947 0.000001 0.039178 0.078648 0.000947 +2 0.038706 0.039178 0.000001 0.081341 0.038706 +3 0.078176 0.078648 0.081341 0.000001 0.078176 +4 0.000001 0.000947 0.038706 0.078176 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f57654f5aa904757e92d4ee9ab2343230c4e72b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001040_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09982150 Before NNI: tree length is 0.09982150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc6c6a35efa652bbd5d0b48fc3cfcbbf53d48ffd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21614550 Before NNI: tree length is 0.21614550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0e8428b076b73f30f6ed8f08650e2d5a9a3e45a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23965450 Before NNI: tree length is 0.23965450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1c3e05a99a10d25237222adf9eed39481a665a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13760650 Before NNI: tree length is 0.13760650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cd7e1f7b4fe8093c2c239c8c421614de94374866 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.069959 0.109686 0.000001 +1 0.000001 0.000001 0.069959 0.109686 0.000001 +2 0.069959 0.069959 0.000001 0.071198 0.069959 +3 0.109686 0.109686 0.071198 0.000001 0.109686 +4 0.000001 0.000001 0.069959 0.109686 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a2d8a6630444afe4f48de747de24306face4ee43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005275 0.081575 0.154288 0.005275 +1 0.005275 0.000001 0.076972 0.149685 0.000001 +2 0.081575 0.076972 0.000001 0.152902 0.076972 +3 0.154288 0.149685 0.152902 0.000001 0.149685 +4 0.005275 0.000001 0.076972 0.149685 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc64cb09e98778ace087674b56353fe934a7a8e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026671 0.232223 0.489120 0.026671 +1 0.026671 0.000001 0.225682 0.482577 0.000001 +2 0.232223 0.225682 0.000001 0.478750 0.225682 +3 0.489120 0.482577 0.478750 0.000001 0.482577 +4 0.026671 0.000001 0.225682 0.482577 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac6499ce5ca16c5d7ffcf443ad70274a1a5fbd22 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13408276 Before NNI: tree length is 0.13408275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ef8bdb5d820f4882a998c752fb99f591bd35b57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48289300 Before NNI: tree length is 1.48289300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d595cb0b574b4957ad7d43d25d1f81d6a60122dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04957550 Before NNI: tree length is 1.04957550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ddf187d007bba6efe78bf141cfe3f32548b7fb0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007351 0.126590 0.185797 0.007351 +1 0.007351 0.000001 0.127201 0.186408 0.000001 +2 0.126590 0.127201 0.000001 0.194063 0.127201 +3 0.185797 0.186408 0.194063 0.000001 0.186408 +4 0.007351 0.000001 0.127201 0.186408 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e8e776e026382c1a6a8958d185a3331eae5378b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40377673 Before NNI: tree length is 0.40377675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001059_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001059_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eea0c92165e8014db2ef5f757aa5bf49647e07f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001059_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35088000 Before NNI: tree length is 0.35088000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b39519462c1200d518696667813391b0ebef17c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039172 0.236261 0.430625 0.024819 +1 0.039172 0.000001 0.234541 0.428905 0.015803 +2 0.236261 0.234541 0.000001 0.443435 0.220189 +3 0.430625 0.428905 0.443435 0.000001 0.414552 +4 0.024819 0.015803 0.220189 0.414552 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..33ee703b2cdcf3d3a954e9d4cd06f8e61780e6dc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012498 0.063661 0.139726 0.012498 +1 0.012498 0.000001 0.067014 0.143078 0.000001 +2 0.063661 0.067014 0.000001 0.136349 0.067014 +3 0.139726 0.143078 0.136349 0.000001 0.143078 +4 0.012498 0.000001 0.067014 0.143078 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..851ae0a1a483faa57a758ac686673cb67ed9baa4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026352 0.327878 0.594439 0.026352 +1 0.026352 0.000001 0.329897 0.596458 0.000001 +2 0.327878 0.329897 0.000001 0.605370 0.329897 +3 0.594439 0.596458 0.605370 0.000001 0.596458 +4 0.026352 0.000001 0.329897 0.596458 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1575a74b31551868f68163f5bc2d4035e2dfa76e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001064_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77802950 Before NNI: tree length is 0.77802950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..33bef0f8a707fcc307adf38be805f4fc464df7a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007752 0.142125 0.295527 0.007752 +1 0.007752 0.000001 0.141283 0.294686 0.000001 +2 0.142125 0.141283 0.000001 0.349047 0.141283 +3 0.295527 0.294686 0.349047 0.000001 0.294686 +4 0.007752 0.000001 0.141283 0.294686 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c528a83ab816d115393abc71b00b5f218f81c393 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001070_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39680529 Before NNI: tree length is 0.39680525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..afe9da8fe7a513e8831c3b5f28b4d1b06ac25157 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009354 0.145562 0.250189 0.010371 +1 0.009354 0.000001 0.146244 0.250871 0.001134 +2 0.145562 0.146244 0.000001 0.265803 0.147261 +3 0.250189 0.250871 0.265803 0.000001 0.251888 +4 0.010371 0.001134 0.147261 0.251888 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a716a602b9952f5b9c4136519500ec85b00e3e09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001072_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33687050 Before NNI: tree length is 0.33687050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..768c7d689748e75541fa21d3dcca6a53bc21fa61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018137 0.199373 0.338069 0.018137 +1 0.018137 0.000001 0.192831 0.331528 0.000001 +2 0.199373 0.192831 0.000001 0.328090 0.192831 +3 0.338069 0.331528 0.328090 0.000001 0.331528 +4 0.018137 0.000001 0.192831 0.331528 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cad80dc458905d10af7b562e2191a5d5c9e8adae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64395689 Before NNI: tree length is 0.64395687 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ff7993ef4f2262ccbfe3694a88236aebf13a8be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69432950 Before NNI: tree length is 0.69432950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8098d09f176b74b8bc52ca5fe436fa02328c2ca6 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.01676450 Before NNI: tree length is 1.01676450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b44361ec32707dfcd7a34110bad5b0a6946ff308 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57593969 Before NNI: tree length is 0.57593975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f0ef883de4a0e37bba6d9295053b6caa2cbd6a64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.164294 0.409891 0.000001 +1 0.000001 0.000001 0.164294 0.409891 0.000001 +2 0.164294 0.164294 0.000001 0.388696 0.164294 +3 0.409891 0.409891 0.388696 0.000001 0.409891 +4 0.000001 0.000001 0.164294 0.409891 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa6dfd07ceaf929be9f2d0a2f30cfd3e06770584 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001085_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48144150 Before NNI: tree length is 0.48144150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..254db71cfc5ffb1970b539d1c3b3b9a3a723deb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002215 0.134609 0.376559 0.002215 +1 0.002215 0.000001 0.135927 0.377876 0.000001 +2 0.134609 0.135927 0.000001 0.392893 0.135927 +3 0.376559 0.377876 0.392893 0.000001 0.377876 +4 0.002215 0.000001 0.135927 0.377876 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001088_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001088_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a7aa2b5753392fa44794b950b409e450934f9b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001088_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.191085 0.572980 0.000001 +1 0.000001 0.000001 0.191085 0.572980 0.000001 +2 0.191085 0.191085 0.000001 0.504137 0.191085 +3 0.572980 0.572980 0.504137 0.000001 0.572980 +4 0.000001 0.000001 0.191085 0.572980 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..44978f816cc4f1e779f58df5edf81ed054417fdd --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.88136250 Before NNI: tree length is 0.88136250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001090_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001090_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a248a87b21f847b848bcfee90389aae2bd88bab1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001090_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.182906 0.489119 0.000001 +1 0.000001 0.000001 0.182906 0.489119 0.000001 +2 0.182906 0.182906 0.000001 0.455640 0.182906 +3 0.489119 0.489119 0.455640 0.000001 0.489119 +4 0.000001 0.000001 0.182906 0.489119 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8bd57807f8ffff24999a8cfee485e9d7d471f00f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.260192 0.459215 0.000001 +1 0.000001 0.000001 0.260192 0.459215 0.000001 +2 0.260192 0.260192 0.000001 0.438657 0.260192 +3 0.459215 0.459215 0.438657 0.000001 0.459215 +4 0.000001 0.000001 0.260192 0.459215 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..36f4e11b6113fb115002aff7b67ee74b5e73f7e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001092_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57903300 Before NNI: tree length is 0.57903300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..65bf9d82cc949229dcf6a8a2921c8d42f3f92790 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012454 0.108567 0.263176 0.012454 +1 0.012454 0.000001 0.105502 0.260111 0.000001 +2 0.108567 0.105502 0.000001 0.232364 0.105502 +3 0.263176 0.260111 0.232364 0.000001 0.260111 +4 0.012454 0.000001 0.105502 0.260111 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32f67dc4e717dce38978b3f282a25cf5a0260295 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001094_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30674850 Before NNI: tree length is 0.30674850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..504d5811569efe63299b821dc7062cda3f2297c8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018102 0.111885 0.251572 0.018102 +1 0.018102 0.000001 0.102312 0.241998 0.000001 +2 0.111885 0.102312 0.000001 0.228522 0.102312 +3 0.251572 0.241998 0.228522 0.000001 0.241998 +4 0.018102 0.000001 0.102312 0.241998 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..827f955913b2efc1ffa5e88797e7465d6b9c0a62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.088841 0.014926 0.185232 0.088841 +1 0.088841 0.000001 0.088791 0.184246 0.000001 +2 0.014926 0.088791 0.000001 0.185183 0.088791 +3 0.185232 0.184246 0.185183 0.000001 0.184246 +4 0.088841 0.000001 0.088791 0.184246 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001099_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001099_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..14858891f5ed9e1d023ad7ebb422416c7c32c67d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001099_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.220528 0.000001 0.169882 0.220661 +1 0.220528 0.000001 0.220528 0.264305 0.006819 +2 0.000001 0.220528 0.000001 0.169882 0.220661 +3 0.169882 0.264305 0.169882 0.000001 0.264438 +4 0.220661 0.006819 0.220661 0.264438 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f658f1fa92391b2632e4fb480262525250deee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.165106 0.003912 0.103618 0.165106 +1 0.165106 0.000001 0.169017 0.168125 0.000001 +2 0.003912 0.169017 0.000001 0.107530 0.169017 +3 0.103618 0.168125 0.107530 0.000001 0.168125 +4 0.165106 0.000001 0.169017 0.168125 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8716c1499cf7acadb775d13732ff1985227854e6 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040621 0.107704 0.268650 0.035981 +1 0.040621 0.000001 0.130259 0.291205 0.012413 +2 0.107704 0.130259 0.000001 0.280720 0.125618 +3 0.268650 0.291205 0.280720 0.000001 0.286564 +4 0.035981 0.012413 0.125618 0.286564 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..341b5437d3644d090b88fa33b106c06f2b2a4920 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23643919 Before NNI: tree length is 0.23643925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ecd3436924f8ea3cc457c949d4715f15010853fd --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001184 0.068754 0.249119 0.012087 +1 0.001184 0.000001 0.067570 0.247935 0.013272 +2 0.068754 0.067570 0.000001 0.224024 0.080841 +3 0.249119 0.247935 0.224024 0.000001 0.261206 +4 0.012087 0.013272 0.080841 0.261206 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eaa386d0af4e4321e8f3afa98e5c3e0bd8265668 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36474312 Before NNI: tree length is 0.36474313 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..91121cbfdf660ec680097fcdd110966a17103985 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008811 0.000001 0.112132 0.007593 +1 0.008811 0.000001 0.008811 0.119018 0.014478 +2 0.000001 0.008811 0.000001 0.112132 0.007593 +3 0.112132 0.119018 0.112132 0.000001 0.115583 +4 0.007593 0.014478 0.007593 0.115583 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5041e597197c8bc11ab4779066816c5abd56b0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001112_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12550267 Before NNI: tree length is 0.12550275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a0faa9b93d35ab4ca0f97dbf4a82495e62442ebf --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013394 0.108238 0.996202 0.060193 +1 0.013394 0.000001 0.099934 0.987897 0.051889 +2 0.108238 0.099934 0.000001 1.003779 0.109620 +3 0.996202 0.987897 1.003779 0.000001 0.997584 +4 0.060193 0.051889 0.109620 0.997584 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b41df18df522f3aedc0366afffc48dc22fac39d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43784081 Before NNI: tree length is 0.43784075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8290c31edeb01662b3b0c931f7c6b50b790872a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11722419 Before NNI: tree length is 0.11722425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..55f9440cc7c5b72fa05169a7fd9ababacf3fdc8a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030713 0.107418 0.319833 0.020702 +1 0.030713 0.000001 0.109798 0.322212 0.014863 +2 0.107418 0.109798 0.000001 0.319430 0.099787 +3 0.319833 0.322212 0.319430 0.000001 0.312202 +4 0.020702 0.014863 0.099787 0.312202 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3df26c1dc1a17b269e592c240f80b01a6e266aa7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14026050 Before NNI: tree length is 0.14026050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..32edfef87a96207174d55669cd106eb12a5021fc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007353 0.139353 0.241955 0.010133 +1 0.007353 0.000001 0.138048 0.240650 0.002780 +2 0.139353 0.138048 0.000001 0.268392 0.140829 +3 0.241955 0.240650 0.268392 0.000001 0.243431 +4 0.010133 0.002780 0.140829 0.243431 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b259da288bdba0ba71e55505486f1fbb3361d6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060700 0.294792 0.527507 0.060700 +1 0.060700 0.000001 0.265977 0.498692 0.000001 +2 0.294792 0.265977 0.000001 0.484892 0.265977 +3 0.527507 0.498692 0.484892 0.000001 0.498692 +4 0.060700 0.000001 0.265977 0.498692 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..205031e7731307f924aee845643e3307a7a17702 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001122_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66953850 Before NNI: tree length is 0.66953850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..bb8cc43c95bf0f9f3f46f66ae67772ec40820b02 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005061 0.030089 0.087348 0.002310 +1 0.005061 0.000001 0.029694 0.086954 0.004824 +2 0.030089 0.029694 