diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b2777769bc800a72dd398840becf41fbd3b5ece0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000003_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022701 0.017735 0.000001 0.000001 +1 0.022701 0.000001 0.024082 0.020577 0.012167 +2 0.017735 0.024082 0.000001 0.017735 0.017735 +3 0.000001 0.020577 0.017735 0.000001 0.000001 +4 0.000001 0.012167 0.017735 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000019_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000019_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ab32ca2dc03149222388899afc603de6603539d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000019_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.085805 0.180055 0.170706 0.086091 +1 0.085805 0.000001 0.140344 0.011057 0.008726 +2 0.180055 0.140344 0.000001 0.142647 0.141483 +3 0.170706 0.011057 0.142647 0.000001 0.001362 +4 0.086091 0.008726 0.141483 0.001362 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dbeda17a3a87b7afb3362569ccd0b5b1d21ea7ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.12662600 Before NNI: tree length is 1.12662600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000029_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000029_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c389f35b23ba8a321dcf00164d2adf487d967b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000029_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026102 1.083153 0.026764 0.026764 +1 0.026102 0.000001 1.057051 0.000662 0.000662 +2 1.083153 1.057051 0.000001 1.056389 0.000001 +3 0.026764 0.000662 1.056389 0.000001 0.000001 +4 0.026764 0.000662 0.000001 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a706eb2bd84b99bf6e159974b7f30aa5bbc242ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000031_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.360024 0.472199 0.361437 0.353837 +1 0.360024 0.000001 0.290536 0.063546 0.009057 +2 0.472199 0.290536 0.000001 0.291950 0.284349 +3 0.361437 0.063546 0.291950 0.000001 0.057358 +4 0.353837 0.009057 0.284349 0.057358 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fad173e69822241e64b1a356d5668c4d9a80b1f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000037_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20265300 Before NNI: tree length is 0.20265300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..37e1c3ef9423fae232bfb469f7e62909b7e1d552 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.202979 0.046098 0.198254 0.194314 +1 0.202979 0.000001 0.391482 0.025791 0.397294 +2 0.046098 0.391482 0.000001 0.386756 0.695852 +3 0.198254 0.025791 0.386756 0.000001 0.392568 +4 0.194314 0.397294 0.695852 0.392568 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92f006a83c08f1e8e72999d334d1d7bd7d548216 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000040_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57729908 Before NNI: tree length is 0.60338538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.78071841 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d7cfafe3a7f2e3e3d4e3bb77611fa25c3000620 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000041_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030139 0.029617 0.028786 0.187682 +1 0.030139 0.000001 0.022071 0.007024 0.182294 +2 0.029617 0.022071 0.000001 0.000001 0.181772 +3 0.028786 0.007024 0.000001 0.000001 0.180941 +4 0.187682 0.182294 0.181772 0.180941 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46c09e0d919bd98212733fd81b218c851e57fdea --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000052_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.827452 2.481677 1.818963 2.752574 +1 1.827452 0.000001 1.787835 0.014298 2.058731 +2 2.481677 1.787835 0.000001 1.804883 1.449971 +3 1.818963 0.014298 1.804883 0.000001 2.075779 +4 2.752574 2.058731 1.449971 2.075779 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ee828435321dce60a1450b30160ab4a8cabb7eb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000060_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32892675 Before NNI: tree length is 0.32892675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..65f41bc530407f582cb346225025695a72d4100d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000063_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.185871 0.400810 0.186391 0.180435 +1 0.185871 0.000001 0.398560 0.011425 0.013046 +2 0.400810 0.398560 0.000001 0.399080 0.393124 +3 0.186391 0.011425 0.399080 0.000001 0.013566 +4 0.180435 0.013046 0.393124 0.013566 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..675e5422d18507ba2c47c5d30ba1147cec5093da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42410550 Before NNI: tree length is 0.42410550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6bd9fcd15f9739f62a07d2411b5b0cfdb73d1e62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.065675 0.177774 0.070949 0.068139 +1 0.065675 0.000001 0.188126 0.018876 0.016066 +2 0.177774 0.188126 0.000001 0.193400 0.190590 +3 0.070949 0.018876 0.193400 0.000001 0.009748 +4 0.068139 0.016066 0.190590 0.009748 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a4f88fa11e4b325183b35054d2bf9db6b7b4760e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000073_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.204095 1.252155 0.204095 0.204095 +1 0.204095 0.000001 1.484012 0.000001 0.000001 +2 1.252155 1.484012 0.000001 1.484012 1.484012 +3 0.204095 0.000001 1.484012 0.000001 0.000001 +4 0.204095 0.000001 1.484012 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f4f94018b2b833b26e035d7a2705f90d4c547bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000076_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.119639 1.131945 1.119801 1.119963 +1 1.119639 0.000001 0.012306 0.000162 0.000324 +2 1.131945 0.012306 0.000001 0.012144 0.011982 +3 1.119801 0.000162 0.012144 0.000001 0.000162 +4 1.119963 0.000324 0.011982 0.000162 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9213a0a7b99374bc1a504728fa7f2458bf80d2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.072107 1.085138 1.072107 1.072107 +1 1.072107 0.000001 0.028420 0.000001 0.000001 +2 1.085138 0.028420 0.000001 0.028420 0.028420 +3 1.072107 0.000001 0.028420 0.000001 0.000001 +4 1.072107 0.000001 0.028420 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..001b911a2db026f2fed6685fd4ccde65f60567e7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000079_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.74104100 Before NNI: tree length is 0.74104100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbf2b9cda692dcd52a6d6e532c1a06b8a642afb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43172233 Before NNI: tree length is 0.43172225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d2f25ab099ef8d4aab83391fde29bced584f671 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000082_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.094683 0.127362 0.097147 0.090565 +1 0.094683 0.000001 0.109555 0.005109 0.035335 +2 0.127362 0.109555 0.000001 0.112019 0.105437 +3 0.097147 0.005109 0.112019 0.000001 0.037799 +4 0.090565 0.035335 0.105437 0.037799 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..448ce1800a1bb9542cf5c78eee0b97cf926f1c2e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.436384 0.953145 0.450897 0.424768 +1 0.436384 0.000001 0.845820 0.026792 0.032653 +2 0.953145 0.845820 0.000001 0.860332 0.834203 +3 0.450897 0.026792 0.860332 0.000001 0.047165 +4 0.424768 0.032653 0.834203 0.047165 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c942ecaaa969d8671f88ae67af26574f01c2cb3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000083_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.14884490 Before NNI: tree length is 1.14884487 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d10b48c95990e8d801b238bb426d60af35f88967 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.82095675 Before NNI: tree length is 0.82095675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c3d93af2a4bd926ec9fe1b58e7a90470d775d23 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000087_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.248109 0.056435 0.019992 0.023689 +1 0.248109 0.000001 0.311144 0.274700 0.278398 +2 0.056435 0.311144 0.000001 0.048181 0.051878 +3 0.019992 0.274700 0.048181 0.000001 0.011210 +4 0.023689 0.278398 0.051878 0.011210 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1db988f7406cc464b69293061c4af52f8cb54bc2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032004 0.137214 0.267296 0.151548 +1 0.032004 0.000001 0.142065 0.264590 0.156399 +2 0.137214 0.142065 0.000001 0.377356 0.230646 +3 0.267296 0.264590 0.377356 0.000001 0.391690 +4 0.151548 0.156399 0.230646 0.391690 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fefc53febf8252baa7ccb72cdcd89fd3a1e23c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.77111637 Before NNI: tree length is 1.77111638 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000096_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000096_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9dc0928da96029ed0298fe58797d389b486934b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000096_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37790185 Before NNI: tree length is 0.37790187 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000099_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000099_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..769e9d1b4b4cef3664dcba7373f44be1c72e356d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000099_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 1.70646758 Before NNI: tree length is 1.73465900 + NNI 1: new tree length is 1.70557275 + Performed 1 NNI(s). + + Before SPR: tree length is 1.73465900 + SPR 1: new tree length is 1.70557275 + Performed 1 SPR(s). + + Explained variance : 0.97072203 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..da9dd3ae71e00c5a35f894089147319f2e524d26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000107_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17664100 Before NNI: tree length is 0.17664100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..696ce5b9c36ae67b5eecad9172dbfa568ed43d35 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000119_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.675913 0.749031 0.750158 +1 0.000001 0.000001 0.343036 0.014813 0.015940 +2 0.675913 0.343036 0.000001 0.344172 0.345299 +3 0.749031 0.014813 0.344172 0.000001 0.009315 +4 0.750158 0.015940 0.345299 0.009315 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f319591c4b4af00235fed7c3c12284e32a0d2ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.163950 0.463345 0.172495 0.172495 +1 0.163950 0.000001 0.422362 0.023136 0.023136 +2 0.463345 0.422362 0.000001 0.430906 0.430906 +3 0.172495 0.023136 0.430906 0.000001 0.000001 +4 0.172495 0.023136 0.430906 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..17dd8ee4b955cf9b26fd8119c007063cd9492b39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59149050 Before NNI: tree length is 0.59049213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.74484275 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000135_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000135_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..45ae9d1a2ce7498439816f83e1623da8e8795a1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000135_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05514575 Before NNI: tree length is 0.05514575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000137_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000137_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c6628b656597cdb8d333b0086f5dce6c91f23e9f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000137_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.138525 1.079670 0.209994 0.230364 +1 0.138525 0.000001 0.941144 0.071469 0.091839 +2 1.079670 0.941144 0.000001 0.910452 0.849305 +3 0.209994 0.071469 0.910452 0.000001 0.061146 +4 0.230364 0.091839 0.849305 0.061146 