0.000001 0.088423 0.029852 +3 0.087348 0.086954 0.088423 0.000001 0.087111 +4 0.002310 0.004824 0.029852 0.087111 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1a2b024fd5f684f7589893a6c0594b85ea16c46b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009464 0.122384 0.141839 0.012867 +1 0.009464 0.000001 0.129104 0.148559 0.019588 +2 0.122384 0.129104 0.000001 0.208249 0.119713 +3 0.141839 0.148559 0.208249 0.000001 0.139169 +4 0.012867 0.019588 0.119713 0.139169 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eaec3307d1d76b715a6f986b642c962fff2a772a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001126_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24942649 Before NNI: tree length is 0.24942650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001127_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001127_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b40b38d51e8fb3d533db2dc47f038de71f69c0c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001127_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003367 0.169277 0.361739 0.015139 +1 0.003367 0.000001 0.167706 0.360168 0.013568 +2 0.169277 0.167706 0.000001 0.372469 0.170163 +3 0.361739 0.360168 0.372469 0.000001 0.362624 +4 0.015139 0.013568 0.170163 0.362624 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5ef1e465c62c76916e40aacc309f4a333a15aaf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.138630 0.535050 0.703932 0.022544 +1 0.138630 0.000001 0.497982 0.666864 0.124728 +2 0.535050 0.497982 0.000001 0.775102 0.521147 +3 0.703932 0.666864 0.775102 0.000001 0.690029 +4 0.022544 0.124728 0.521147 0.690029 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..35d28982fe879f948b53c1ea13075fddd912de63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001128_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.06214375 Before NNI: tree length is 1.06214375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f1eedb58bb3c61d3809241099158ab047587d7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017423 0.130724 0.350698 0.015989 +1 0.017423 0.000001 0.113301 0.333275 0.001433 +2 0.130724 0.113301 0.000001 0.305809 0.114734 +3 0.350698 0.333275 0.305809 0.000001 0.334709 +4 0.015989 0.001433 0.114734 0.334709 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8e885a5ee04ed27748c24409a2d42c6673083f43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001129_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39361515 Before NNI: tree length is 0.39361513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..216d05e84980cbcd7d89517c7b7fde1b4dfb5ffb --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030080 0.250183 0.406631 0.028024 +1 0.030080 0.000001 0.246182 0.402631 0.027893 +2 0.250183 0.246182 0.000001 0.365099 0.247996 +3 0.406631 0.402631 0.365099 0.000001 0.404445 +4 0.028024 0.027893 0.247996 0.404445 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd935ddcc54c9328967456c3a3c70e4c7ea756a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77689971 Before NNI: tree length is 0.77689975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b33ecc8721d8cccd9158eed5977c2c9719e1e29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17282523 Before NNI: tree length is 0.17282525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f540e190b5d5bb7e61aa3aa63708016a06b3a3c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043016 0.476559 0.863865 0.036513 +1 0.043016 0.000001 0.487110 0.874416 0.033226 +2 0.476559 0.487110 0.000001 0.907107 0.480607 +3 0.863865 0.874416 0.907107 0.000001 0.867913 +4 0.036513 0.033226 0.480607 0.867913 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..24d2c3a744b2dd6c62cb5c9be6b7463bdb4d254a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004900 0.121953 0.233084 0.011381 +1 0.004900 0.000001 0.118829 0.229960 0.008258 +2 0.121953 0.118829 0.000001 0.216766 0.117613 +3 0.233084 0.229960 0.216766 0.000001 0.228745 +4 0.011381 0.008258 0.117613 0.228745 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42be46bedfbc5effedb94c8cc7992a9c08a7906a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31699565 Before NNI: tree length is 0.31699563 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..259900f1d61fb236825b8b7f0b5e8a3585e0efa9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037044 0.206370 0.336079 0.010165 +1 0.037044 0.000001 0.213834 0.343543 0.034511 +2 0.206370 0.213834 0.000001 0.343076 0.203837 +3 0.336079 0.343543 0.343076 0.000001 0.333546 +4 0.010165 0.034511 0.203837 0.333546 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..45c420320de365fa8b6d3013601b68b349ba3518 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011281 0.070682 0.175357 0.000001 +1 0.011281 0.000001 0.065807 0.170482 0.011281 +2 0.070682 0.065807 0.000001 0.191136 0.070682 +3 0.175357 0.170482 0.191136 0.000001 0.175357 +4 0.000001 0.011281 0.070682 0.175357 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6090503ba1fe3270362105be3ec44b1ba4b7943a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001370 0.008315 0.105066 0.000001 +1 0.001370 0.000001 0.006946 0.103696 0.001370 +2 0.008315 0.006946 0.000001 0.096751 0.008315 +3 0.105066 0.103696 0.096751 0.000001 0.105066 +4 0.000001 0.001370 0.008315 0.105066 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbfc52f4e814c641966268fd0c124ee3ae0d0a84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.61376000 Before NNI: tree length is 0.61376000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b217008162e2d30a4eeafefa91dbe9c7b652921 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55064486 Before NNI: tree length is 0.55064487 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f732cab005e0ba1e740265e9572a877539fa5cfc --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35686978 Before NNI: tree length is 0.35686975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c685e694fb90562f0a1cc767321767e5ab3c4107 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033298 0.247432 0.621681 0.012244 +1 0.033298 0.000001 0.236908 0.611157 0.029863 +2 0.247432 0.236908 0.000001 0.663301 0.243997 +3 0.621681 0.611157 0.663301 0.000001 0.618246 +4 0.012244 0.029863 0.243997 0.618246 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..66c75485f7e4a4017b4df57df11e24ecfd7f382f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001149_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.78199850 Before NNI: tree length is 0.78199850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42b51b4d42303d9c26d677cdb26083053e434c09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002132 0.019847 0.120708 0.000001 +1 0.002132 0.000001 0.020089 0.120950 0.002132 +2 0.019847 0.020089 0.000001 0.126232 0.019847 +3 0.120708 0.120950 0.126232 0.000001 0.120708 +4 0.000001 0.002132 0.019847 0.120708 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de842039e1201b3ce4f2b9b510fe74d3f4527c4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042357 0.162001 0.318106 0.044374 +1 0.042357 0.000001 0.137333 0.293438 0.002067 +2 0.162001 0.137333 0.000001 0.265157 0.139350 +3 0.318106 0.293438 0.265157 0.000001 0.295455 +4 0.044374 0.002067 0.139350 0.295455 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001155_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001155_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a02059a53a65a0d963a963cc831902fa4fc3d17b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001155_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12534839 Before NNI: tree length is 0.12534837 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ffdaf4bd7a1ea07de2f784cc95469721eed4bada --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005719 0.054361 0.254120 0.019365 +1 0.005719 0.000001 0.060080 0.259839 0.025084 +2 0.054361 0.060080 0.000001 0.240125 0.050670 +3 0.254120 0.259839 0.240125 0.000001 0.250428 +4 0.019365 0.025084 0.050670 0.250428 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ff0c81cb4fa57696813ac3b258cc4c8959d21df5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016200 0.157945 0.510229 0.015024 +1 0.016200 0.000001 0.174145 0.526429 0.031225 +2 0.157945 0.174145 0.000001 0.520018 0.164217 +3 0.510229 0.526429 0.520018 0.000001 0.516501 +4 0.015024 0.031225 0.164217 0.516501 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4fe6ace4ebafa966a39e9d7943189d05d0dcae3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001157_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.62094425 Before NNI: tree length is 0.62094425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..51cb3f292a496e2e7bed0ef0bff1c252908d90d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029173 0.209154 0.552528 0.033441 +1 0.029173 0.000001 0.212831 0.556205 0.005331 +2 0.209154 0.212831 0.000001 0.582046 0.217099 +3 0.552528 0.556205 0.582046 0.000001 0.560473 +4 0.033441 0.005331 0.217099 0.560473 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a09b2bbe0762dd181a5766a8bf4457f372494a47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001158_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69308850 Before NNI: tree length is 0.69308850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..91dd54a8f590f717f32a6d9dabe718663e190dc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006456 0.036300 0.220188 0.000572 +1 0.006456 0.000001 0.042756 0.226644 0.005884 +2 0.036300 0.042756 0.000001 0.216829 0.036872 +3 0.220188 0.226644 0.216829 0.000001 0.220760 +4 0.000572 0.005884 0.036872 0.220760 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a42bbb74c9ac3f8a68c947c50ba21956d4f92de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006768 0.212353 0.116289 0.005348 +1 0.006768 0.000001 0.212098 0.116034 0.002518 +2 0.212353 0.212098 0.000001 0.298848 0.210678 +3 0.116289 0.116034 0.298848 0.000001 0.114613 +4 0.005348 0.002518 0.210678 0.114613 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001165_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001165_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1ce4d1646a478826a21b9c02dcaba61c39d52a4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001165_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14472200 Before NNI: tree length is 0.14472200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a137079d86976df009a0804ecb825b54091bef4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007404 0.056880 0.048647 0.015595 +1 0.007404 0.000001 0.056277 0.048044 0.014991 +2 0.056880 0.056277 0.000001 0.036000 0.041367 +3 0.048647 0.048044 0.036000 0.000001 0.033133 +4 0.015595 0.014991 0.041367 0.033133 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e40ff01f6346431dd7d75bf267e30a8018a7c48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001169_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07420448 Before NNI: tree length is 0.07420450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..20289234268b748f7408572395dcfdd3cd2f6f37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29769550 Before NNI: tree length is 0.29769550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7fb2ab039c29553206de1a5e6e9d4bdfb46412b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.080369 0.336397 0.534560 0.080369 +1 0.080369 0.000001 0.284157 0.482320 0.000001 +2 0.336397 0.284157 0.000001 0.488432 0.284157 +3 0.534560 0.482320 0.488432 0.000001 0.482320 +4 0.080369 0.000001 0.284157 0.482320 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b421d3dba6ef32c45c234c5bfd61f9fbda084326 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001177_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69375950 Before NNI: tree length is 0.69375950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..22641387a648cbbe461531deb0eda0f7dd939e76 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009711 0.108929 0.262348 0.010071 +1 0.009711 0.000001 0.111919 0.265337 0.006228 +2 0.108929 0.111919 0.000001 0.254823 0.112278 +3 0.262348 0.265337 0.254823 0.000001 0.265696 +4 0.010071 0.006228 0.112278 0.265696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6f302a6e9b64e976333ad01082375cd2f0eb0e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15607500 Before NNI: tree length is 0.15607500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001182_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001182_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f450ba1091f0452963c77c805e04e4ca9b990d9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001182_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.94045460 Before NNI: tree length is 0.94045462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9fb5f3ee1bc93818dd922c9cdfbc49cfc1fdaaaf --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006483 0.079784 0.160853 0.006483 +1 0.006483 0.000001 0.085215 0.166284 0.000001 +2 0.079784 0.085215 0.000001 0.163971 0.085215 +3 0.160853 0.166284 0.163971 0.000001 0.166284 +4 0.006483 0.000001 0.085215 0.166284 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..49c5f03479b8a6192dd9070ce4de12a4c2dc1d80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004304 0.173308 0.286289 0.010281 +1 0.004304 0.000001 0.171846 0.284826 0.008818 +2 0.173308 0.171846 0.000001 0.294372 0.171113 +3 0.286289 0.284826 0.294372 0.000001 0.284094 +4 0.010281 0.008818 0.171113 0.284094 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001186_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001186_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..80082b117bf281e1bcc3692cb1ccb623ab0046c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001186_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26164211 Before NNI: tree length is 0.26164213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d64827a5f504f09e1f77bb45869f595453d67ff0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011992 0.165764 0.268504 0.018135 +1 0.011992 0.000001 0.165107 0.267847 0.017479 +2 0.165764 0.165107 0.000001 0.227786 0.166089 +3 0.268504 0.267847 0.227786 0.000001 0.268830 +4 0.018135 0.017479 0.166089 0.268830 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d00207586ddfef224f28e77e631da5c5798d401b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001187_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34592496 Before NNI: tree length is 0.34592500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f00b613ae73d4f80b7f1537b6e778dd2d015831e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19524875 Before NNI: tree length is 0.19524875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..99c0b3cc4fea410d796efec6fa0d2a5d2eff2c0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41042889 Before NNI: tree length is 0.41042888 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ceda9f35b1721d1519444a527212e45e11f78710 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007180 0.149921 0.423880 0.007180 +1 0.007180 0.000001 0.144236 0.418195 0.000001 +2 0.149921 0.144236 0.000001 0.361630 0.144236 +3 0.423880 0.418195 0.361630 0.000001 0.418195 +4 0.007180 0.000001 0.144236 0.418195 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..59b08741fb96bab6db17b8511f1d16a55cae1921 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030054 0.282168 0.402152 0.035952 +1 0.030054 0.000001 0.261331 0.381316 0.020276 +2 0.282168 0.261331 0.000001 0.385759 0.272390 +3 0.402152 0.381316 0.385759 0.000001 0.392374 +4 0.035952 0.020276 0.272390 0.392374 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..411ffd5a8a74d3625d61b9de6db8a4c222e054ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086165 0.238684 0.347884 0.058608 +1 0.086165 0.000001 0.181187 0.290387 0.027557 +2 0.238684 0.181187 0.000001 0.281518 0.180077 +3 0.347884 0.290387 0.281518 0.000001 0.289277 +4 0.058608 0.027557 0.180077 0.289277 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..afd32d3d8498cb469c676899afcaca15a1e10ebb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.100384 0.346889 0.000001 +1 0.000001 0.000001 0.100384 0.346889 0.000001 +2 0.100384 0.100384 0.000001 0.356480 0.100384 +3 0.346889 0.346889 0.356480 0.000001 0.346889 +4 0.000001 0.000001 0.100384 0.346889 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..f331c6ac09925dd5f9854b499b2b1bfef579f8aa --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.632384 0.391741 0.489240 0.051853 +1 0.632384 0.000001 0.416477 0.462207 0.624825 +2 0.391741 0.416477 0.000001 0.273332 0.384182 +3 0.489240 0.462207 0.273332 0.000001 0.481680 +4 0.051853 0.624825 0.384182 0.481680 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1a3397dc8ed9fee76fb3ee3d6017ed07493aeddb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.020705 0.041847 0.000001 +1 0.000001 0.000001 0.020705 0.041847 0.000001 +2 0.020705 0.020705 0.000001 0.037583 0.020705 +3 0.041847 0.041847 0.037583 0.000001 0.041847 +4 0.000001 0.000001 0.020705 0.041847 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..df162acf5c7bb3e2a83a3790e071cd7ba0f2f6ab --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086707 0.081374 0.154806 0.000001 +1 0.086707 0.000001 0.065366 0.112613 0.086707 +2 0.081374 0.065366 0.000001 0.133465 0.081374 +3 0.154806 0.112613 0.133465 0.000001 0.154806 +4 0.000001 0.086707 0.081374 0.154806 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..b4401ac138ee1b27af17a45b626e4e4ab3d0917a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.011976 0.000001 +1 0.000001 0.000001 0.000001 0.011976 0.000001 +2 0.000001 0.000001 0.000001 0.011976 0.000001 +3 0.011976 0.011976 0.011976 0.000001 0.011976 +4 0.000001 0.000001 0.000001 0.011976 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a3ab4ae4a54bfd0cecf753f7223f4623f24b5f1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42412650 Before NNI: tree length is 0.42412650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..aeec69c344ff7d6e2b2837b1e3c8cff16d32b5a5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027437 0.416651 0.731154 0.007953 +1 0.027437 0.000001 0.407538 0.722041 0.020868 +2 0.416651 0.407538 0.000001 0.813433 0.410082 +3 0.731154 0.722041 0.813433 0.000001 0.724585 +4 0.007953 0.020868 0.410082 0.724585 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d1d78754c4a5dabbef0e484c6c13d7f9c469b74a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021535 0.376922 0.577546 0.018091 +1 0.021535 0.000001 0.376824 0.577448 0.038394 +2 0.376922 0.376824 0.000001 0.576914 0.393781 +3 0.577546 0.577448 0.576914 0.000001 0.594405 +4 0.018091 0.038394 0.393781 0.594405 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b30e3301d489a7bcce552fc27af28537153d6dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001214_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79388450 Before NNI: tree length is 0.79388450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a0c2535e024a374d0cd441bd2aff6ae042851fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.292187 0.294764 0.000001 +1 0.000001 0.000001 0.292187 0.294764 0.000001 +2 0.292187 0.292187 0.000001 0.354310 0.292187 +3 0.294764 0.294764 0.354310 0.000001 0.294764 +4 0.000001 0.000001 0.292187 0.294764 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e6311ef2996f56a950a03dc30dca411a07cbd18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81876600 Before NNI: tree length is 0.81876600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f648d059c4108d3b220f9edf6debb07a6163141 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008644 0.238057 0.406003 0.007013 +1 0.008644 0.000001 0.242756 0.410702 0.006601 +2 0.238057 0.242756 0.000001 0.408153 0.241124 +3 0.406003 0.410702 0.408153 0.000001 0.409070 +4 0.007013 0.006601 0.241124 0.409070 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..06c7c29452f9d3c578610f428330819dbc23f6ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001223_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53526275 Before NNI: tree length is 0.53526275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb31e5ea7ece5f549b4704dfd8697b462ace7e75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015100 0.255674 0.254465 0.000001 +1 0.015100 0.000001 0.254795 0.253585 0.015100 +2 0.255674 0.254795 0.000001 0.355143 0.255674 +3 0.254465 0.253585 0.355143 0.000001 0.254465 +4 0.000001 0.015100 0.255674 0.254465 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c28e87d6de1c1280ac8b6132f53b6260886548fc --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.68184400 Before NNI: tree length is 0.68184400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6dbf3ce53ed4a8f35a7e62f09b10b373a9e6b038 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.075462 0.296059 0.679057 0.062524 +1 0.075462 0.000001 0.302911 0.685910 0.018691 +2 0.296059 0.302911 0.000001 0.573412 0.289973 +3 0.679057 0.685910 0.573412 0.000001 0.672972 +4 0.062524 0.018691 0.289973 0.672972 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f87ac457ac19e1872f42bc6d3a94132bc79bf1b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001228_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81829781 Before NNI: tree length is 0.81829775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a0c99885a2c9aa8b242e760e3376dc84347b8847 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005952 0.202144 0.503049 0.007463 +1 0.005952 0.000001 0.199067 0.499972 0.005963 +2 0.202144 0.199067 0.000001 0.529362 0.202155 +3 0.503049 0.499972 0.529362 0.000001 0.503061 +4 0.007463 0.005963 0.202155 0.503061 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7534ca3d86475a2842cf979c71ec87004a3a34de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001232_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.62245215 Before NNI: tree length is 0.62245213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b47cd0f05e8cf7f52c8c7872826a3e2c0cc6354b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.00353927 Before NNI: tree length is 1.00353925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7672330b7451a59d8d7afbc87f277cf756217837 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.059712 0.159462 0.002905 +1 0.000001 0.000001 0.059712 0.159462 0.002905 +2 0.059712 0.059712 0.000001 0.178616 0.060388 +3 0.159462 0.159462 0.178616 0.000001 0.160138 +4 0.002905 0.002905 0.060388 0.160138 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2743ee8256dcba21b2f15d9ca3be1ee4a184648 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66147504 Before NNI: tree length is 0.66147500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cc89404fd42c8161a86077e849efeae95648a85 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.83493765 Before NNI: tree length is 0.83493762 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6f7baa2889390ff18babdad6800c9e2190f84d37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035269 0.049120 0.323203 0.028643 +1 0.035269 0.000001 0.047960 0.333881 0.020655 +2 0.049120 0.047960 0.000001 0.347732 0.041334 +3 0.323203 0.333881 0.347732 0.000001 0.327255 +4 0.028643 0.020655 0.041334 0.327255 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d1d159c680da6ef86fe8e9f56d6b6b613556d077 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003964 0.037542 1.079418 0.030857 +1 0.003964 0.000001 0.041402 1.083278 0.034718 +2 0.037542 0.041402 0.000001 1.072646 0.047402 +3 1.079418 1.083278 1.072646 0.000001 1.089278 +4 0.030857 0.034718 0.047402 1.089278 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28afd0d7f82f83ad2ea621de6cb53fd1ef0b9b48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001247_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.11907375 Before NNI: tree length is 1.11907375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..24d31315be6a6f7904d09c4e1668018426e2fd1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27582125 Before NNI: tree length is 0.27582125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8796c8ab8c152a3aebfc7d2450cdc19d66648c8f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42665225 Before NNI: tree length is 0.42665225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..58bc478481b55498cab7d723814cf8a8b536c57c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015685 0.278236 1.039023 0.043013 +1 0.015685 0.000001 0.277409 1.038196 0.031696 +2 0.278236 0.277409 0.000001 1.213022 0.304737 +3 1.039023 1.038196 1.213022 0.000001 1.065524 +4 0.043013 0.031696 0.304737 1.065524 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8ffa5691c10c3bfdb73eb6347fa9ecc446237fc0 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010645 0.101402 0.196253 0.019048 +1 0.010645 0.000001 0.095305 0.190156 0.012951 +2 0.101402 0.095305 0.000001 0.195181 0.093342 +3 0.196253 0.190156 0.195181 0.000001 0.188193 +4 0.019048 0.012951 0.093342 0.188193 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..89108b4a6160ef3d3345d3f2a132c5a2c73f17c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55909135 Before NNI: tree length is 0.55909138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..fb09ea4e66a2b1f65cb145aa3de3c9a17b9b332b --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016109 0.229891 0.216922 0.016109 +1 0.016109 0.000001 0.230652 0.217683 0.000001 +2 0.229891 0.230652 0.000001 0.228470 0.230652 +3 0.216922 0.217683 0.228470 0.000001 0.217683 +4 0.016109 0.000001 0.230652 0.217683 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..63f1ae96d8a2feef27fd0642ff248cd067ba5dc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.071903 0.203689 0.009712 +1 0.000001 0.000001 0.071903 0.203689 0.009712 +2 0.071903 0.071903 0.000001 0.188101 0.075916 +3 0.203689 0.203689 0.188101 0.000001 0.207702 +4 0.009712 0.009712 0.075916 0.207702 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c425a5509fc0f901f85d112d1d6004c3f56c07e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057507 0.630409 0.581695 0.065638 +1 0.057507 0.000001 0.687915 0.593524 0.077467 +2 0.630409 0.687915 0.000001 1.212104 0.696047 +3 0.581695 0.593524 1.212104 0.000001 0.572499 +4 0.065638 0.077467 0.696047 0.572499 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..298a10709e43e8770af09b8061394945f0546109 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001842 0.308638 1.100971 0.011051 +1 0.001842 0.000001 0.310480 1.102812 0.012893 +2 0.308638 0.310480 0.000001 1.113261 0.298823 +3 1.100971 1.102812 1.113261 0.000001 1.091155 +4 0.011051 0.012893 0.298823 1.091155 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f9401f2e9839f5eb76fb1ab792bfce1d31a55e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07046817 Before NNI: tree length is 0.07046813 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1afab4e78d6f49b14c286ef63cfd0d58bd693364 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039043 0.496833 0.701366 0.113744 +1 0.039043 0.000001 0.488855 0.693388 0.105766 +2 0.496833 0.488855 0.000001 0.609961 0.520676 +3 0.701366 0.693388 0.609961 0.000001 0.725209 +4 0.113744 0.105766 0.520676 0.725209 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b84c7e619a00ed3c31725331b596ec53a858ad6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001267_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.98840600 Before NNI: tree length is 0.98840600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f0195054bd96cb75347ceec239d86605fedb6992 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004669 0.082248 0.209908 0.001871 +1 0.004669 0.000001 0.084928 0.212588 0.005647 +2 0.082248 0.084928 0.000001 0.187106 0.083226 +3 0.209908 0.212588 0.187106 0.000001 0.210886 +4 0.001871 0.005647 0.083226 0.210886 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64e5b687042da542a8e54ab2d0b568e89cf8418d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15599118 Before NNI: tree length is 0.15599125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..100cb3a26e8c02e0d749e5b281eb9cf9f572daa0 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004721 0.166516 0.279687 0.000001 +1 0.004721 0.000001 0.171095 0.284266 0.004721 +2 0.166516 0.171095 0.000001 0.293235 0.166516 +3 0.279687 0.284266 0.293235 0.000001 0.279687 +4 0.000001 0.004721 0.166516 0.279687 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..62bf3eb2e71a2c75cb6dc995801cdb7e5fe56ae2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26369490 Before NNI: tree length is 0.26369487 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..47d84eb1aa76304dd7c931527354a96235282e9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003261 0.074747 0.047500 0.001939 +1 0.003261 0.000001 0.077029 0.049783 0.004222 +2 0.074747 0.077029 0.000001 0.091573 0.074195 +3 0.047500 0.049783 0.091573 0.000001 0.046948 +4 0.001939 0.004222 0.074195 0.046948 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a9166b359c16e38ce301a09017fb6e0bcbacd955 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001278_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11037536 Before NNI: tree length is 0.11037538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0ae0700207de962382b5e7db4224a26dea84371 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26518325 Before NNI: tree length is 0.26518325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42a2d3fdff72b6197c506f37830dd9adf77c67fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023098 0.257116 0.514784 0.004731 +1 0.023098 0.000001 0.261032 0.518700 0.021864 +2 0.257116 0.261032 0.000001 0.548111 0.255881 +3 0.514784 0.518700 0.548111 0.000001 0.513550 +4 0.004731 0.021864 0.255881 0.513550 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..66649f3d33591e509f11e9cbc683b476cc0540d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001284_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67526089 Before NNI: tree length is 0.67526088 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..c2b22589ec2776123490641cfb4bb8f12e8c2dda --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008503 0.092257 0.171445 0.007585 +1 0.008503 0.000001 0.092094 0.171281 0.014544 +2 0.092257 0.092094 0.000001 0.152885 0.098298 +3 0.171445 0.171281 0.152885 0.000001 0.177486 +4 0.007585 0.014544 0.098298 0.177486 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a70866745acdcba6e71aca2a516f89c845e16bf3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30122550 Before NNI: tree length is 0.30122550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..79da73d30b1dfab2d7cdc0bc1a40906d7198dbd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22867950 Before NNI: tree length is 0.22867950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbb587c3ddfeaa823b2bdec1dbf0f4adcec199e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005794 0.305647 0.412108 0.003216 +1 0.005794 0.000001 0.307445 0.413907 0.002578 +2 0.305647 0.307445 0.000001 0.708288 0.304867 +3 0.412108 0.413907 0.708288 0.000001 0.411328 +4 0.003216 0.002578 0.304867 0.411328 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3415a81eb38d1f3aba9f107c759d09b4aa2fbe2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001294_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71681763 Before NNI: tree length is 0.71681763 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001295_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001295_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2d56864c53d9cd79deecb63c0be13bdd7ad3fba9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001295_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029258 0.068775 0.464338 0.002670 +1 0.029258 0.000001 0.070631 0.466194 0.029258 +2 0.068775 0.070631 0.000001 0.457303 0.068775 +3 0.464338 0.466194 0.457303 0.000001 0.464338 +4 0.002670 0.029258 0.068775 0.464338 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4248e70e4d1a83c487a9271d21ff95d3085037a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.214615 0.251186 0.035955 +1 0.000001 0.000001 0.214615 0.251186 0.035955 +2 0.214615 0.214615 0.000001 0.239580 0.238189 +3 0.251186 0.251186 0.239580 0.000001 0.274760 +4 0.035955 0.035955 0.238189 0.274760 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b1278fa2cf75fbc1d1ba4822548d75a34211e79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001296_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38245550 Before NNI: tree length is 0.38245550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4642fd9bf1e1d993b7fa900e0c75ff50abc4973d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035981 0.392603 0.050899 0.044608 +1 0.035981 0.000001 0.397417 0.044787 0.038496 +2 0.392603 0.397417 0.000001 0.412335 0.406044 +3 0.050899 0.044787 0.412335 0.000001 0.048122 +4 0.044608 0.038496 0.406044 0.048122 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb05c4e85cfcee899a85dbec20be37c75b09f687 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001298_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46376850 Before NNI: tree length is 0.46376850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b49c9164a5af7f59d04465e5c5c1ff3456b337b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.103347 0.124877 0.012097 +1 0.000001 0.000001 0.103347 0.124877 0.012097 +2 0.103347 0.103347 0.000001 0.121811 0.106031 +3 0.124877 0.124877 0.121811 0.000001 0.127561 +4 0.012097 0.012097 0.106031 0.127561 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe6e5e8b3a8ef4b9a7d6d66a5eea594d0d9df018 