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000139_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000139_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9022eb65b2e7225448f5852da71b65f597997016 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000139_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.201679 0.267068 0.231652 0.205368 +1 0.201679 0.000001 0.212012 0.073547 0.047263 +2 0.267068 0.212012 0.000001 0.241984 0.215701 +3 0.231652 0.073547 0.241984 0.000001 0.058657 +4 0.205368 0.047263 0.215701 0.058657 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9540d27fc92bcca955f13c85b4a22e729b7e25a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.139431 0.249435 0.139581 0.139581 +1 0.139431 0.000001 0.249436 0.001731 0.001731 +2 0.249435 0.249436 0.000001 0.249585 0.249585 +3 0.139581 0.001731 0.249585 0.000001 0.000001 +4 0.139581 0.001731 0.249585 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000143_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000143_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..577d40ff41488bf4ea3e76f55163822be9a81566 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000143_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.96709537 Before NNI: tree length is 0.96709538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000146_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000146_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31f56302d713f9ed41abb271c1475be6f346e7fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000146_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18694423 Before NNI: tree length is 0.18694425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f0cc49bca4d7f7d9c6767080f0181915fd040c59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.122159 0.196205 0.126900 0.126900 +1 0.122159 0.000001 0.193046 0.016869 0.016869 +2 0.196205 0.193046 0.000001 0.197787 0.197787 +3 0.126900 0.016869 0.197787 0.000001 0.000001 +4 0.126900 0.016869 0.197787 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d1813853a8aa1aedc37d2bf1fe071a6bfa98076 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000148_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26651050 Before NNI: tree length is 0.26651050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7898f01bd7bd630bdbb14b5b2957c682d64fb1fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047263 0.132556 0.047150 0.046957 +1 0.047263 0.000001 0.131776 0.004751 0.002296 +2 0.132556 0.131776 0.000001 0.131662 0.131470 +3 0.047150 0.004751 0.131662 0.000001 0.004445 +4 0.046957 0.002296 0.131470 0.004445 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4695d02edfe8d65c0d0ffcb9e91b656ed0a6d2d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000149_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15911130 Before NNI: tree length is 0.15911125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000150_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000150_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04978c4034bbbd4a52f81565298fc1b97beaf72f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000150_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26515700 Before NNI: tree length is 0.26515700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000151_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000151_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0e2be1cca3fa5e714193a7535e9b36612760d240 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000151_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.836891 0.789885 0.848510 0.842062 +1 0.836891 0.000001 0.691081 0.019570 0.013122 +2 0.789885 0.691081 0.000001 0.702701 0.696253 +3 0.848510 0.019570 0.702701 0.000001 0.011853 +4 0.842062 0.013122 0.696253 0.011853 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4566863a856de4e742f9393c3572039ab4dccf43 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000154_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.36194150 Before NNI: tree length is 1.36194150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f10840a75c7dd10532aa37409b0122d9f852a61a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.794426 0.556217 0.794426 0.013228 +1 0.794426 0.000001 0.813600 0.000001 0.795927 +2 0.556217 0.813600 0.000001 0.813600 0.557718 +3 0.794426 0.000001 0.813600 0.000001 0.795927 +4 0.013228 0.795927 0.557718 0.795927 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02a4b494daf4f84b8edff0867b533eb2a023aa64 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000156_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08948650 Before NNI: tree length is 1.08948650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000158_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000158_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..66754909c50cd009ac408e7d156fc3d7039eb4ab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000158_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.403182 0.346952 0.397378 0.391531 +1 0.403182 0.000001 0.428875 0.013405 0.027392 +2 0.346952 0.428875 0.000001 0.423070 0.417223 +3 0.397378 0.013405 0.423070 0.000001 0.021588 +4 0.391531 0.027392 0.417223 0.021588 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000159_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000159_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..806df57459ddaa0bea2892b0a16c502128897eaa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000159_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.664289 1.756949 0.660513 0.687934 +1 0.664289 0.000001 1.161939 0.376939 0.404360 +2 1.756949 1.161939 0.000001 1.161525 1.090075 +3 0.660513 0.376939 1.161525 0.000001 0.092510 +4 0.687934 0.404360 1.090075 0.092510 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000161_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000161_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..475b6967bd90c3e7cdceec26ae974ce0ca997a63 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000161_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.67884583 Before NNI: tree length is 1.67884575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99001206 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000163_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000163_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1b8af30486d8eaa76d5a8abdedb606a27930a53 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000163_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23977575 Before NNI: tree length is 0.23977575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..60b168462e056f5572e0bb27486b9f76a17ea9a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084975 0.089613 0.086420 0.087524 +1 0.084975 0.000001 0.093491 0.001445 0.003037 +2 0.089613 0.093491 0.000001 0.094936 0.096040 +3 0.086420 0.001445 0.094936 0.000001 0.004482 +4 0.087524 0.003037 0.096040 0.004482 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000169_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000169_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b851dc56630de510e6dc4129df9949e3256857fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000169_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.441622 1.456016 1.396978 1.444679 +1 1.441622 0.000001 2.769540 0.206442 0.003058 +2 1.456016 2.769540 0.000001 2.724896 2.772597 +3 1.396978 0.206442 2.724896 0.000001 0.209499 +4 1.444679 0.003058 2.772597 0.209499 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000171_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000171_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..272345bb82c05fc7ea5070e3fe70a22b59253e83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000171_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17383000 Before NNI: tree length is 0.17383000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fae0546496e931ec2bf0d8df91d7f1b5b6e0bee8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000179_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53231650 Before NNI: tree length is 0.53231650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000182_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000182_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..41c15fbebb74979d41a6db18c7280dc1c886016a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000182_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041057 0.074352 0.041057 0.041057 +1 0.041057 0.000001 0.097086 0.000001 0.000001 +2 0.074352 0.097086 0.000001 0.097086 0.097086 +3 0.041057 0.000001 0.097086 0.000001 0.000001 +4 0.041057 0.000001 0.097086 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12136ea51f0725bb3995794531e05cb61cbee7a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000188_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23361350 Before NNI: tree length is 0.23361350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..31e457304d891a1eff4ea9b0b939501e0ce41f84 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.308598 0.463735 0.291804 0.302479 +1 0.308598 0.000001 0.416739 0.022377 0.025945 +2 0.463735 0.416739 0.000001 0.399945 0.410620 +3 0.291804 0.022377 0.399945 0.000001 0.016258 +4 0.302479 0.025945 0.410620 0.016258 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9322eeb573e78f9376efebabff55b72d0e37a57d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000189_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60724050 Before NNI: tree length is 0.60724050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000197_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000197_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2bf7c6ad53643c3ca86ba32863308a200f99ddbf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000197_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23149530 Before NNI: tree length is 0.23149525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f11af29e86f7119a3ae0587eb3a8f45dd21eb010 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000204_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.100954 0.134896 0.103708 0.103399 +1 0.100954 0.000001 0.186396 0.003413 0.018431 +2 0.134896 0.186396 0.000001 0.189151 0.188842 +3 0.103708 0.003413 0.189151 0.000001 0.021186 +4 0.103399 0.018431 0.188842 0.021186 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..06e51ee664d99b313302dd3a7cfab8b2389c1edb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.741966 0.685263 0.731899 0.731858 +1 0.741966 0.000001 0.321449 0.076336 0.076295 +2 0.685263 0.321449 0.000001 0.311382 0.311341 +3 0.731899 0.076336 0.311382 0.000001 0.005588 +4 0.731858 0.076295 0.311341 0.005588 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f995cf7cd0a68b98f7d99757329bd11cac56ce4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000207_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91024700 Before NNI: tree length is 0.91024700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000208_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000208_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa713d9bb353fa5991d0812898cae0b07b49db35 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000208_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31663525 Before NNI: tree length is 0.31663525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000209_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000209_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..934adc7f97d03ffa3d1444c4b50fac8fe65b296d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000209_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.765999 1.090782 0.751385 0.745364 +1 0.765999 0.000001 1.047620 0.042982 0.064207 +2 1.090782 1.047620 0.000001 1.033006 1.026986 +3 0.751385 0.042982 1.033006 0.000001 0.049592 +4 0.745364 0.064207 1.026986 0.049592 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5fd7950545cfcd5611587722798c55bcfc56d32b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000210_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26361171 Before NNI: tree length is 0.26361175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000212_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000212_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c347503242d5581e9261a40aecb6d8f000671ad4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000212_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21298765 