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001299_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18240850 Before NNI: tree length is 0.18240850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..744bdfdeef562894e57108f98365684012421d94 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.03564883 Before NNI: tree length is 1.03564875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7c6859b3496a0f4175fadd2968f8a2b9152b7a2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02492550 Before NNI: tree length is 0.02492550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..439da77490fee6c1d58a841b7ede5f114aed5815 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10654469 Before NNI: tree length is 0.10654475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001306_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001306_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a44a0bfb10f9f5815fa6a394eaf7d55b6cc7723 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001306_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06236499 Before NNI: tree length is 0.06236500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..00fdc3746509f68f873f53628390285e917bfb75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 2.130813 2.113381 2.107245 2.125265 +1 2.130813 0.000001 0.033473 0.051491 0.031245 +2 2.113381 0.033473 0.000001 0.034060 0.027926 +3 2.107245 0.051491 0.034060 0.000001 0.045944 +4 2.125265 0.031245 0.027926 0.045944 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..63298bed2d53a30aeb5954f91b39c30d893f351e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.262825 0.226502 0.289553 0.005197 +1 0.262825 0.000001 0.276346 0.325576 0.268022 +2 0.226502 0.276346 0.000001 0.303075 0.231699 +3 0.289553 0.325576 0.303075 0.000001 0.294750 +4 0.005197 0.268022 0.231699 0.294750 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001310_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001310_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..614a6b7a955edff2b866e993961bbc09d1db59d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001310_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.078629 0.238648 0.129294 0.031313 +1 0.078629 0.000001 0.209488 0.100134 0.085241 +2 0.238648 0.209488 0.000001 0.197545 0.245259 +3 0.129294 0.100134 0.197545 0.000001 0.135906 +4 0.031313 0.085241 0.245259 0.135906 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..24fdba83cec73199c628c2c95325b5542bcde344 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016228 0.269358 0.418797 0.019616 +1 0.016228 0.000001 0.264497 0.413937 0.014755 +2 0.269358 0.264497 0.000001 0.466060 0.260290 +3 0.418797 0.413937 0.466060 0.000001 0.409729 +4 0.019616 0.014755 0.260290 0.409729 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..e82e1c9e77f04e1c01ef34da3bf932cc8147e207 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018222 0.062111 0.098498 0.017476 +1 0.018222 0.000001 0.065046 0.101432 0.014286 +2 0.062111 0.065046 0.000001 0.114430 0.064300 +3 0.098498 0.101432 0.114430 0.000001 0.100686 +4 0.017476 0.014286 0.064300 0.100686 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001315_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001315_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9398622913678c176342ca6d106f2d0719e06615 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001315_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04476150 Before NNI: tree length is 1.04476150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c0fc8427552a59f26835d704c447d26f99a85a1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44314250 Before NNI: tree length is 0.44314250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001318_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001318_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e2482616508ad940893836facef409925224add --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001318_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56323735 Before NNI: tree length is 0.56323738 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e08f94d9fcaecd8f767c11cab7c10e72a32dd9fe --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.52018100 Before NNI: tree length is 1.52018100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..01e33e87652bb70ccbb1d3db40d70e9acd87ede5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.073257 0.476464 1.227513 0.060655 +1 0.073257 0.000001 0.521200 1.272249 0.105392 +2 0.476464 0.521200 0.000001 1.232908 0.466878 +3 1.227513 1.272249 1.232908 0.000001 1.217927 +4 0.060655 0.105392 0.466878 1.217927 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f6e41903d84f35726229ae17497ada990e018a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001323_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.55297375 Before NNI: tree length is 1.55297375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..6ddcb8b84d0b77837dd1b7daa76c9e965e5433c9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.093068 0.648132 1.709557 0.029506 +1 0.093068 0.000001 0.584383 1.645809 0.073421 +2 0.648132 0.584383 0.000001 2.007263 0.628485 +3 1.709557 1.645809 2.007263 0.000001 1.689911 +4 0.029506 0.073421 0.628485 1.689911 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..72eef442d65e80dd288b760771de90f191e752e7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028995 0.083686 0.280036 0.013921 +1 0.028995 0.000001 0.085948 0.282298 0.026086 +2 0.083686 0.085948 0.000001 0.294263 0.080776 +3 0.280036 0.282298 0.294263 0.000001 0.277126 +4 0.013921 0.026086 0.080776 0.277126 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001326_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001326_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b16d857a3f77f36d479af600dd3db86d0741103 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001326_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.68104131 Before NNI: tree length is 0.68104125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7752b87c948eb2b2951fbbb37d4f1135116634cf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39778365 Before NNI: tree length is 0.39778362 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3b2df024babf9243631d5620b128b6decb1ff833 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009137 0.025570 0.090875 0.014473 +1 0.009137 0.000001 0.029862 0.095166 0.011795 +2 0.025570 0.029862 0.000001 0.091510 0.035197 +3 0.090875 0.095166 0.091510 0.000001 0.100501 +4 0.014473 0.011795 0.035197 0.100501 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1cde8b90de88e12b710051562ec643a7944464d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001330_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11925694 Before NNI: tree length is 0.11925700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1ce25869a7b0ed4d379ff7bc6e2664dbfae3a3fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040648 0.227772 0.367782 0.033699 +1 0.040648 0.000001 0.207999 0.348009 0.008683 +2 0.227772 0.207999 0.000001 0.315888 0.201050 +3 0.367782 0.348009 0.315888 0.000001 0.341060 +4 0.033699 0.008683 0.201050 0.341060 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0500cdae52828a76bc535d0b78be7a918411268 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001331_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46702550 Before NNI: tree length is 0.46702550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f897ca9d8d28210083d8ee08c7e499e10a0acee8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51853403 Before NNI: tree length is 0.51853400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001333_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001333_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9bd2de257d9275b44e831fbadf7f8d9b36479e81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001333_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14028206 Before NNI: tree length is 0.14028200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..363f8cb42bc4d80ff03581f9337b434fb4a21e0e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010569 0.118453 0.178731 0.009523 +1 0.010569 0.000001 0.116123 0.176400 0.002857 +2 0.118453 0.116123 0.000001 0.178922 0.115077 +3 0.178731 0.176400 0.178922 0.000001 0.175354 +4 0.009523 0.002857 0.115077 0.175354 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d3458a9ba3b24eada4feeea354ddabe1add6a0cd --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013062 0.154287 0.016778 0.019129 +1 0.013062 0.000001 0.149907 0.012399 0.014749 +2 0.154287 0.149907 0.000001 0.146298 0.144553 +3 0.016778 0.012399 0.146298 0.000001 0.011140 +4 0.019129 0.014749 0.144553 0.011140 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..22774d56a9229a159c498486dab0646cef8176a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027583 0.566421 0.609263 0.039096 +1 0.027583 0.000001 0.557128 0.599971 0.029803 +2 0.566421 0.557128 0.000001 1.039561 0.561454 +3 0.609263 0.599971 1.039561 0.000001 0.604296 +4 0.039096 0.029803 0.561454 0.604296 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ae34081510d91c9f0047252334f503bb2cd8f97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001341_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.13383213 Before NNI: tree length is 1.13383213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ab50f73a79b4637aeb6baba141e3b8ed858377f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40330850 Before NNI: tree length is 0.40330850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9861229ef66cfd1b4bb5be726c4f5be88b8c53bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018556 0.171500 0.164495 0.014079 +1 0.018556 0.000001 0.168612 0.161607 0.018589 +2 0.171500 0.168612 0.000001 0.203606 0.171533 +3 0.164495 0.161607 0.203606 0.000001 0.164528 +4 0.014079 0.018589 0.171533 0.164528 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7a659b6666f66439ad0212d24fd2c24336f230a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001346_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28469050 Before NNI: tree length is 0.28469050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4c8c746553f2d69475dcb18a4c30b9a60a535c0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14506075 Before NNI: tree length is 0.14506075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001348_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001348_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..91e6f83ca7ae3b3643a57c732301910c90c438c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001348_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045577 0.130737 0.350812 0.043740 +1 0.045577 0.000001 0.127981 0.356922 0.062626 +2 0.130737 0.127981 0.000001 0.442082 0.147786 +3 0.350812 0.356922 0.442082 0.000001 0.367861 +4 0.043740 0.062626 0.147786 0.367861 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..7fb4dfc99ddfed2eeec8dfddc598142bac3640a9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012903 0.071422 0.265420 0.013000 +1 0.012903 0.000001 0.078128 0.272126 0.019706 +2 0.071422 0.078128 0.000001 0.249609 0.070450 +3 0.265420 0.272126 0.249609 0.000001 0.264448 +4 0.013000 0.019706 0.070450 0.264448 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..076e6a467251260304af95fb1ebfd7999d2bc428 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47715600 Before NNI: tree length is 0.47715600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001355_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001355_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eb45aa1186eae445d1627962f187c5e5be7b809e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001355_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.068898 0.131239 0.007792 +1 0.000001 0.000001 0.068898 0.131239 0.007792 +2 0.068898 0.068898 0.000001 0.147487 0.067280 +3 0.131239 0.131239 0.147487 0.000001 0.129621 +4 0.007792 0.007792 0.067280 0.129621 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e8a412c50933cca5f9812bff013e89c3f9154882 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.391098 1.066906 0.000001 +1 0.000001 0.000001 0.391098 1.066906 0.000001 +2 0.391098 0.391098 0.000001 0.976010 0.391098 +3 1.066906 1.066906 0.976010 0.000001 1.066906 +4 0.000001 0.000001 0.391098 1.066906 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..52127a80d179d50336a9b6e7679fa14cb348ec3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001359_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.21700800 Before NNI: tree length is 1.21700800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001360_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001360_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..49c5681a5cc7ff20847aa3a37e1ddda29e88c14a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001360_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15039300 Before NNI: tree length is 0.15039300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b881ec186993b6f502494ef9458fd4f63495780 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.236874 0.868575 0.273900 0.242237 +1 0.236874 0.000001 0.733037 0.416506 0.164385 +2 0.868575 0.733037 0.000001 1.048207 0.796086 +3 0.273900 0.416506 1.048207 0.000001 0.421869 +4 0.242237 0.164385 0.796086 0.421869 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8e386ac18131f5bf511d26642325edd4089b2f79 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06930375 Before NNI: tree length is 0.06930375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef990ee46a7af7db0177ec55a35b2238f029c6cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.020858 0.056319 0.000001 +1 0.000001 0.000001 0.020858 0.056319 0.000001 +2 0.020858 0.020858 0.000001 0.035460 0.020858 +3 0.056319 0.056319 0.035460 0.000001 0.056319 +4 0.000001 0.000001 0.020858 0.056319 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..883fe9bf37b1fa75e706cbae5d80aad5ea9db777 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001367_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05631950 Before NNI: tree length is 0.05631950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..56ece2417a61f684af07c7804a94e75bba019faa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.039191 0.000001 +1 0.000001 0.000001 0.000001 0.039191 0.000001 +2 0.000001 0.000001 0.000001 0.039191 0.000001 +3 0.039191 0.039191 0.039191 0.000001 0.039191 +4 0.000001 0.000001 0.000001 0.039191 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b42278af07ff7f021848cef391536c3bc3147f1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011281 0.086287 0.170185 0.018877 +1 0.011281 0.000001 0.089499 0.173397 0.007596 +2 0.086287 0.089499 0.000001 0.141786 0.097095 +3 0.170185 0.173397 0.141786 0.000001 0.180993 +4 0.018877 0.007596 0.097095 0.180993 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b9bf9404411b99deb929eff64fbe2cecab55cc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001371_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21397150 Before NNI: tree length is 0.21397150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001372_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001372_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..912464f6f93d9825c58d4ed9cd17dc4209172573 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001372_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014079 0.057059 0.146922 0.014075 +1 0.014079 0.000001 0.069813 0.159675 0.007663 +2 0.057059 0.069813 0.000001 0.139887 0.069809 +3 0.146922 0.159675 0.139887 0.000001 0.159672 +4 0.014075 0.007663 0.069809 0.159672 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31c98e2758a857056246cc084bd11306ee3d5c51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14343700 Before NNI: tree length is 0.14343700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f927cab74ff4ae0ec0da9e8fedcab33de7d82197 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09408150 Before NNI: tree length is 0.09408150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001376_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001376_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..29c29b96c19f9ac6b80359e6f792bf7836f1f8ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001376_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14641950 Before NNI: tree length is 0.14641950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2fc28d5610c5267e0dd69d5530e3079154654558 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07363000 Before NNI: tree length is 0.07363000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..11fd7a1a783fefd4672800d9677791ab58dbfabf --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.016902 0.156476 0.000001 +1 0.000001 0.000001 0.016902 0.156476 0.000001 +2 0.016902 0.016902 0.000001 0.143531 0.016902 +3 0.156476 0.156476 0.143531 0.000001 0.156476 +4 0.000001 0.000001 0.016902 0.156476 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a8253e5be5521c6cf9f9dd23d22cd1d658ddf4b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00522350 Before NNI: tree length is 0.00522350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999997 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2e09fe78eca982310e3698769d02f54dac753fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01271750 Before NNI: tree length is 0.01271750 + 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/OG0001390_tree_id.txt.dist.phylip 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 new file mode 100644 index 0000000000000000000000000000000000000000..6a273dc1b7fe07be8d6170699ab84da731fa3b15 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.079356 0.000001 +1 0.000001 0.000001 0.000001 0.079356 0.000001 +2 0.000001 0.000001 0.000001 0.079356 0.000001 +3 0.079356 0.079356 0.079356 0.000001 0.079356 +4 0.000001 0.000001 0.000001 0.079356 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf513bc0a6e328e49462c9a801d3dab90a0c2b02 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.007685 0.038417 0.000001 +1 0.000001 0.000001 0.007685 0.038417 0.000001 +2 0.007685 0.007685 0.000001 0.030732 0.007685 +3 0.038417 0.038417 0.030732 0.000001 0.038417 +4 0.000001 0.000001 0.007685 0.038417 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..51bcf2891609718cda9a9fcaecfe083bb539e50e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05500977 Before NNI: tree length is 0.05500975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4e48405c0dd5a2d1e7c76a5b2a1050d94c82652f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.000001 0.000001 +1 0.000001 0.000001 0.000001 0.000001 0.000001 +2 0.000001 0.000001 0.000001 0.000001 0.000001 +3 0.000001 0.000001 0.000001 0.000001 0.000001 +4 0.000001 0.000001 0.000001 0.000001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..599985b3e3ea3a1afb38757b1a759122baffb83f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001393_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00000250 Before NNI: tree length is 0.00000250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : -4460149039706124200828622340096.