Before NNI: tree length is 0.21298762 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..79a85dc24fd31907c293537fe8b9b48591dfaa88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000213_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79490425 Before NNI: tree length is 0.79490425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000218_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000218_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4358b8472dc08df08660536a55069b57cff7288e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000218_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44387100 Before NNI: tree length is 0.44387100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3015ec28a20cc0e2d7b183dcc04091210191d91b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.073280 0.155242 0.073280 0.073280 +1 0.073280 0.000001 0.096064 0.000001 0.000001 +2 0.155242 0.096064 0.000001 0.096064 0.096064 +3 0.073280 0.000001 0.096064 0.000001 0.000001 +4 0.073280 0.000001 0.096064 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..34443cf6cdd73504661bc8e67b7f4fd1b721a283 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000220_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16229400 Before NNI: tree length is 0.16229400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000221_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000221_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d55a13708b3f8ee175c2943c0d8de851761593e4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000221_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86287900 Before NNI: tree length is 0.86287900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b1a93cf07c6e69fcc4b975a81f2e11ed9fbfc33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.175325 0.534573 0.170973 0.174709 +1 0.175325 0.000001 0.588529 0.013484 0.004912 +2 0.534573 0.588529 0.000001 0.584177 0.587914 +3 0.170973 0.013484 0.584177 0.000001 0.012869 +4 0.174709 0.004912 0.587914 0.012869 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..489d4b5a967838d3df30795c330ba845e0db412e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000225_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65592791 Before NNI: tree length is 0.65592787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000228_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000228_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c335bff72957888a5cb64f9240dd0286d3dc0b3f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000228_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53705725 Before NNI: tree length is 0.53705725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8aeacb1dd3a15b2cb678f2c7a7d86c23583bfa8c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.78005875 Before NNI: tree length is 0.78005875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000233_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000233_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a3051f21c252d49655b6cdba4eab4d2af79dd4d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000233_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.248285 0.938641 0.264148 0.256823 +1 0.248285 0.000001 0.872306 0.040004 0.032679 +2 0.938641 0.872306 0.000001 0.888169 0.880844 +3 0.264148 0.040004 0.888169 0.000001 0.025487 +4 0.256823 0.032679 0.880844 0.025487 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7aaf4f8ed82b3db80d1fce52343f75525a73d115 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.111732 0.532661 0.109020 0.109020 +1 0.111732 0.000001 0.543618 0.008071 0.008071 +2 0.532661 0.543618 0.000001 0.540905 0.540905 +3 0.109020 0.008071 0.540905 0.000001 0.000001 +4 0.109020 0.008071 0.540905 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000236_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000236_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5bc8ae8ed7b91867de39106c3b17ac4bab7ea393 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000236_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37925132 Before NNI: tree length is 0.37925125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0355eebf5f56f4583221439ac230560f497ac5c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25842335 Before NNI: tree length is 0.25842338 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000249_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000249_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d96e8801b4fb7e1c4c48ba5f779c976798882c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000249_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.92359250 Before NNI: tree length is 0.92359250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ec273ed48afd2ceeb135683b4cf57a325acdf27 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.407947 1.075431 0.399601 0.440484 +1 0.407947 0.000001 1.025972 0.008346 0.032537 +2 1.075431 1.025972 0.000001 1.017626 1.058509 +3 0.399601 0.008346 1.017626 0.000001 0.040883 +4 0.440484 0.032537 1.058509 0.040883 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000256_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000256_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0122361258c5fd6ee27d685a2586c3b579dfb392 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000256_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15044611 Before NNI: tree length is 0.15044612 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000257_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000257_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5890c80576d21462148ace2b9c9441fa589a32e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000257_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12353350 Before NNI: tree length is 0.12353350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000259_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000259_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4efbc868557afe1e9d9174cdf3ca306fb3deba2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000259_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.10208725 Before NNI: tree length is 1.10208725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1422722a33f958a1632ce0a2642a8c8d1a3be800 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000261_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29731550 Before NNI: tree length is 0.29731550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b627c6b31bf49d04b3bddcaa65fe6b69c8bf3fe0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000266_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.569089 0.538925 0.569089 0.806012 +1 0.569089 0.000001 0.037046 0.000001 0.276435 +2 0.538925 0.037046 0.000001 0.037046 0.273969 +3 0.569089 0.000001 0.037046 0.000001 0.276435 +4 0.806012 0.276435 0.273969 0.276435 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000273_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000273_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e03705d08cb16ce5fa07eb3d02e2e6cf2d193db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000273_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17164925 Before NNI: tree length is 0.17164925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b37cac4bc772df5171b04271bfd45be254063bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77335700 Before NNI: tree length is 0.77335700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3f194a832739a88ba2025945159ee4b6f90da217 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025088 0.378385 0.020989 0.020989 +1 0.025088 0.000001 0.363319 0.009916 0.009916 +2 0.378385 0.363319 0.000001 0.363212 0.363212 +3 0.020989 0.009916 0.363212 0.000001 0.000001 +4 0.020989 0.009916 0.363212 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000278_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000278_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ca1476a96e80bcbbb794b8c962c0bc4e810f156 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000278_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15088360 Before NNI: tree length is 0.15088363 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000279_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000279_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9feea56f7d68cc063523c51db63c45565436a2f7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000279_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021084 0.030571 0.024591 0.022222 +1 0.021084 0.000001 0.023496 0.003507 0.003485 +2 0.030571 0.023496 0.000001 0.027003 0.024634 +3 0.024591 0.003507 0.027003 0.000001 0.006992 +4 0.022222 0.003485 0.024634 0.006992 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000280_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000280_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8cc8d40fbef19b1b250b7158e7779b955a5f544 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000280_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.49588549 Before NNI: tree length is 1.49588550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8330303ab967bb5c34a4c5158b4965b41325739 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055632 0.142659 0.055632 0.055632 +1 0.055632 0.000001 0.140319 0.000001 0.000001 +2 0.142659 0.140319 0.000001 0.140319 0.140319 +3 0.055632 0.000001 0.140319 0.000001 0.000001 +4 0.055632 0.000001 0.140319 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1479f97e7733a078536fd8d1e45e16331e18c3d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59659850 Before NNI: tree length is 0.59659850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000287_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000287_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8833099a61d81c94d6327e0e156e7c0e5731f9a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000287_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10664700 Before NNI: tree length is 0.10664700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd4aa7351d31d19e71e328317000857470f5b78b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.069988 0.208938 0.074360 0.076659 +1 0.069988 0.000001 0.227331 0.007988 0.010288 +2 0.208938 0.227331 0.000001 0.231703 0.234002 +3 0.074360 0.007988 0.231703 0.000001 0.005792 +4 0.076659 0.010288 0.234002 0.005792 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000296_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000296_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..437d30eb776f4290e99b32c1be4cf2e347cf8f5d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000296_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.210985 0.455048 0.225969 0.216474 +1 0.210985 0.000001 0.426271 0.030259 0.020764 +2 0.455048 0.426271 0.000001 0.441256 0.431760 +3 0.225969 0.030259 0.441256 0.000001 0.009495 +4 0.216474 0.020764 0.431760 0.009495 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000297_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000297_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3efa203f66b11912facdcbe75f192b9572790397 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000297_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011161 0.186791 0.011161 0.006782 +1 0.011161 0.000001 0.181655 0.000001 0.004813 +2 0.186791 0.181655 0.000001 0.181655 0.180443 +3 0.011161 0.000001 0.181655 0.000001 0.004813 +4 0.006782 0.004813 0.180443 0.004813 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000299_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000299_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a582ad39ffc2117f8ee47caf5269c1c53008c4ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000299_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.32609525 Before NNI: tree length is 2.32609525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000301_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000301_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e0b5b8d70c716890433bcb3e3e7d6535ad21469a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000301_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.167295 0.314872 