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58972e01553a048edd2b97d351be489698ceae0f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55988150 Before NNI: tree length is 0.55988150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..41f63eba4f52040f5daa7ae947c920695cde7011 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.050555 0.339309 0.700704 0.000001 +1 0.050555 0.000001 0.288755 0.650149 0.050555 +2 0.339309 0.288755 0.000001 0.573838 0.339309 +3 0.700704 0.650149 0.573838 0.000001 0.700704 +4 0.000001 0.050555 0.339309 0.700704 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001397_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001397_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18a1b74efb1a6d808cda27bf0bf0378d0a4d8177 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001397_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07368100 Before NNI: tree length is 0.07368100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..44021c2883535a307ddda7317b8f5ec66da780fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00654800 Before NNI: tree length is 0.00654800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999997 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75a3f98652ebe71d61f29ce62b07548f0421f0ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04947750 Before NNI: tree length is 0.04947750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0633df2b23d55ca965acf9727da4ab81776ca47a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002609 0.036907 0.114035 0.001305 +1 0.002609 0.000001 0.034297 0.111426 0.001305 +2 0.036907 0.034297 0.000001 0.087278 0.035602 +3 0.114035 0.111426 0.087278 0.000001 0.112731 +4 0.001305 0.001305 0.035602 0.112731 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa0f247d1ce8a71780beab7d5cc1193e20a89b6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001402_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11911009 Before NNI: tree length is 0.11911013 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7ab70873aa1fc3a6d793cdb86841acd0b68535a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42549136 Before NNI: tree length is 0.42549138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001407_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001407_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41bf7e8ad3f731bcc98890469f25af66d7bbffb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001407_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38167500 Before NNI: tree length is 0.38167500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1768501ad65ae6a61dea5aabfcc69b820c8d3526 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005864 0.125258 0.145192 0.017148 +1 0.005864 0.000001 0.120516 0.140449 0.012406 +2 0.125258 0.120516 0.000001 0.176009 0.118562 +3 0.145192 0.140449 0.176009 0.000001 0.138496 +4 0.017148 0.012406 0.118562 0.138496 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..24e06109641e086be0d0e9df5de1a9b0c6766b40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001408_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22901637 Before NNI: tree length is 0.22901637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..403673b5f4dadad00782b7b012657216127ff9c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039515 0.266093 0.341191 0.024464 +1 0.039515 0.000001 0.257321 0.332418 0.043519 +2 0.266093 0.257321 0.000001 0.352648 0.270097 +3 0.341191 0.332418 0.352648 0.000001 0.345195 +4 0.024464 0.043519 0.270097 0.345195 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..5e6e91aa13c886224ef398ae07033945e7acd6ac --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022148 0.485918 0.700612 0.006737 +1 0.022148 0.000001 0.489451 0.704145 0.015797 +2 0.485918 0.489451 0.000001 0.649291 0.479566 +3 0.700612 0.704145 0.649291 0.000001 0.694260 +4 0.006737 0.015797 0.479566 0.694260 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..cb24ec3eadfa501637c8d02b89a1ab82ca094932 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003877 0.059436 0.075574 0.002926 +1 0.003877 0.000001 0.056542 0.072680 0.005632 +2 0.059436 0.056542 0.000001 0.078472 0.061191 +3 0.075574 0.072680 0.078472 0.000001 0.077329 +4 0.002926 0.005632 0.061191 0.077329 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c24b91b9b72c959b01d65044c2f4a9bd5cc10405 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.39545710 Before NNI: tree length is 1.39545712 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc2210f58f18a903df4478747c509d790c7510e2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27724400 Before NNI: tree length is 0.27724400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a2254df3c50dbc3f96ff40c7664de3dff8ecb04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57169975 Before NNI: tree length is 0.57169975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b79857c9d78aca21fcdb1b5718368efa2dc77e03 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56567350 Before NNI: tree length is 0.56567350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d507b90022ff6a328d75cadac54f6393c8021755 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.142146 0.287688 0.000001 +1 0.000001 0.000001 0.142146 0.287688 0.000001 +2 0.142146 0.142146 0.000001 0.262359 0.142146 +3 0.287688 0.287688 0.262359 0.000001 0.287688 +4 0.000001 0.000001 0.142146 0.287688 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e49eb480e7a0c7d7786290aaf03d26eb4c3b8074 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11258500 Before NNI: tree length is 0.11258500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8806d1098e2139fc334bd22f13d6ca6a06afda1c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47342050 Before NNI: tree length is 0.47342050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d50a43ed805968bfc751496ea5f8b8e274bf3e73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.429316 0.545296 0.000001 +1 0.000001 0.000001 0.429316 0.545296 0.000001 +2 0.429316 0.429316 0.000001 0.561845 0.429316 +3 0.545296 0.545296 0.561845 0.000001 0.545296 +4 0.000001 0.000001 0.429316 0.545296 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8d33d4337153ca0b29b0157ec08a5b040ad6112 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001428_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76822950 Before NNI: tree length is 0.76822950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001429_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001429_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18e666dcadf94ace5183a008da2741342e722ae9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001429_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38063500 Before NNI: tree length is 0.38063500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..16f5595ebf0f9bbda495e196fd582b58f109f052 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59970500 Before NNI: tree length is 0.59970500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69939ed2d241cbaa24fa92f3ca8bab3196609cbb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014570 0.116336 0.121744 0.033583 +1 0.014570 0.000001 0.101766 0.107174 0.019013 +2 0.116336 0.101766 0.000001 0.117747 0.102614 +3 0.121744 0.107174 0.117747 0.000001 0.108022 +4 0.033583 0.019013 0.102614 0.108022 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001442_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001442_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..92f43065f1507d645767a9ea49cbdbcb930f479a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001442_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004461 0.163339 0.218184 0.012660 +1 0.004461 0.000001 0.165930 0.220775 0.015251 +2 0.163339 0.165930 0.000001 0.287423 0.160123 +3 0.218184 0.220775 0.287423 0.000001 0.214968 +4 0.012660 0.015251 0.160123 0.214968 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001443_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001443_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..30ce1535fc9027109772a3b1291da7717786d73b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001443_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27880735 Before NNI: tree length is 0.27880737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..1e5e91ec9dc67a54dcd9448743a3987ebe711c0c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006762 0.158959 0.205155 0.020361 +1 0.006762 0.000001 0.157797 0.203994 0.019199 +2 0.158959 0.157797 0.000001 0.192118 0.162851 +3 0.205155 0.203994 0.192118 0.000001 0.209048 +4 0.020361 0.019199 0.162851 0.209048 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f91ad266f71662641b4ceb9944176efab46da51d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08859575 Before NNI: tree length is 0.08859575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b669c4440229e929743523b898945b3949d1914 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17066021 Before NNI: tree length is 0.17066025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d38e07a21909f88ce5b014e5d38e7756b09e40a8 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026116 0.020610 0.017395 0.018023 +1 0.026116 0.000001 0.015339 0.022430 0.023058 +2 0.020610 0.015339 0.000001 0.016923 0.017552 +3 0.017395 0.022430 0.016923 0.000001 0.011591 +4 0.018023 0.023058 0.017552 0.011591 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf048c5bf09739209fb2fe2e10fc98739e7fedb6 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10995911 Before NNI: tree length is 0.10995912 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f15b6b86c39e1e2caca2c0d5c12d2b8c2d93f32 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.386749 0.379816 0.387289 0.094113 +1 0.386749 0.000001 0.006933 0.460753 0.357469 +2 0.379816 0.006933 0.000001 0.453821 0.350537 +3 0.387289 0.460753 0.453821 0.000001 0.358009 +4 0.094113 0.357469 0.350537 0.358009 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71addab8982de70ba56c0b0dd0d4091e050b0e29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.352634 0.366980 0.692040 0.054551 +1 0.352634 0.000001 0.029950 0.610602 0.387353 +2 0.366980 0.029950 0.000001 0.624949 0.401699 +3 0.692040 0.610602 0.624949 0.000001 0.726760 +4 0.054551 0.387353 0.401699 0.726760 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..708ca8d536c85b07bfeb3bad8170dd3ee94270c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37368789 Before NNI: tree length is 0.37368788 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001461_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001461_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c54b18269a56bcd9130d80dc4082c8e99d6c7f00 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001461_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04660750 Before NNI: tree length is 0.04660750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2fdf6efd47c98f895c70d617e26471e1facb4f4b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29713500 Before NNI: tree length is 0.29713500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b89279e9e606cf01c181a651ac2fa40b4b2660b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008798 0.043424 0.099068 0.005657 +1 0.008798 0.000001 0.052221 0.107866 0.014455 +2 0.043424 0.052221 0.000001 0.098715 0.042787 +3 0.099068 0.107866 0.098715 0.000001 0.098432 +4 0.005657 0.014455 0.042787 0.098432 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a86e45e477bd9795a15698c2b896dcc796e305d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001464_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13191161 Before NNI: tree length is 0.13191162 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..00d47c9d1910cf4f76e5a2710bb2080127cc22de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029785 0.518319 0.537779 0.015459 +1 0.029785 0.000001 0.518207 0.537667 0.015347 +2 0.518319 0.518207 0.000001 0.434005 0.502860 +3 0.537779 0.537667 0.434005 0.000001 0.522320 +4 0.015459 0.015347 0.502860 0.522320 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..40dbb9097918ef636c31217d8962becb3ad822bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048114 0.150444 0.303766 0.005806 +1 0.048114 0.000001 0.170084 0.323407 0.044735 +2 0.150444 0.170084 0.000001 0.286733 0.147064 +3 0.303766 0.323407 0.286733 0.000001 0.300387 +4 0.005806 0.044735 0.147064 0.300387 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001467_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001467_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd0742081c7dd01b297593f6b754501e638f17f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001467_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23838865 Before NNI: tree length is 0.23838863 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92841316534532f560e180e270752690b95d1d54 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36773480 Before NNI: tree length is 0.36773475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7600d2873982518adc06fc9886422f6d7112b2cb --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.78747650 Before NNI: tree length is 0.78747650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001476_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001476_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb73c8ba2f28b053bdbce92bd182ff4224d784e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001476_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.092792 0.369298 0.695186 0.018864 +1 0.092792 0.000001 0.410572 0.736460 0.094860 +2 0.369298 0.410572 0.000001 0.811607 0.371366 +3 0.695186 0.736460 0.811607 0.000001 0.697254 +4 0.018864 0.094860 0.371366 0.697254 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..879fa92846f5579c8efc67e24538bb6501a66bf7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73957225 Before NNI: tree length is 0.73957225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..50599e7b63af43a6ffd5043d6bab148f57bfb948 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032544 0.306737 0.466495 0.033246 +1 0.032544 0.000001 0.312091 0.471849 0.038599 +2 0.306737 0.312091 0.000001 0.446256 0.298998 +3 0.466495 0.471849 0.446256 0.000001 0.458755 +4 0.033246 0.038599 0.298998 0.458755 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdae8ea235f01e4111aec780b2d1a57a5a972bef --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.50858700 Before NNI: tree length is 1.50858700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..157b0cfd02c8a464d02e05b7e1f1035082e00305 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.87958400 Before NNI: tree length is 0.87958400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5381b25e40121b76ec377b2bcdb628ebdb1996c4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29980440 Before NNI: tree length is 0.29980438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a4227d350c11b1cdb4aef7436c19f038b2ba7a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.007134 0.067872 0.000001 +1 0.000001 0.000001 0.007134 0.067872 0.000001 +2 0.007134 0.007134 0.000001 0.069011 0.007134 +3 0.067872 0.067872 0.069011 0.000001 0.067872 +4 0.000001 0.000001 0.007134 0.067872 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..52fe75068dd5f63987faca70b2a0a3f50b1d9384 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028359 0.080619 0.195931 0.028359 +1 0.028359 0.000001 0.093844 0.209155 0.000001 +2 0.080619 0.093844 0.000001 0.197323 0.093844 +3 0.195931 0.209155 0.197323 0.000001 0.209155 +4 0.028359 0.000001 0.093844 0.209155 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..96991bb4ba9c10caba9e7d038aed2bc245f35229 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.082818 0.078643 0.000001 +1 0.000001 0.000001 0.082818 0.078643 0.000001 +2 0.082818 0.082818 0.000001 0.134092 0.082818 +3 0.078643 0.078643 0.134092 0.000001 0.078643 +4 0.000001 0.000001 0.082818 0.078643 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f8088ae1ff58015fafaef0dd8081df5e5bdbabca --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41000950 Before NNI: tree length is 0.41000950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..c106aa59cabed4f98478afab5603ccb7f1d9b5c5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.199872 0.405956 0.039542 +1 0.000001 0.000001 0.199872 0.405956 0.039542 +2 0.199872 0.199872 0.000001 0.454354 0.209623 +3 0.405956 0.405956 0.454354 0.000001 0.415708 +4 0.039542 0.039542 0.209623 0.415708 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..b946febded2f7db41c27ec00fa06e24f7135f45e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.359892 0.362031 0.003967 +1 0.000001 0.000001 0.359892 0.362031 0.003967 +2 0.359892 0.359892 0.000001 0.304469 0.356029 +3 0.362031 0.362031 0.304469 0.000001 0.358168 +4 0.003967 0.003967 0.356029 0.358168 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f271422e2b60f3e4276abd0357c207e3da03ced5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47840700 Before NNI: tree length is 0.47840700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001493_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001493_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e598f6f6979fd7de0be42d2666b57da0854877bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001493_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007990 0.123565 0.335902 0.002635 +1 0.007990 0.000001 0.124535 0.336873 0.009189 +2 0.123565 0.124535 0.000001 0.324451 0.124763 +3 0.335902 0.336873 0.324451 0.000001 0.337101 +4 0.002635 0.009189 0.124763 0.337101 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f345374481e8998cc77e6ed06d4c01a318d353b0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04093900 Before NNI: tree length is 1.04093900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e602ff115e7f7cc7c160bf24c2555acf3210e4f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58443700 Before NNI: tree length is 0.58443700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001497_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001497_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fb8192ec14234adf9cbb22041d0c309c1029db5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001497_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22535150 Before NNI: tree length is 0.22535150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..58a5509cd2274de8f7def054f2662344f00d62d6 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010357 0.130099 0.131745 0.004748 +1 0.010357 0.000001 0.131005 0.132652 0.009642 +2 0.130099 0.131005 0.000001 0.117542 0.129385 +3 0.131745 0.132652 0.117542 0.000001 0.131031 +4 0.004748 0.009642 0.129385 0.131031 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..24f903ad7a81474308c92c6d0b72edb3ff8e9343 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013446 0.376487 0.317947 0.009214 +1 0.013446 0.000001 0.372984 0.314443 0.016647 +2 0.376487 0.372984 0.000001 0.390081 0.379688 +3 0.317947 0.314443 0.390081 0.000001 0.321147 +4 0.009214 0.016647 0.379688 0.321147 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e94cc66d2b760988108b8fa3aa9dcf91525b7bf5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005292 0.110593 0.226287 0.008920 +1 0.005292 0.000001 0.111485 0.227179 0.003944 +2 0.110593 0.111485 0.000001 0.226111 0.115113 +3 0.226287 0.227179 0.226111 0.000001 0.230807 +4 0.008920 0.003944 0.115113 0.230807 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..975550881deb4f9be4616b4975f84ffdf9ea4a0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001502_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28837350 Before NNI: tree length is 0.28837350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c31992e5d3074652f9d2cefc3255d1f2e63d5aad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18076425 Before NNI: tree length is 0.18076425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001508_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001508_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a7866671d30dbfa0e110151fc52bd390cc5c294 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001508_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36192025 Before NNI: tree length is 0.36192025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2969b85c17ff343cfa6cdefc1b39279cbcd72166 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010732 0.152582 0.221097 0.012356 +1 0.010732 0.000001 0.150284 0.218798 0.023088 +2 0.152582 0.150284 0.000001 0.206981 0.164938 +3 0.221097 0.218798 0.206981 0.000001 0.233453 +4 0.012356 0.023088 0.164938 0.233453 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8a18f37b02ae14eb23c58e8c6e448fd26ca106f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.05844300 Before NNI: tree length is 1.05844300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf57a4f6a8e3ae315f05b75cbf9e23158c80864f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.06514184 Before NNI: tree length is 1.06514188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..07b593498e3b2e565fc86f753bc3eef49d432167 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028480 0.034608 0.391324 0.015941 +1 0.028480 0.000001 0.044882 0.401597 0.042028 +2 0.034608 0.044882 0.000001 0.394507 0.048156 +3 0.391324 0.401597 0.394507 0.000001 0.404872 +4 0.015941 0.042028 0.048156 0.404872 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ae87cce0549ea3bbf2dad35656357a1f2d685624 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024208 0.009172 0.057182 0.023675 +1 0.024208 0.000001 0.021262 0.065531 0.006208 +2 0.009172 0.021262 0.000001 0.054236 0.020728 +3 0.057182 0.065531 0.054236 0.000001 0.064997 +4 0.023675 0.006208 0.020728 0.064997 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e554baa9cb27759f97f0d97f601c00dcc2b2e99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001519_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07941063 Before NNI: tree length is 0.07941063 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a3f38de535e8dacc1abd066d5a37080c83a1973 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51718550 Before NNI: tree length is 0.51718550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..954cf79cb3776d6db4e32b5397b33e992e7d9a33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.150057 0.187958 0.349217 0.000001 +1 0.150057 0.000001 0.092725 0.312522 0.150057 +2 0.187958 0.092725 0.000001 0.350424 0.187958 +3 0.349217 0.312522 0.350424 0.000001 0.349217 +4 0.000001 0.150057 0.187958 0.349217 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46e0994b69206a3264f0a13ae24abd3cf64e13a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023670 0.088092 0.370147 0.000001 +1 0.023670 0.000001 0.078029 0.360083 0.023670 +2 0.088092 0.078029 0.000001 0.324207 0.088092 +3 0.370147 0.360083 0.324207 0.000001 0.370147 +4 0.000001 0.023670 0.088092 0.370147 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..355a51b47b65323e1858f32fdca8d493e505171e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001523_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39802682 Before NNI: tree length is 0.39802675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001527_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001527_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..821930a0354d8fe7ee3add0733b3ff93f36e7c84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001527_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23635230 Before NNI: tree length is 0.23635225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b31c811a06f488af365dc51312f85a44c082f185 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.63020431 Before NNI: tree length is 0.63020425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..38f25764c2688908a0c558daa85525ce8ec18906 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028919 0.068381 0.284638 0.023077 +1 0.028919 0.000001 0.075610 0.291867 0.030306 +2 0.068381 0.075610 0.000001 0.271294 0.052278 +3 0.284638 0.291867 0.271294 0.000001 0.268535 +4 0.023077 0.030306 0.052278 0.268535 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..92679dea4c5c5856c08c25cec43b241be178190b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043331 0.137868 0.286559 0.010306 +1 0.043331 0.000001 0.129462 0.278153 0.046442 +2 0.137868 0.129462 0.000001 0.302709 0.140979 +3 0.286559 0.278153 0.302709 0.000001 0.289669 +4 0.010306 0.046442 0.140979 0.289669 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e8420cb217984622f5ba731fe1d3069c2c856bf0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042887 0.206610 0.518836 0.034228 +1 0.042887 0.000001 0.170356 0.482583 0.015021 +2 0.206610 0.170356 0.000001 0.507423 0.178743 +3 0.518836 0.482583 0.507423 0.000001 0.490970 +4 0.034228 0.015021 0.178743 0.490970 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..01261eaf2b9fe6e50eff14b1ce2450858cb430f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001533_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.62293210 Before NNI: tree length is 0.62293212 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..98c95b761dfc7064bb78abc0884f20d7c955926b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31430930 Before NNI: tree length is 0.31430925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..977981de78327e91f6d4f55f22fa1398ba2ffd4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.083521 0.296597 0.670061 0.000001 +1 0.083521 0.000001 0.272021 0.645486 0.083521 +2 0.296597 0.272021 0.000001 0.668158 0.296597 +3 0.670061 0.645486 0.668158 0.000001 0.670061 +4 0.000001 0.083521 0.296597 0.670061 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a28a2e151957dc5d2a5b9d994572f30ecfd59b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001535_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.84688120 Before NNI: tree length is 0.84688125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a3854a6f68ace8d8340f35a96f8a3149257d1029 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009901 0.178719 0.249541 0.001704 +1 0.009901 0.000001 0.183711 0.254532 0.009573 +2 0.178719 0.183711 0.000001 0.267080 0.178391 +3 0.249541 0.254532 0.267080 0.000001 0.249212 +4 0.001704 0.009573 0.178391 0.249212 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..19f6db91e03744f0c50015cf852957221f105b2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001536_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35580414 Before NNI: tree length is 0.35580413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa13fc0976bdae6de6b5f658ce0bf4768b57a53e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.87558775 Before NNI: tree length is 0.87558775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..85abe0834602a9c7a98c206feee1378364dd8fc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026668 0.494369 0.896330 0.046962 +1 0.026668 0.000001 0.490867 0.892828 0.043460 +2 0.494369 0.490867 0.000001 0.714642 0.473848 +3 0.896330 0.892828 0.714642 0.000001 0.875809 +4 0.046962 0.043460 0.473848 0.875809 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..84b7b252c974ea1c8b3de21383e1697da6c69f6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000485 0.018352 0.020316 0.009193 +1 0.000485 0.000001 0.018837 0.020801 0.008708 +2 0.018352 0.018837 0.000001 0.014472 0.027545 +3 0.020316 0.020801 0.014472 0.000001 0.029509 +4 0.009193 0.008708 0.027545 0.029509 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6962859eefa242cfe3a6ddede14996cb76c3f2df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001541_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03576300 Before NNI: tree length is 0.03576300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8e47be1a066cb08d8019dd5ed20e54896440b653 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01336450 Before NNI: tree length is 0.01336450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..11dfdf07fb4e89435502e765379b908808d66dbf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034334 0.361629 0.287394 0.035519 +1 0.034334 0.000001 0.348510 0.274275 0.006873 +2 0.361629 0.348510 0.000001 0.307756 0.349695 +3 0.287394 0.274275 0.307756 0.000001 0.275460 +4 0.035519 0.006873 0.349695 0.275460 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..446d9fee2911e26dfad454be2132aa1f67d19b11 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53281039 Before NNI: tree length is 0.53281037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..99cb0020c94feddc273987f8d58ff5b9327f2469 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003837 0.295003 0.275582 0.008282 +1 0.003837 0.000001 0.291892 0.272470 0.005171 +2 0.295003 0.291892 0.000001 0.311219 0.293352 +3 0.275582 0.272470 0.311219 0.000001 0.273930 +4 0.008282 0.005171 0.293352 0.273930 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9571e2dd482800128aa4f0a455dc3521724e89c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017697 0.168509 0.257377 0.000001 +1 0.017697 0.000001 0.175393 0.264261 0.017697 +2 0.168509 0.175393 0.000001 0.258404 0.168509 +3 0.257377 0.264261 0.258404 0.000001 0.257377 +4 0.000001 0.017697 0.168509 0.257377 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3968a6a000928086c68470f0cbfffdf393c6e621 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001562_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35443600 Before NNI: tree length is 0.35443600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..caa20b0cdf9bc7c146e82bf323702a372f7b80f7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035748 0.585537 0.492320 0.000001 +1 0.035748 0.000001 0.617643 0.524426 0.035748 +2 0.585537 0.617643 0.000001 0.763458 0.585537 +3 0.492320 0.524426 0.763458 0.000001 0.492320 +4 0.000001 0.035748 0.585537 0.492320 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cdf3463916992f2cdb6b4987e1f1052fbebc5ef8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016075 0.032340 0.034696 0.016075 +1 0.016075 0.000001 0.031857 0.029503 0.000001 +2 0.032340 0.031857 0.000001 0.050478 0.031857 +3 0.034696 0.029503 0.050478 0.000001 0.029503 +4 0.016075 0.000001 0.031857 0.029503 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b28221f5452bbbe23d76bf863e1730530dd78570 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11118689 Before NNI: tree length is 0.11118687 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..a40a09d9a51f35858fc7f6111bf29d94ec7af0c4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007467 0.024811 0.017989 0.008952 +1 0.007467 0.000001 0.026615 0.013632 0.010755 +2 0.024811 0.026615 0.000001 0.037136 0.026043 +3 0.017989 0.013632 0.037136 0.000001 0.021277 +4 0.008952 0.010755 0.026043 0.021277 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9550b34c341b22510b09a55536073fd2f7ee3fb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037853 0.478025 0.032623 0.025111 +1 0.037853 0.000001 0.492838 0.047436 0.039924 +2 0.478025 0.492838 0.000001 0.475973 