0.178806 0.175975 +1 0.167295 0.000001 0.268787 0.026108 0.023277 +2 0.314872 0.268787 0.000001 0.280297 0.277466 +3 0.178806 0.026108 0.280297 0.000001 0.002830 +4 0.175975 0.023277 0.277466 0.002830 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000303_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000303_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b9bbe81e8dd9976f953a7466fdb3c66e8856595 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000303_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.38354875 Before NNI: tree length is 1.38354875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000310_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000310_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31574889019d2752114fd8c62d4a9409e925ddbb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000310_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49247400 Before NNI: tree length is 0.49247400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000314_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000314_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3019cbd60a0edc5d6a0b3ce26348fe361f99cac9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000314_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.238064 0.147920 0.238064 0.237021 +1 0.238064 0.000001 0.207738 0.000001 0.001042 +2 0.147920 0.207738 0.000001 0.207738 0.206696 +3 0.238064 0.000001 0.207738 0.000001 0.001042 +4 0.237021 0.001042 0.206696 0.001042 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dac24211f87c93738a0a68e9c0949f7f6b986a13 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000316_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36296239 Before NNI: tree length is 0.36296238 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a64ca0dcde6125ebb3a2c9b876459438f2f739f5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.209431 0.673379 0.209431 0.166443 +1 0.209431 0.000001 0.531447 0.000001 0.164891 +2 0.673379 0.531447 0.000001 0.531447 0.628838 +3 0.209431 0.000001 0.531447 0.000001 0.164891 +4 0.166443 0.164891 0.628838 0.164891 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3098520aeddec37ae2e691874e45fca8c60b2414 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000320_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76808023 Before NNI: tree length is 0.76808025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad691a99ed4d109feda708df4c9f883898de5dde --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000322_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.342916 0.343206 0.358488 0.342916 +1 0.342916 0.000001 0.343314 0.016967 0.000001 +2 0.343206 0.343314 0.000001 0.358887 0.343314 +3 0.358488 0.016967 0.358887 0.000001 0.016967 +4 0.342916 0.000001 0.343314 0.016967 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000326_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000326_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3f5a0e22432d450c1b024bfc75ebbe6b0c1309b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000326_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.483720 0.678832 0.488189 0.488558 +1 0.483720 0.000001 0.741048 0.028869 0.009569 +2 0.678832 0.741048 0.000001 0.745516 0.745885 +3 0.488189 0.028869 0.745516 0.000001 0.033706 +4 0.488558 0.009569 0.745885 0.033706 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000330_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000330_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e142323edb781b6e99270d6a1cb6301a92ed810d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000330_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.301826 0.268739 0.301826 0.301826 +1 0.301826 0.000001 0.161670 0.000001 0.000001 +2 0.268739 0.161670 0.000001 0.161670 0.161670 +3 0.301826 0.000001 0.161670 0.000001 0.000001 +4 0.301826 0.000001 0.161670 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a40a31b039f2978bb29cfff4e4ec50a654f1ed5b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045355 0.538866 0.047068 0.046569 +1 0.045355 0.000001 0.532443 0.031412 0.030912 +2 0.538866 0.532443 0.000001 0.534156 0.533656 +3 0.047068 0.031412 0.534156 0.000001 0.001994 +4 0.046569 0.030912 0.533656 0.001994 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000337_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000337_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1c95b35db6ac901c953482f8b84286d3f124002 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000337_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.85073625 Before NNI: tree length is 0.85073625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000339_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000339_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..16de3ddbbfad6437303eebbeb4255a21ade150a4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000339_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69467250 Before NNI: tree length is 0.69467250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000342_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000342_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9ddfdcc7fc4bee481ea6843f8b2187812a2ce60 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000342_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25128600 Before NNI: tree length is 0.25128600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000345_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000345_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..39fc2623f7754ae794b3c914ff87d73d39c76ce8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000345_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.644789 0.638618 0.630152 0.648169 +1 0.644789 0.000001 0.512029 0.070415 0.040764 +2 0.638618 0.512029 0.000001 0.497393 0.515409 +3 0.630152 0.070415 0.497393 0.000001 0.073795 +4 0.648169 0.040764 0.515409 0.073795 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000346_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000346_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71066208237491cf8c98341f03deef8c5d9a4ef5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000346_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.319046 0.331796 0.356289 0.321333 +1 0.319046 0.000001 0.291666 0.063642 0.021147 +2 0.331796 0.291666 0.000001 0.328909 0.293953 +3 0.356289 0.063642 0.328909 0.000001 0.065928 +4 0.321333 0.021147 0.293953 0.065928 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000351_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000351_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b0e44329a6ae2763ddcf2a1d307f0c1c0c19b8ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000351_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.451032 0.290362 0.459369 0.455796 +1 0.451032 0.000001 0.349815 0.016323 0.012750 +2 0.290362 0.349815 0.000001 0.358152 0.354579 +3 0.459369 0.016323 0.358152 0.000001 0.011599 +4 0.455796 0.012750 0.354579 0.011599 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..97164d1b90ad289b6f6a3aef43aafa34d9dfb4f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000357_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17032125 Before NNI: tree length is 0.17032125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2ce3511e385658d39761deccde8c6e783afa3d6d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000358_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.136175 0.142776 0.139352 0.134735 +1 0.136175 0.000001 0.017418 0.009375 0.011771 +2 0.142776 0.017418 0.000001 0.020595 0.018371 +3 0.139352 0.009375 0.020595 0.000001 0.014948 +4 0.134735 0.011771 0.018371 0.014948 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000362_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000362_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af0367244e1c46259ba3545994526157b01bd844 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000362_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.312827 0.379420 0.303392 0.303392 +1 0.312827 0.000001 0.417113 0.025313 0.025313 +2 0.379420 0.417113 0.000001 0.407678 0.407678 +3 0.303392 0.025313 0.407678 0.000001 0.000001 +4 0.303392 0.025313 0.407678 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000366_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000366_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72c43d287f2291f245b3dbc91775ad4a31afcf80 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000366_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64830773 Before NNI: tree length is 0.64830775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94e9afa3471525a6847b8301bc8a5553df48633a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18768963 Before NNI: tree length is 0.18768962 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000369_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000369_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..469d6e372d84ccf73ea865ab4f614cc3cf61ff21 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000369_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.189873 0.265442 0.188894 0.189126 +1 0.189873 0.000001 0.288919 0.003670 0.007224 +2 0.265442 0.288919 0.000001 0.287941 0.288172 +3 0.188894 0.003670 0.287941 0.000001 0.006246 +4 0.189126 0.007224 0.288172 0.006246 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a8dc97f2b2666cbb9747a2beda36ceab95f7694 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000372_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.073803 0.408906 0.093204 0.062233 +1 0.073803 0.000001 0.387025 0.076227 0.080811 +2 0.408906 0.387025 0.000001 0.411330 0.415913 +3 0.093204 0.076227 0.411330 0.000001 0.100212 +4 0.062233 0.080811 0.415913 0.100212 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000373_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000373_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3e20e311a7c1a7476ff0c4b6bb1dae1a760dd06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000373_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19181857 Before NNI: tree length is 0.19181850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000382_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000382_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c9f212be42cfc4318fecef9c3db769ac968a8dd3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000382_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36664790 Before NNI: tree length is 0.36664788 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46a56bc8cef163f2ee95477078beb80f1ef4b8b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.074563 0.148634 0.074563 0.074563 +1 0.074563 0.000001 0.116982 0.000001 0.000001 +2 0.148634 0.116982 0.000001 0.116982 0.116982 +3 0.074563 0.000001 0.116982 0.000001 0.000001 +4 0.074563 0.000001 0.116982 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..34ca6af73db6ffe4848d6abd482fd6f322e7d3b0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000393_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17009050 Before NNI: tree length is 0.17009050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ce4a843f9842549b97e99c4d2f7ebea474d04045 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000395_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044137 0.036756 0.044137 0.044137 +1 0.044137 0.000001 0.051998 0.000001 0.000001 +2 0.036756 0.051998 0.000001 0.051998 0.051998 +3 0.044137 0.000001 0.051998 0.000001 0.000001 +4 0.044137 0.000001 0.051998 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000406_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000406_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2bdaeec98c8b6fa2b4249517db1e3cc4cde96edf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000406_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037259 0.092435 0.039832 0.033550 +1 0.037259 0.000001 0.088163 0.011960 0.005679 +2 0.092435 0.088163 0.000001 0.090735 0.084453 +3 0.039832 0.011960 0.090735 0.000001 0.006344 +4 0.033550 0.005679 0.084453 0.006344 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000410_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000410_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c14edd552ae4f2e13feeb44e5989d6cb43bdc4a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000410_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.98682100 Before NNI: tree length is 1.98682100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e0cdbe54c3b20bf150ca45fac09d62ef1ad76dc2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023161 0.039112 0.023161 0.023161 +1 0.023161 0.000001 0.060453 0.000001 0.000001 +2 0.039112 0.060453 0.000001 0.060453 0.060453 +3 0.023161 0.000001 0.060453 0.000001 0.000001 +4 0.023161 0.000001 0.060453 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd5235aab0571a335eee653468a8987555aa7bff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000412_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06136400 Before NNI: tree length is 0.06136400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000413_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000413_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0750f63a67fc4b14b6f90d2825f62d5f54688de3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000413_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.113951 0.233539 0.116223 0.113130 +1 0.113951 0.000001 0.183475 0.008097 0.016060 +2 0.233539 0.183475 0.000001 0.185747 0.182654 +3 0.116223 0.008097 0.185747 0.000001 0.018333 +4 0.113130 0.016060 0.182654 0.018333 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000415_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000415_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d5ccaa33c70c8a5ffda7eac9eb91b8a679b67c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000415_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20766580 Before NNI: tree length is 0.20766575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d44202249b0231de2c3142eca9de1f7ce2832881 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060835 0.257387 0.063608 0.063339 +1 0.060835 0.000001 0.256318 0.023918 0.012329 +2 0.257387 0.256318 0.000001 0.259092 0.258822 +3 0.063608 0.023918 0.259092 0.000001 0.026422 +4 0.063339 0.012329 0.258822 0.026422 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a2b04257f1242f032b01e2758a98337e239353cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068209 0.075204 0.068209 0.068209 +1 0.068209 0.000001 0.065936 0.000001 0.000001 +2 0.075204 0.065936 0.000001 0.065936 0.065936 +3 0.068209 0.000001 0.065936 0.000001 0.000001 +4 0.068209 0.000001 0.065936 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a36b23b4908f13cd35d8d94319679f05c228d42 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000423_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10467550 Before NNI: tree length is 0.10467550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000429_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000429_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8d14bafd6409dd4b2ea2bf05f858ea4f764df61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000429_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.145423 0.732793 0.145423 0.145423 +1 0.145423 0.000001 0.724965 0.000001 0.000001 +2 0.732793 0.724965 0.000001 0.724965 0.724965 +3 0.145423 0.000001 0.724965 0.000001 0.000001 +4 0.145423 0.000001 0.724965 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000431_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000431_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e4ced30ae6a18845be6f0daee9eaf2c64a1463c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000431_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24961823 Before NNI: tree length is 0.24961825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c805ea40579899231541d8805dfc3e54857df3a4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000436_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.338012 0.582257 0.338136 0.316041 +1 0.338012 0.000001 0.593373 0.016464 0.032225 +2 0.582257 0.593373 0.000001 0.593496 0.571402 +3 0.338136 0.016464 0.593496 0.000001 0.032349 +4 0.316041 0.032225 0.571402 0.032349 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000438_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000438_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dfa39226d52fbd5af1cb144768191342a4838b7b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000438_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.75556750 Before NNI: tree length is 0.75556750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55ebf422f82ab13ced2b3ade0e4c56123a425398 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.392525 2.263424 0.392525 0.392525 +1 0.392525 0.000001 2.304240 0.000001 0.000001 +2 2.263424 2.304240 0.000001 2.304240 2.304240 +3 0.392525 0.000001 2.304240 0.000001 0.000001 +4 0.392525 0.000001 2.304240 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..501a9112ef7772d926ad1db8e4fc64708ab3a8f1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000441_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.48009550 Before NNI: tree length is 2.48009550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000442_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000442_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c0546d950db7a3a580445412366499fff0178c79 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000442_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.843296 1.234826 0.817336 0.811726 +1 0.843296 0.000001 1.173512 0.541952 0.536343 +2 1.234826 1.173512 0.000001 1.147552 1.141943 +3 0.817336 0.541952 1.147552 0.000001 0.016647 +4 0.811726 0.536343 1.141943 0.016647 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd90469aae0e98eb69f421933145fc0f58ac2a9c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.346466 0.643996 0.356473 0.348860 +1 0.346466 0.000001 0.491903 0.010006 0.008154 +2 0.643996 0.491903 0.000001 0.501909 0.494296 +3 0.356473 0.010006 0.501909 0.000001 0.018160 +4 0.348860 0.008154 0.494296 0.018160 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000451_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000451_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac210ef4ba886632d0642cb924dcd3946745658a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000451_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52809100 Before NNI: tree length is 0.52809100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000452_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000452_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..77d1f8fed07649202109e60443816eea06091d12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000452_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76258372 Before NNI: tree length is 0.76258375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c67cfd30b67c2f018ea969636a7ad7960773259 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.817416 1.078408 0.802751 0.808587 +1 0.817416 0.000001 1.067757 0.042727 0.026984 +2 1.078408 1.067757 0.000001 1.053092 1.058928 +3 0.802751 0.042727 1.053092 0.000001 0.033899 +4 0.808587 0.026984 1.058928 0.033899 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e19bc3149c9abcf562a26c93dca23bb98aa5d74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000453_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.50489925 Before NNI: tree length is 1.50489925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000455_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000455_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3388ac38906f18fb66dc60758472265a19aacd34 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000455_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44137236 Before NNI: tree length is 0.44137238 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d0ae83c66e3384b4da5059ac9e8a5b255d3ab26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081922 0.307899 0.084403 0.076187 +1 0.081922 0.000001 0.291886 0.004243 0.010478 +2 0.307899 0.291886 0.000001 0.294367 0.286151 +3 0.084403 0.004243 0.294367 0.000001 0.012960 +4 0.076187 0.010478 0.286151 0.012960 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000460_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000460_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3800495e44ae3992f8bf4ab4b5dc1d05feb15e5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000460_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.564722 0.552991 0.579034 0.563930 +1 0.564722 0.000001 0.491158 0.020783 0.005679 +2 0.552991 0.491158 0.000001 0.505471 0.490366 +3 0.579034 0.020783 0.505471 0.000001 0.015104 +4 0.563930 0.005679 0.490366 0.015104 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f5744e2fb159d1d10502ca2e6652b0648620281d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000462_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086608 0.324270 0.086608 0.080655 +1 0.086608 0.000001 0.332989 0.000001 0.007279 +2 0.324270 0.332989 0.000001 0.332989 0.327036 +3 0.086608 0.000001 0.332989 0.000001 0.007279 +4 0.080655 0.007279 0.327036 0.007279 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000463_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000463_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..59c31e6f6debfef3abfcfb04b75c757d39c65d91 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000463_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.158900 0.340094 0.159576 0.156186 +1 0.158900 0.000001 0.355521 0.009974 0.011742 +2 0.340094 0.355521 0.000001 0.356198 0.352807 +3 0.159576 0.009974 0.356198 0.000001 0.012419 +4 0.156186 0.011742 0.352807 0.012419 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3805305d613faabbac7dea2edc5e5fa19ce8becf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.228908 0.353082 0.216795 0.216343 +1 0.228908 0.000001 0.346203 0.012113 0.012565 +2 0.353082 0.346203 0.000001 0.334090 0.333637 +3 0.216795 0.012113 0.334090 0.000001 0.000453 +4 0.216343 0.012565 0.333637 0.000453 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c1e655c96a78c2704f862fe45af795b8b7f35e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000468_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46409653 Before NNI: tree length is 0.46409650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000472_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000472_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e8bf60773e60e33b712661d6f961524732934df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000472_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.229099 0.218647 0.224451 0.227244 +1 0.229099 0.000001 0.209973 0.004648 0.002795 +2 0.218647 0.209973 0.000001 0.205325 0.208118 +3 0.224451 0.004648 0.205325 0.000001 0.002793 +4 0.227244 0.002795 0.208118 0.002793 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000475_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000475_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f3417a19e442106f4a6de4d00ed22f75a7fc127 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000475_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77177970 Before NNI: tree length is 0.77177975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000477_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000477_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..60e46994643cb90d595bac02aac96ad95a9994dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000477_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51387550 Before NNI: tree length is 0.51387550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000480_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000480_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..414eb32fa1e81242d16756d3aea9e1ee2ad3e181 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000480_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22362325 Before NNI: tree length is 0.22362325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000482_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000482_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3391f3ce6d377e5dcadb9f3630c5baf34b8f6969 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000482_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.992872 0.986029 1.010667 1.010667 +1 0.992872 0.000001 0.465642 0.490279 0.490279 +2 0.986029 