0.462525 +3 0.032623 0.047436 0.475973 0.000001 0.023058 +4 0.025111 0.039924 0.462525 0.023058 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9877e3bbd3e256a335e62c793449ae1d90a27298 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001568_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52444875 Before NNI: tree length is 0.52444875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..310bdbf24be60030288378a764c23e02244ff453 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.095186 0.038876 0.904259 0.019274 +1 0.095186 0.000001 0.079329 0.960604 0.085783 +2 0.038876 0.079329 0.000001 0.904294 0.029473 +3 0.904259 0.960604 0.904294 0.000001 0.894857 +4 0.019274 0.085783 0.029473 0.894857 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8b6bb23d8ca78261b9efdddd4a56a5fe81ce4828 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025257 0.081070 0.536846 0.023821 +1 0.025257 0.000001 0.083624 0.539401 0.011985 +2 0.081070 0.083624 0.000001 0.536676 0.082189 +3 0.536846 0.539401 0.536676 0.000001 0.537965 +4 0.023821 0.011985 0.082189 0.537965 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9076922bc94cd3d4fd541a7d81fdd10d610772ba --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023411 0.304685 0.559092 0.027490 +1 0.023411 0.000001 0.304549 0.558956 0.009282 +2 0.304685 0.304549 0.000001 0.585145 0.308627 +3 0.559092 0.558956 0.585145 0.000001 0.563035 +4 0.027490 0.009282 0.308627 0.563035 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..05adb7baddf1666ff92340f593e56db7c86ec585 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.099089 0.614816 0.792300 0.039863 +1 0.099089 0.000001 0.636794 0.814278 0.075833 +2 0.614816 0.636794 0.000001 0.935790 0.591560 +3 0.792300 0.814278 0.935790 0.000001 0.769044 +4 0.039863 0.075833 0.591560 0.769044 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c33271c8bd37167562b43b97834c9a33cc16a882 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001578_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.24029000 Before NNI: tree length is 1.24029000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46a8f422df946fb11a14473c7121726c0c20609f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012483 0.259040 0.024321 0.011684 +1 0.012483 0.000001 0.259790 0.025072 0.015798 +2 0.259040 0.259790 0.000001 0.259623 0.262355 +3 0.024321 0.025072 0.259623 0.000001 0.027636 +4 0.011684 0.015798 0.262355 0.027636 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..ac80f8d7813a669b2d4df2854de636ff10f9507d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004403 0.321883 0.007829 0.003421 +1 0.004403 0.000001 0.324318 0.010264 0.000982 +2 0.321883 0.324318 0.000001 0.323309 0.323336 +3 0.007829 0.010264 0.323309 0.000001 0.009282 +4 0.003421 0.000982 0.323336 0.009282 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c63346cb9f69afb55b6e9f43dd32fd16466f6cf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58296792 Before NNI: tree length is 0.58296800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6328a7c2364395b97b91324e3169145a54f7ab2d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10039900 Before NNI: tree length is 0.10039900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b58a278c9aa0acd2ef17349203a539827c57edb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005766 0.000001 0.026706 0.005337 +1 0.005766 0.000001 0.005766 0.032125 0.005115 +2 0.000001 0.005766 0.000001 0.026706 0.005337 +3 0.026706 0.032125 0.026706 0.000001 0.031696 +4 0.005337 0.005115 0.005337 0.031696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d7aaa6858483a2a5419e7783fcf0b5ce0c7d87a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001585_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03464200 Before NNI: tree length is 0.03464200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..65c59af8470eea6f0190f3121b9db3094843295d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30769435 Before NNI: tree length is 0.30769437 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b207d0e670247f433e0cc766e08239b4b4f3fd85 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40244200 Before NNI: tree length is 0.40244200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d6659677db4229e19d1ea67f754313a1bbdb7229 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015529 0.059755 0.035020 0.015410 +1 0.015529 0.000001 0.062174 0.037438 0.017829 +2 0.059755 0.062174 0.000001 0.042751 0.053373 +3 0.035020 0.037438 0.042751 0.000001 0.028638 +4 0.015410 0.017829 0.053373 0.028638 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dc88b6ecdeec3830d444dcfa7f13e41711a9b89c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007332 0.067366 0.043294 0.007319 +1 0.007332 0.000001 0.062112 0.038040 0.003882 +2 0.067366 0.062112 0.000001 0.076923 0.063916 +3 0.043294 0.038040 0.076923 0.000001 0.039845 +4 0.007319 0.003882 0.063916 0.039845 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63f1b07a0db5702b4ae9f7ffc066e3cf99dda219 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001591_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09676511 Before NNI: tree length is 0.09676513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..071044ffbf613ab4eafd31cf3a4a2e9ba08b9de3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010001 0.125773 0.060811 0.008720 +1 0.010001 0.000001 0.115773 0.050811 0.002810 +2 0.125773 0.115773 0.000001 0.100803 0.118583 +3 0.060811 0.050811 0.100803 0.000001 0.053621 +4 0.008720 0.002810 0.118583 0.053621 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0906719f7fbd7b6abf45a33b17cfdf9e762a450d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26930423 Before NNI: tree length is 0.26930425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d9c1bacf87278e19474a155dc6f686a7456c3c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.19655125 Before NNI: tree length is 1.19655125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a39acf689ec4ba44361e360d78303da42f15460 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69626800 Before NNI: tree length is 0.69626800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..091c479c8be97161cd22edffa78e7f3149014a83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.072592 0.554732 1.737095 0.074481 +1 0.072592 0.000001 0.549999 1.732363 0.045104 +2 0.554732 0.549999 0.000001 1.700595 0.551888 +3 1.737095 1.732363 1.700595 0.000001 1.734252 +4 0.074481 0.045104 0.551888 1.734252 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001602_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001602_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6935fded7cc509bc446076e354b20d91e9cf3d6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001602_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.051404 0.086716 0.000001 +1 0.000001 0.000001 0.051404 0.086716 0.000001 +2 0.051404 0.051404 0.000001 0.063259 0.051404 +3 0.086716 0.086716 0.063259 0.000001 0.086716 +4 0.000001 0.000001 0.051404 0.086716 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..310e5664e110ca6dc377746bc21050a978c966f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003919 0.048659 0.008522 0.009039 +1 0.003919 0.000001 0.047966 0.007829 0.008346 +2 0.048659 0.047966 0.000001 0.048601 0.045749 +3 0.008522 0.007829 0.048601 0.000001 0.008981 +4 0.009039 0.008346 0.045749 0.008981 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2df90a52a941909f47958cc0f2230c23f4d4e0c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001607_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05756850 Before NNI: tree length is 0.05756850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..e26dbe2c29dab3bc6059e4d0f4f601293ac89ee4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036248 0.049715 0.036821 0.016061 +1 0.036248 0.000001 0.037586 0.028349 0.020356 +2 0.049715 0.037586 0.000001 0.041816 0.033823 +3 0.036821 0.028349 0.041816 0.000001 0.020928 +4 0.016061 0.020356 0.033823 0.020928 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..d023c157c9a5edf6bba32cbbee315cd5b4c5520f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007349 0.049017 0.103290 0.005785 +1 0.007349 0.000001 0.050940 0.105213 0.008714 +2 0.049017 0.050940 0.000001 0.134453 0.050382 +3 0.103290 0.105213 0.134453 0.000001 0.104655 +4 0.005785 0.008714 0.050382 0.104655 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001614_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001614_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f70c5224e682d1e252186500b5b347a64f67bc81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001614_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56996458 Before NNI: tree length is 0.56996463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3bf6b5f96bbbb7a2a9fbc64fadd044d0dfee10cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018159 0.272982 0.080641 0.018159 +1 0.018159 0.000001 0.268542 0.076201 0.000001 +2 0.272982 0.268542 0.000001 0.241992 0.268542 +3 0.080641 0.076201 0.241992 0.000001 0.076201 +4 0.018159 0.000001 0.268542 0.076201 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..66765160d85a275f5d05ad999a124bbe013abc63 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002767 0.027920 0.026831 0.005293 +1 0.002767 0.000001 0.028417 0.027328 0.005790 +2 0.027920 0.028417 0.000001 0.039991 0.028198 +3 0.026831 0.027328 0.039991 0.000001 0.027109 +4 0.005293 0.005790 0.028198 0.027109 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ab4323d25c460cd179eab4a68bfc337c0782477 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25530125 Before NNI: tree length is 0.25530125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f1cad6f33f82b31e17325c2a7088ea77d00ba87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41649350 Before NNI: tree length is 0.41649350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..35795b9a6164e29ad57bcd1dd428ec4bc96bed31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010013 0.468593 0.731119 0.111611 +1 0.010013 0.000001 0.470273 0.732799 0.113290 +2 0.468593 0.470273 0.000001 0.782041 0.455455 +3 0.731119 0.732799 0.782041 0.000001 0.717980 +4 0.111611 0.113290 0.455455 0.717980 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc2e8a63b9cc4715e021362f0743cfc7db6d9311 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03979032 Before NNI: tree length is 0.03979025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3118571975038f568e8dbf05c6d738c2e0b1abf8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03669600 Before NNI: tree length is 0.03669600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001642_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001642_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ce900989cb2f474d777175f1eae00f20bbc7c167 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001642_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.074677 0.185436 0.059193 0.189005 +1 0.074677 0.000001 0.177219 0.096669 0.226481 +2 0.185436 0.177219 0.000001 0.207429 0.337241 +3 0.059193 0.096669 0.207429 0.000001 0.186114 +4 0.189005 0.226481 0.337241 0.186114 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001645_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001645_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..84e61ffa5188662fb71c628ab6fc74989496b98e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001645_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.24505569 Before NNI: tree length is 1.24505575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..4d1188515f8e07315c1d1453b68bae8ffc524f68 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003840 0.206333 0.490051 0.011294 +1 0.003840 0.000001 0.202493 0.486211 0.007453 +2 0.206333 0.202493 0.000001 0.428386 0.202000 +3 0.490051 0.486211 0.428386 0.000001 0.485718 +4 0.011294 0.007453 0.202000 0.485718 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001649_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001649_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3d01e2d1532139a7c029f13b03f476948c070ea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001649_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.618285 0.860788 0.003060 +1 0.000001 0.000001 0.618285 0.860788 0.003060 +2 0.618285 0.618285 0.000001 1.369418 0.615501 +3 0.860788 0.860788 1.369418 0.000001 0.858004 +4 0.003060 0.003060 0.615501 0.858004 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..67d269047382bc95248c59479dcf8933b88091b0 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028166 0.060399 0.363884 0.033552 +1 0.028166 0.000001 0.070646 0.374131 0.043799 +2 0.060399 0.070646 0.000001 0.378444 0.065071 +3 0.363884 0.374131 0.378444 0.000001 0.368555 +4 0.033552 0.043799 0.065071 0.368555 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5708f76a181ac7cfb01643e2f9dd914adbac7260 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48541438 Before NNI: tree length is 0.48541438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001655_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001655_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0de3e1cbafcad7d64e13e60b9c119f3e05c84bb8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001655_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011486 0.295915 0.726605 0.060124 +1 0.011486 0.000001 0.307401 0.738091 0.071611 +2 0.295915 0.307401 0.000001 0.783452 0.352898 +3 0.726605 0.738091 0.783452 0.000001 0.783588 +4 0.060124 0.071611 0.352898 0.783588 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001656_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001656_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..077cf345d3eaf7da643a1ddb804b9ef552412bfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001656_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51282930 Before NNI: tree length is 0.51282925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..368fbfc4fde759cb49d2b783003da16113948eb2 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.278999 0.419550 0.000001 +1 0.000001 0.000001 0.278999 0.419550 0.000001 +2 0.278999 0.278999 0.000001 0.405070 0.278999 +3 0.419550 0.419550 0.405070 0.000001 0.419550 +4 0.000001 0.000001 0.278999 0.419550 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..22322986f175505281d0a82e7c71e2d8cb3bd7c4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049641 0.073237 0.061035 0.049641 +1 0.049641 0.000001 0.085186 0.041424 0.000001 +2 0.073237 0.085186 0.000001 0.096580 0.085186 +3 0.061035 0.041424 0.096580 0.000001 0.041424 +4 0.049641 0.000001 0.085186 0.041424 0.000001 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..9471ccaa4243e7d890d60d1452aa2ef9d1cd264f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031542 0.091069 0.021806 0.031542 +1 0.031542 0.000001 0.093292 0.020462 0.000001 +2 0.091069 0.093292 0.000001 0.083556 0.093292 +3 0.021806 0.020462 0.083556 0.000001 0.020462 +4 0.031542 0.000001 0.093292 0.020462 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..60c606b86a2ae728e2306efc4500d6e40a4d501b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45660561 Before NNI: tree length is 0.45660563 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001662_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001662_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd3b70f88e4e40cee8f9c10162c51e20c1a28de9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001662_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05659950 Before NNI: tree length is 0.05659950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001664_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001664_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6c36a3d3a3fdb435b13195cff84bed69e2e6cf4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001664_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02481820 Before NNI: tree length is 0.02481825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..8bbd18e8c25e913d895d384e1a30a9b9c0bced99 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020905 0.047252 0.045808 0.000001 +1 0.020905 0.000001 0.048623 0.047179 0.020905 +2 0.047252 0.048623 0.000001 0.047829 0.047252 +3 0.045808 0.047179 0.047829 0.000001 0.045808 +4 0.000001 0.020905 0.047252 0.045808 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001669_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001669_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1bd84dfa064e3ad797172cfb84fb90fdcc72be0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001669_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12610563 Before NNI: tree length is 