0.465642 0.000001 0.333087 0.333087 +3 1.010667 0.490279 0.333087 0.000001 0.000001 +4 1.010667 0.490279 0.333087 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4ab8f5319006df3f826179749ba288d415a79610 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.069094 0.145788 0.199643 0.196881 +1 0.069094 0.000001 0.138567 0.192422 0.189659 +2 0.145788 0.138567 0.000001 0.119921 0.117159 +3 0.199643 0.192422 0.119921 0.000001 0.006029 +4 0.196881 0.189659 0.117159 0.006029 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0cd18cc075006f6f21e03ae65eef0035f138770b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000483_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26524590 Before NNI: tree length is 0.26524588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000484_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000484_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d85b8d652d7d048cc99000add2ec439666dea2e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000484_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033561 0.127093 0.126756 0.130151 +1 0.033561 0.000001 0.138691 0.138354 0.141749 +2 0.127093 0.138691 0.000001 0.013002 0.016397 +3 0.126756 0.138354 0.013002 0.000001 0.003519 +4 0.130151 0.141749 0.016397 0.003519 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff1dc4aba1a1f359f1a537bc2552d91aaebfd295 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000486_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33100266 Before NNI: tree length is 0.33100262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000488_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000488_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..636225467fe5e22abd4120d6b7684d1658e0ac14 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000488_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36096950 Before NNI: tree length is 0.36096950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000493_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000493_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f1a96faaedc855dd4fa3284e4cb95d778be3ad3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000493_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08158300 Before NNI: tree length is 0.08158300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..454ac3ed7ef4c9a5c78d52b803a8c70b051f222f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013990 0.037668 0.010457 0.022865 +1 0.013990 0.000001 0.032450 0.005239 0.019306 +2 0.037668 0.032450 0.000001 0.028121 0.042984 +3 0.010457 0.005239 0.028121 0.000001 0.015773 +4 0.022865 0.019306 0.042984 0.015773 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd3b70f88e4e40cee8f9c10162c51e20c1a28de9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000499_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05659950 Before NNI: tree length is 0.05659950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d15ec6bf7802d0d90a09caca7d517266a49cd01f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.073237 0.096580 0.085186 0.085186 +1 0.073237 0.000001 0.061035 0.049641 0.049641 +2 0.096580 0.061035 0.000001 0.041424 0.041424 +3 0.085186 0.049641 0.041424 0.000001 0.000001 +4 0.085186 0.049641 0.041424 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..917a4f55f01cc600771fda971193b57b9a6b952d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000502_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13044150 Before NNI: tree length is 0.13044150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000503_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000503_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4b59445f1882880da442af5670eafd2e4641afb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000503_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55181050 Before NNI: tree length is 0.55181050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000506_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000506_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dabe8d359b76be5baf96aa13e15170990c8b72c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000506_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.295915 0.783452 0.307401 0.352898 +1 0.295915 0.000001 0.726605 0.011486 0.060124 +2 0.783452 0.726605 0.000001 0.738091 0.783588 +3 0.307401 0.011486 0.738091 0.000001 0.071611 +4 0.352898 0.060124 0.783588 0.071611 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000509_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000509_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5708f76a181ac7cfb01643e2f9dd914adbac7260 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000509_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48541438 Before NNI: tree length is 0.48541438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000512_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000512_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..17867bf0f407bbcfa002ba6f643aa66ab686e9f3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000512_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.618285 1.369418 0.618285 0.615501 +1 0.618285 0.000001 0.860788 0.000001 0.003060 +2 1.369418 0.860788 0.000001 0.860788 0.858004 +3 0.618285 0.000001 0.860788 0.000001 0.003060 +4 0.615501 0.003060 0.858004 0.003060 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7b33f78b302c4b85b23d8719afe2c2684bebd6d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000513_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.206325 0.428386 0.202276 0.202000 +1 0.206325 0.000001 0.490043 0.004049 0.011719 +2 0.428386 0.490043 0.000001 0.485994 0.485718 +3 0.202276 0.004049 0.485994 0.000001 0.007670 +4 0.202000 0.011719 0.485718 0.007670 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000514_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000514_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..027b5205aea48fa1e967e2d70abe8b2699ca3134 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000514_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53024850 Before NNI: tree length is 0.53024850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000517_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000517_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6771ce83a5a3a76939bdcee29f83da32dd59b2f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000517_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.500547 0.902746 0.500547 0.499170 +1 0.500547 0.000001 1.037844 0.000001 0.006739 +2 0.902746 1.037844 0.000001 1.037844 1.036467 +3 0.500547 0.000001 1.037844 0.000001 0.006739 +4 0.499170 0.006739 1.036467 0.006739 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0e1dff037bb900c8e7c4157d01eb3f2a123aa524 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034514 0.031280 0.034514 0.030456 +1 0.034514 0.000001 0.017535 0.000001 0.013667 +2 0.031280 0.017535 0.000001 0.017535 0.013477 +3 0.034514 0.000001 0.017535 0.000001 0.013667 +4 0.030456 0.013667 0.013477 0.013667 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f90b22297e9cc4c6035b475e00b23ff6725f854 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000521_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04646950 Before NNI: tree length is 0.04646950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000522_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000522_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74bd40d7a9907e08b1d2f5fb31550be77ec84239 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000522_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013821 0.011997 0.013821 0.021840 +1 0.013821 0.000001 0.018682 0.000001 0.014485 +2 0.011997 0.018682 0.000001 0.018682 0.026701 +3 0.013821 0.000001 0.018682 0.000001 0.014485 +4 0.021840 0.014485 0.026701 0.014485 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000523_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000523_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be08fda7d1ac144578251f80b853faad7bc62dc4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000523_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020878 0.018698 0.020878 0.010079 +1 0.020878 0.000001 0.012894 0.000001 0.010799 +2 0.018698 0.012894 0.000001 0.012894 0.008620 +3 0.020878 0.000001 0.012894 0.000001 0.010799 +4 0.010079 0.010799 0.008620 0.010799 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000524_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000524_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2dce7c8d2699cfe66fc405013c91e38ad91e6beb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000524_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02285600 Before NNI: tree length is 0.02285600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000529_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000529_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4196101a689114af886802f74ade233449091cf4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000529_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.266773 0.193792 0.259741 0.424151 +1 0.266773 0.000001 0.265227 0.007032 0.173314 +2 0.193792 0.265227 0.000001 0.258194 0.422604 +3 0.259741 0.007032 0.258194 0.000001 0.166281 +4 0.424151 0.173314 0.422604 0.166281 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d4cde5eaf79ede8a723c9a9d87a426433d31335d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.276044 0.249140 0.268987 0.268987 +1 0.276044 0.000001 0.294742 0.020117 0.020117 +2 0.249140 0.294742 0.000001 0.287685 0.287685 +3 0.268987 0.020117 0.287685 0.000001 0.000001 +4 0.268987 0.020117 0.287685 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc52816af93a02b15d64df8fe91e0fcc009bf867 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000538_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.112452 0.170237 0.113510 0.113510 +1 0.112452 0.000001 0.085363 0.006485 0.006485 +2 0.170237 0.085363 0.000001 0.086422 0.086422 +3 0.113510 0.006485 0.086422 0.000001 0.000001 +4 0.113510 0.006485 0.086422 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d57b396b958e37a217876de5130cc3a68db68ce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86778150 Before NNI: tree length is 0.86778150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c219e761bcb0f7ca898cc716813bbb58315cd6f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15159100 Before NNI: tree length is 0.15159100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d90e76e8d5d1ea4bf3ebf6e73a9dd1fc562bb1e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000552_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.503435 0.517710 0.506360 0.501701 +1 0.503435 0.000001 0.069666 0.034657 0.064900 +2 0.517710 0.069666 0.000001 0.072591 0.079175 +3 0.506360 0.034657 0.072591 0.000001 0.067825 +4 0.501701 0.064900 0.079175 0.067825 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b9a0ea23ba7b187d7e5b492d3cfa48e8daa79a13 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049715 0.041816 0.037586 0.033823 +1 0.049715 0.000001 0.036821 0.036248 0.016061 +2 0.041816 0.036821 0.000001 0.028349 0.020928 +3 0.037586 0.036248 0.028349 0.000001 0.020356 +4 0.033823 0.016061 0.020928 0.020356 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb21cf3afd4429b7c2200988461dc015c1b6c1ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000553_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07631967 Before NNI: tree length is 0.07631975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..587298d7d92e4dfdfe3aa502b6f4e941b0ba2e49 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.070055 0.174823 0.045819 0.056946 +1 0.070055 0.000001 0.125744 0.036009 0.028249 +2 0.174823 0.125744 0.000001 0.140777 0.133017 +3 0.045819 0.036009 0.140777 0.000001 0.022901 +4 0.056946 0.028249 0.133017 0.022901 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c25b13eb1f8d27fa385a9336ce1b274e67c33c1b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000557_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19876775 Before NNI: tree length is 0.19876775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000559_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000559_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..861e309ebe255a05e3304fda4dee23e8158b1e70 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000559_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10069050 Before NNI: tree length is 0.10069050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000560_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000560_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f57db788779278fb1d55b25516112ad9434b53cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000560_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045373 0.045786 0.041280 0.046224 +1 0.045373 0.000001 0.039230 0.004093 0.011850 +2 0.045786 0.039230 0.000001 0.035137 0.040080 +3 0.041280 0.004093 0.035137 0.000001 0.007757 +4 0.046224 0.011850 0.040080 0.007757 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5638f7a80172cab2b90790162640e4d301fa804d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000566_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.262636 0.564233 0.251234 0.251234 +1 0.262636 0.000001 0.550204 0.026864 0.026864 +2 0.564233 0.550204 0.000001 0.538802 0.538802 +3 0.251234 0.026864 0.538802 0.000001 0.000001 +4 0.251234 0.026864 0.538802 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000567_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000567_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6b61ea13a2ac9c76a8d4d91818ef8c41262b8dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000567_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.729097 1.040100 0.722932 0.733384 +1 0.729097 0.000001 0.569705 0.024381 0.031698 +2 1.040100 0.569705 0.000001 0.563540 0.573992 +3 0.722932 0.024381 0.563540 0.000001 0.028667 +4 0.733384 0.031698 0.573992 0.028667 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000568_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000568_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0906719f7fbd7b6abf45a33b17cfdf9e762a450d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000568_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26930423 Before NNI: tree length is 0.26930425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000570_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000570_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63f1b07a0db5702b4ae9f7ffc066e3cf99dda219 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000570_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09676511 Before NNI: tree length is 0.09676513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000571_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000571_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..14333fa5ecf5df86c4e60fadc76889bcb413cf00 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000571_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059755 0.042751 0.062174 0.053373 +1 0.059755 0.000001 0.035020 0.015529 0.015410 +2 0.042751 0.035020 0.000001 0.037438 0.028638 +3 0.062174 0.015529 0.037438 0.000001 0.017829 +4 0.053373 0.015410 0.028638 0.017829 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000574_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000574_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..162bbf12877a855732d62240bb28f9a9c630b6af --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000574_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.672984 1.118784 0.692042 0.688958 +1 0.672984 0.000001 1.017149 0.125356 0.122271 +2 1.118784 1.017149 0.000001 1.036207 1.033123 +3 0.692042 0.125356 1.036207 0.000001 0.108135 +4 0.688958 0.122271 1.033123 0.108135 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8218cd9cbd665d8815b688bc934d4f34c2602dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46936100 Before NNI: tree length is 0.46936100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000584_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000584_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c680840c7d15e39c31503badd60987b5dcac3700 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000584_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.108341 0.359573 0.106999 0.106999 +1 0.108341 0.000001 0.381804 0.010982 0.010982 +2 0.359573 0.381804 0.000001 0.380462 0.380462 +3 0.106999 0.010982 0.380462 0.000001 0.000001 +4 0.106999 0.010982 0.380462 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..475ff3d42252be7af31688bedcb9d7cf765cb8ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081070 0.536676 0.083843 0.081881 +1 0.081070 0.000001 0.536846 0.025564 0.023603 +2 0.536676 0.536846 0.000001 0.539619 0.537658 +3 0.083843 0.025564 0.539619 0.000001 0.011985 +4 0.081881 0.023603 0.537658 0.011985 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a90d1ed83b9bbf49eb3bd6fa2fdbdb9846375ea --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000587_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59647641 Before NNI: tree length is 0.59647637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000589_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000589_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e53f2be7e0b28e1b9defbb8b83c4b38bc57a84ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000589_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039949 0.904294 0.079329 0.029123 +1 0.039949 0.000001 0.904609 0.096259 0.019274 +2 0.904294 0.904609 0.000001 0.960604 0.893784 +3 0.079329 0.096259 0.960604 0.000001 0.085434 +4 0.029123 0.019274 0.893784 0.085434 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000591_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000591_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f57dbe6cfe511608473ef72091499891fa08038c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000591_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 2.113381 0.034060 0.033473 0.027926 +1 2.113381 0.000001 2.107245 2.130813 2.125265 +2 0.034060 2.107245 0.000001 0.051491 0.045944 +3 0.033473 2.130813 0.051491 0.000001 0.031245 +4 0.027926 2.125265 0.045944 0.031245 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000594_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000594_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f22e2f04f9a9ac577b98861545e1f284878aca40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000594_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52444864 Before NNI: tree length is 0.52444863 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000595_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000595_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c2294ecf0259d0929e9a6dff650a1aad85266e3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000595_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04661519 Before NNI: tree length is 0.04661525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000596_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000596_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7de4f19dd07fae8fe2a36445dc993208ee540a37 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000596_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.089687 0.089793 0.089908 0.091096 +1 0.089687 0.000001 0.020303 0.018269 0.019456 +2 0.089793 0.020303 0.000001 0.020525 0.021712 +3 0.089908 0.018269 0.020525 0.000001 0.002913 +4 0.091096 0.019456 0.021712 0.002913 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad2c3e5038c8f6753e1155302d57cc5d4e8cc2cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.95458500 Before NNI: tree length is 0.95458500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000601_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000601_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6434320b4d0d4742476da58933f6e170ad70f6d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000601_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53202125 Before NNI: tree length is 0.53202125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000604_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000604_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e46f3c554191d2e810a1e086721de2f687b4096 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000604_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45334463 Before NNI: tree length is 0.45334463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000606_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000606_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c634b75a3891da88831be55c7262b561c714fafb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000606_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.277377 0.253497 0.278001 0.286154 +1 0.277377 0.000001 0.269980 0.000624 0.008777 +2 0.253497 0.269980 0.000001 0.270605 0.278757 +3 0.278001 0.000624 0.270605 0.000001 0.008153 +4 0.286154 0.008777 0.278757 0.008153 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000608_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000608_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..446d9fee2911e26dfad454be2132aa1f67d19b11 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000608_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53281039 Before NNI: tree length is 0.53281037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000609_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000609_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a7f63ee8ec80843e13bda129adf1fd914981df4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000609_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08297475 Before NNI: tree length is 0.08297475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55e012d6cb4a104ac5c646acdff49a2b3a5b2fcb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.627899 1.604237 1.619933 1.667968 +1 1.627899 0.000001 0.185971 0.020713 0.040069 +2 1.604237 0.185971 0.000001 0.178005 0.226040 +3 1.619933 0.020713 0.178005 0.000001 0.060782 +4 1.667968 0.040069 0.226040 0.060782 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bcc44ad9080aebbe45659c05c9346a645193dcc2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000611_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.75549600 Before NNI: tree length is 1.75549600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..65d4b37eb3cdf332d21c1dea44735edcf07b3cc0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29465250 Before NNI: tree length is 0.29465250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac2b71aee00527a519f99cc39063df7e9ce9cbc3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000613_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25637650 Before NNI: tree length is 0.25637650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a8626f1eedf677ba83456502ecc8632bd48b893 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060744 0.275624 0.057558 0.047056 +1 0.060744 0.000001 0.282742 0.013258 0.014391 +2 0.275624 0.282742 0.000001 0.279555 0.269053 +3 0.057558 0.013258 0.279555 0.000001 0.011205 +4 0.047056 0.014391 0.269053 0.011205 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..25deb83706f241cf7023bc4e0e14b6fb5a25ffbd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000615_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31494215 Before NNI: tree length is 0.31494213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000617_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000617_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b0ab0b0c3bfbd540db8149c5c38b10306c6bdd40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000617_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.361629 0.307756 0.348510 0.349695 +1 0.361629 0.000001 0.287394 0.034334 0.035519 +2 0.307756 0.287394 0.000001 0.274275 0.275460 +3 0.348510 0.034334 0.274275 0.000001 0.006873 +4 0.349695 0.035519 0.275460 0.006873 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bb898e37af088f4171dc4271d3fd7336fc3bded --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000618_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03557617 Before NNI: tree length is 0.03557613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1f1c41cb80be46d23b959fb9aa734394a56e2827 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.179413 0.255090 0.137395 0.176491 +1 0.179413 0.000001 