0.12610562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f2ceefc80e7386684cab828fd5231171f2c76c17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068847 0.169348 0.438715 0.071811 +1 0.068847 0.000001 0.201861 0.471227 0.016217 +2 0.169348 0.201861 0.000001 0.449988 0.204824 +3 0.438715 0.471227 0.449988 0.000001 0.474191 +4 0.071811 0.016217 0.204824 0.474191 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8edd5cc039c97a3a2117dc64674d889f23993aa6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012500 0.063470 0.249736 0.012500 +1 0.012500 0.000001 0.072153 0.258419 0.000001 +2 0.063470 0.072153 0.000001 0.255079 0.072153 +3 0.249736 0.258419 0.255079 0.000001 0.258419 +4 0.012500 0.000001 0.072153 0.258419 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4fffb004c0c7e9f3b5e67b379d8b72a6fc43f508 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23542450 Before NNI: tree length is 0.23542450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..636225467fe5e22abd4120d6b7684d1658e0ac14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36096950 Before NNI: tree length is 0.36096950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001674_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001674_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a57627926620ad4f984e1afb839b8c784b41061e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001674_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.180602 0.380076 0.000001 +1 0.000001 0.000001 0.180602 0.380076 0.000001 +2 0.180602 0.180602 0.000001 0.398307 0.180602 +3 0.380076 0.380076 0.398307 0.000001 0.380076 +4 0.000001 0.000001 0.180602 0.380076 0.000001 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..24abd3959f2c660d48d7a1cf296a769365cd947a --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33100266 Before NNI: tree length is 0.33100263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55cd6d2599e3d93fbc3535c88ed51c00f230ab13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.138194 0.033561 0.138692 0.141742 +1 0.138194 0.000001 0.126595 0.013038 0.003548 +2 0.033561 0.126595 0.000001 0.127093 0.130143 +3 0.138692 0.013038 0.127093 0.000001 0.016586 +4 0.141742 0.003548 0.130143 0.016586 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001679_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001679_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d32c56c6d3281b83380a9318c102cdf5d9da28f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001679_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26524600 Before NNI: tree length is 0.26524600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..988fb5c0b9bcd263d13f276d2e6beb4d401010c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028407 0.162228 0.411258 0.013009 +1 0.028407 0.000001 0.161430 0.410460 0.029066 +2 0.162228 0.161430 0.000001 0.412988 0.162887 +3 0.411258 0.410460 0.412988 0.000001 0.411917 +4 0.013009 0.029066 0.162887 0.411917 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..60e46994643cb90d595bac02aac96ad95a9994dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001683_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51387550 Before NNI: tree length is 0.51387550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..26354d6fd7a65ad8e488487c8ddf2ea380826519 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004648 0.229099 0.209973 0.002795 +1 0.004648 0.000001 0.224451 0.205325 0.002793 +2 0.229099 0.224451 0.000001 0.218647 0.227244 +3 0.209973 0.205325 0.218647 0.000001 0.208118 +4 0.002795 0.002793 0.227244 0.208118 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..56b7043ee62b87db0411394ea72361f095da3e85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001688_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32932950 Before NNI: tree length is 0.32932950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a21d13ad04be0166b8a5b5acd77be00b5ea4f788 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001784 0.396886 0.466551 0.059353 +1 0.001784 0.000001 0.398670 0.468335 0.061137 +2 0.396886 0.398670 0.000001 0.590136 0.420981 +3 0.466551 0.468335 0.590136 0.000001 0.490646 +4 0.059353 0.061137 0.420981 0.490646 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bd679f78744c67697e90b4b5e584f5b924fc26c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001690_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77029450 Before NNI: tree length is 0.77029450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f671b702d69f65e5f36f608754191957e9b33042 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48167250 Before NNI: tree length is 1.48167250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02ce3b0720c6be934a52461c9145cf51e4e3324d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43709700 Before NNI: tree length is 0.43709700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c69b00f8436cdcd4f62458557214d9c5a3acef3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011366 0.325011 0.231131 0.010501 +1 0.011366 0.000001 0.322283 0.228403 0.002333 +2 0.325011 0.322283 0.000001 0.339354 0.321419 +3 0.231131 0.228403 0.339354 0.000001 0.227538 +4 0.010501 0.002333 0.321419 0.227538 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e887b4042c5293c793933d6e5f1c63613e3bee66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001698_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45280114 Before NNI: tree length is 0.45280112 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..11bee489c56af91e2a70d9ccbb5a05b3240f489f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020696 0.564722 0.491158 0.005644 +1 0.020696 0.000001 0.579035 0.505471 0.015070 +2 0.564722 0.579035 0.000001 0.552991 0.563983 +3 0.491158 0.505471 0.552991 0.000001 0.490420 +4 0.005644 0.015070 0.563983 0.490420 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001702_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001702_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7fe2765445a551d789533428c443736f3f3624f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001702_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004243 0.081922 0.291886 0.010478 +1 0.004243 0.000001 0.084403 0.294367 0.012960 +2 0.081922 0.084403 0.000001 0.307899 0.076187 +3 0.291886 0.294367 0.307899 0.000001 0.286151 +4 0.010478 0.012960 0.076187 0.286151 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de0369d951fbba5aa95d900a475d18da72a6f9e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048490 0.818776 1.069117 0.026984 +1 0.048490 0.000001 0.802752 1.053092 0.032539 +2 0.818776 0.802752 0.000001 1.078408 0.802825 +3 1.069117 1.053092 1.078408 0.000001 1.053166 +4 0.026984 0.032539 0.802825 1.053166 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b753735e8befbc9b3e3b9485a5904b550f5edc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001706_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.50489977 Before NNI: tree length is 1.50489975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d17b29cc65d38eb5bd53a33022266d6606ce2cb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028435 0.174549 0.405628 0.044068 +1 0.028435 0.000001 0.179025 0.410104 0.028845 +2 0.174549 0.179025 0.000001 0.398616 0.194658 +3 0.405628 0.410104 0.398616 0.000001 0.425737 +4 0.044068 0.028845 0.194658 0.425737 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8d024292e1b5ddc1872d89433a4c73fa9f1d661 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024589 0.385429 0.949605 0.021665 +1 0.024589 0.000001 0.384756 0.948931 0.005747 +2 0.385429 0.384756 0.000001 1.057527 0.381832 +3 0.949605 0.948931 1.057527 0.000001 0.946007 +4 0.021665 0.005747 0.381832 0.946007 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..c488246864db5a1ba00524b55092b5523ae2b755 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086087 0.036420 0.528934 0.009637 +1 0.086087 0.000001 0.093769 0.550349 0.080342 +2 0.036420 0.093769 0.000001 0.536617 0.030676 +3 0.528934 0.550349 0.536617 0.000001 0.523190 +4 0.009637 0.080342 0.030676 0.523190 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39b772934a5c3d35a8e65a8cc9c41ccab82851a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000365 0.037915 0.863271 0.000365 +1 0.000365 0.000001 0.038280 0.862906 0.000730 +2 0.037915 0.038280 0.000001 0.901185 0.037550 +3 0.863271 0.862906 0.901185 0.000001 0.863636 +4 0.000365 0.000730 0.037550 0.863636 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f51c1da4e9b26c797cccff23a5ab8cfa5cd4865 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001714_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.90118583 Before NNI: tree length is 0.90118587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001715_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001715_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..886c32c19e697759b4e900776bf0a7711348422b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001715_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.75646239 Before NNI: tree length is 0.75646237 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d66e2cee3d8df33f80d1a485c0d725c2868411f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.233245 0.645070 0.000001 +1 0.000001 0.000001 0.233245 0.645070 0.000001 +2 0.233245 0.233245 0.000001 0.713782 0.233245 +3 0.645070 0.645070 0.713782 0.000001 0.645070 +4 0.000001 0.000001 0.233245 0.645070 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..633a1e67afa34afea388052c6b9497ababd30c0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.275604 1.021769 0.000001 +1 0.000001 0.000001 0.275604 1.021769 0.000001 +2 0.275604 0.275604 0.000001 1.063885 0.275604 +3 1.021769 1.021769 1.063885 0.000001 1.021769 +4 0.000001 0.000001 0.275604 1.021769 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5535d318d05bf6d1f9a6ff6db5206005cff646b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001719_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.18063000 Before NNI: tree length is 1.18063000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a86aaa17aaca12800658bd4160831646b93e273a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030141 0.120054 0.661627 0.030141 +1 0.030141 0.000001 0.133207 0.674780 0.000001 +2 0.120054 0.133207 0.000001 0.686159 0.133207 +3 0.661627 0.674780 0.686159 0.000001 0.674780 +4 0.030141 0.000001 0.133207 0.674780 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dfa39226d52fbd5af1cb144768191342a4838b7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001720_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.75556750 Before NNI: tree length is 0.75556750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e4ced30ae6a18845be6f0daee9eaf2c64a1463c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24961823 Before NNI: tree length is 0.24961825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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 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 new file mode 100644 index 0000000000000000000000000000000000000000..e3c067e30a68ba80068d6fac849b71ee8f351bde --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008572 1.231948 0.629152 0.004559 +1 0.008572 0.000001 1.227595 0.624799 0.005865 +2 1.231948 1.227595 0.000001 1.648474 1.229241 +3 0.629152 0.624799 1.648474 0.000001 0.626445 +4 0.004559 0.005865 1.229241 0.626445 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eb6101df93949d6147a6a3d0040fe9ccdaa78fdd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057635 0.132316 0.032780 0.009726 +1 0.057635 0.000001 0.154061 0.072948 0.060030 +2 0.132316 0.154061 0.000001 0.147629 0.134711 +3 0.032780 0.072948 0.147629 0.000001 0.035175 +4 0.009726 0.060030 0.134711 0.035175 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7822ea958bf54f68ec31adb577e479386aed161 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001729_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20211300 Before NNI: tree length is 0.20211300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bfc219c18a45d23983ebf0f2abefecbdf7809473 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009519 0.035920 0.296628 0.002807 +1 0.009519 0.000001 0.044866 0.305574 0.008222 +2 0.035920 0.044866 0.000001 0.322780 0.038153 +3 0.296628 0.305574 0.322780 0.000001 0.298861 +4 0.002807 0.008222 0.038153 0.298861 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85b91ca9a4cf3d7e58a879f05ed543b124f809e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001730_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33765125 Before NNI: tree length is 0.33765125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4753e86e18a51abd396cb0d9ed5741852ffffd99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.068209 0.065936 0.000001 +1 0.000001 0.000001 0.068209 0.065936 0.000001 +2 0.068209 0.068209 0.000001 0.075204 0.068209 +3 0.065936 0.065936 0.075204 0.000001 0.065936 +4 0.000001 0.000001 0.068209 0.065936 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..35a2d384b125669e4f75c47d10ad4edf013e8874 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026363 0.048299 0.331637 0.015271 +1 0.026363 0.000001 0.058464 0.343233 0.022248 +2 0.048299 0.058464 0.000001 0.365169 0.047372 +3 0.331637 0.343233 0.365169 0.000001 0.332142 +4 0.015271 0.022248 0.047372 0.332142 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..595a593c4004053f206e6c939f906b1f225aa33a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001734_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39639461 Before NNI: tree length is 0.39639463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c46f35c94632db1af561a63afffa94ca039f6d2e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27828675 Before NNI: tree length is 0.27828675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41c1f2ca8179e7a7aa5b491286d53e36fd285223 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46296585 Before NNI: tree length is 0.46296587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de5a0b85c30f06879e557dcfe5e6b1ca292e211b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.119922 0.612885 0.788007 0.177662 +1 0.119922 0.000001 0.598397 0.773519 0.099696 +2 0.612885 0.598397 0.000001 0.817200 0.656137 +3 0.788007 0.773519 0.817200 0.000001 0.831259 +4 0.177662 0.099696 0.656137 0.831259 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..01770de59bf8581d1e62d03b17b64e5852b4de4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001745_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.24048100 Before NNI: tree length is 1.24048100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001746_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001746_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..62ff9448e292369886daacb292a8780eb489a379 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001746_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014312 0.207670 0.380841 0.017711 +1 0.014312 0.000001 0.204509 0.377680 0.007300 +2 0.207670 0.204509 0.000001 0.355755 0.207908 +3 0.380841 0.377680 0.355755 0.000001 0.381079 +4 0.017711 0.007300 0.207908 0.381079 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001749_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001749_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78ab2e72893b2ec37cbd62e5fdf32a89e146be76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001749_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001228 0.245676 0.353661 0.007185 +1 0.001228 0.000001 0.246904 0.354889 0.008413 +2 0.245676 0.246904 0.000001 0.508478 0.247906 +3 0.353661 0.354889 0.508478 0.000001 0.355892 +4 0.007185 0.008413 0.247906 0.355892 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0695bef3cc3bf52979788b2409bdf4c0d500d415 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019965 0.067818 0.148616 0.007696 +1 0.019965 0.000001 0.071139 0.151936 0.016039 +2 0.067818 0.071139 0.000001 0.139808 0.063892 +3 0.148616 0.151936 0.139808 0.000001 0.144690 +4 0.007696 0.016039 0.063892 0.144690 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..733e11e0c0db453a05f1cd404792337b0dadbc84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001752_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19164880 Before NNI: tree length is 0.19164875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 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_fastme_stat.txt 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_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3900e9386c6ab9bb5a0b81f3c578fcd35a3a556c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69193250 Before NNI: tree length is 0.69193250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000