0.318240 0.053828 0.023501 +2 0.255090 0.318240 0.000001 0.276223 0.315318 +3 0.137395 0.053828 0.276223 0.000001 0.050906 +4 0.176491 0.023501 0.315318 0.050906 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d22c1cd4cdf298e2ab0a39328db7f04ad992aee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000625_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39256620 Before NNI: tree length is 0.39256625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000627_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000627_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a28a2e151957dc5d2a5b9d994572f30ecfd59b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000627_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.84688120 Before NNI: tree length is 0.84688125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000628_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000628_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..98c95b761dfc7064bb78abc0884f20d7c955926b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000628_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31430930 Before NNI: tree length is 0.31430925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000630_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000630_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..371e9dbb253027ed8521e6f487a7ed4bb46b616a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000630_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39555000 Before NNI: tree length is 0.39555000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000631_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000631_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6bd79554970ac27bb56bedcd1d5eaf7a952f4aa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000631_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14538550 Before NNI: tree length is 0.14538550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000637_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000637_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..288ed2f0e8d8bf62ad965dc40e213b1c55fb7f12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000637_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.166342 0.356039 0.124197 0.166342 +1 0.166342 0.000001 0.433850 0.099173 0.000001 +2 0.356039 0.433850 0.000001 0.391705 0.433850 +3 0.124197 0.099173 0.391705 0.000001 0.099173 +4 0.166342 0.000001 0.433850 0.099173 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000640_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000640_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6258d00b89b6e6056e10cc7a461db21652cf4a6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000640_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47121175 Before NNI: tree length is 0.47121175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28ef18acc1eb00234d4f750bca6a657e23d7a584 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44434075 Before NNI: tree length is 0.44434075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..94b7bce372553affa10f3b70220717fdfeae2658 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.342284 0.555861 0.348718 0.313491 +1 0.342284 0.000001 0.364234 0.032725 0.088207 +2 0.555861 0.364234 0.000001 0.370668 0.335441 +3 0.348718 0.032725 0.370668 0.000001 0.094641 +4 0.313491 0.088207 0.335441 0.094641 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9bd1eb4e9a3cab6e80b77cda9ed509c04fadbcdf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000645_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.68047600 Before NNI: tree length is 0.68047600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f55d2b53fb20a0f82ffba4114d38854b57e7398 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.177492 0.244234 0.181053 0.160184 +1 0.177492 0.000001 0.291017 0.006846 0.061815 +2 0.244234 0.291017 0.000001 0.294578 0.273710 +3 0.181053 0.006846 0.294578 0.000001 0.065377 +4 0.160184 0.061815 0.273710 0.065377 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9d79c8eaeb652a204f6ea62974dcf769f4dbfe0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000648_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38382896 Before NNI: tree length is 0.38382900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b752879504134850945c8f3658d1c9266c90d95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.475744 0.830612 0.460880 0.482652 +1 0.475744 0.000001 0.703421 0.018836 0.096229 +2 0.830612 0.703421 0.000001 0.688557 0.710329 +3 0.460880 0.018836 0.688557 0.000001 0.081365 +4 0.482652 0.096229 0.710329 0.081365 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6eaa289677c8064c556c14c5de5eca2f2263791b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.144284 0.338796 0.144284 0.144820 +1 0.144284 0.000001 0.294908 0.000001 0.002033 +2 0.338796 0.294908 0.000001 0.294908 0.295445 +3 0.144284 0.000001 0.294908 0.000001 0.002033 +4 0.144820 0.002033 0.295445 0.002033 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f95020b66e6fb6d930dd5db603be05b5fde75ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000650_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39027921 Before NNI: tree length is 0.39027925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000652_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000652_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c08927283b0010efed32144d42665cb57b0f3b86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000652_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.107447 0.183025 0.106662 0.110569 +1 0.107447 0.000001 0.177446 0.000949 0.003884 +2 0.183025 0.177446 0.000001 0.176661 0.180568 +3 0.106662 0.000949 0.176661 0.000001 0.004071 +4 0.110569 0.003884 0.180568 0.004071 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000655_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000655_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8868fd4a5657a5269b1e72afbd64aa2f619e6f4d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000655_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.23331675 Before NNI: tree length is 1.23331675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000657_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000657_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c31992e5d3074652f9d2cefc3255d1f2e63d5aad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000657_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18076425 Before NNI: tree length is 0.18076425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f87d6101d6490bc5018733e7e8ace7a4845feef6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.376487 0.390081 0.372984 0.379688 +1 0.376487 0.000001 0.317947 0.013446 0.009214 +2 0.390081 0.317947 0.000001 0.314443 0.321147 +3 0.372984 0.013446 0.314443 0.000001 0.016647 +4 0.379688 0.009214 0.321147 0.016647 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f2d0e205d5b89becf8190dd3c9b641ad3fd5753 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000663_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55343612 Before NNI: tree length is 0.55343612 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dbf834c935f75adae4d49415bedcf7b4269128db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.130099 0.117542 0.131005 0.129385 +1 0.130099 0.000001 0.131745 0.010357 0.004748 +2 0.117542 0.131745 0.000001 0.132652 0.131031 +3 0.131005 0.010357 0.132652 0.000001 0.009642 +4 0.129385 0.004748 0.131031 0.009642 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..727563bdcab4c22253d7cefe39af69adc7bc6f28 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000665_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19734150 Before NNI: tree length is 0.19734150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fb8192ec14234adf9cbb22041d0c309c1029db5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000667_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22535150 Before NNI: tree length is 0.22535150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000668_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000668_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..741e9f69d0c9b4219c8be83bfd096afe8ac7ee5d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000668_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.319504 0.342908 0.323471 0.321624 +1 0.319504 0.000001 0.298626 0.011851 0.010004 +2 0.342908 0.298626 0.000001 0.302592 0.300745 +3 0.323471 0.011851 0.302592 0.000001 0.011289 +4 0.321624 0.010004 0.300745 0.011289 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d1cba179bcc485338f642089fe02bd85c64087d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.149201 0.506985 0.153795 0.148192 +1 0.149201 0.000001 0.471262 0.025019 0.012822 +2 0.506985 0.471262 0.000001 0.475856 0.470253 +3 0.153795 0.025019 0.475856 0.000001 0.024010 +4 0.148192 0.012822 0.470253 0.024010 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c4ea7f53eabc90359f59e67de356892a1bb8f973 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000674_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.359892 0.304469 0.359892 0.356029 +1 0.359892 0.000001 0.362031 0.000001 0.003967 +2 0.304469 0.362031 0.000001 0.362031 0.358168 +3 0.359892 0.000001 0.362031 0.000001 0.003967 +4 0.356029 0.003967 0.358168 0.003967 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..230471200eedf84b540932712fcf1a3dfe04f2d7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.080619 0.197323 0.093844 0.093844 +1 0.080619 0.000001 0.195931 0.028359 0.028359 +2 0.197323 0.195931 0.000001 0.209155 0.209155 +3 0.093844 0.028359 0.209155 0.000001 0.000001 +4 0.093844 0.028359 0.209155 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1804e9b3c1abe754c6be2816679746abc33406ea --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000678_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25772870 Before NNI: tree length is 0.25772875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000683_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000683_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..26bbf40f2055229522d56a4919d5b054b33f44e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000683_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.229242 1.288858 0.211612 0.239635 +1 0.229242 0.000001 1.278296 0.103314 0.124702 +2 1.288858 1.278296 0.000001 1.260665 1.288688 +3 0.211612 0.103314 1.260665 0.000001 0.113706 +4 0.239635 0.124702 1.288688 0.113706 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a0c3adff4439c254d2be3f39067eb98b7273e7c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.387110 0.830474 0.298939 0.387733 +1 0.387110 0.000001 0.839374 0.145587 0.029777 +2 0.830474 0.839374 0.000001 0.751202 0.839997 +3 0.298939 0.145587 0.751202 0.000001 0.146209 +4 0.387733 0.029777 0.839997 0.146209 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3acf479c94aca02eee0c886ec95009d7fc807847 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000690_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.07238650 Before NNI: tree length is 1.07238650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000692_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000692_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..014584151fe276dfefdac95b66caec82ac40afee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000692_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36192438 Before NNI: tree length is 0.36192438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f6d28b1eee7e45fd4dcedb4409df85dc0a2af4e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.61800700 Before NNI: tree length is 0.61800700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000695_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000695_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1bb5ed2ab0c4ab720320ff5c4ccb90aa23583b0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000695_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.251403 0.271296 0.258643 0.248329 +1 0.251403 0.000001 0.240931 0.029721 0.013644 +2 0.271296 0.240931 0.000001 0.248172 0.237857 +3 0.258643 0.029721 0.248172 0.000001 0.026647 +4 0.248329 0.013644 0.237857 0.026647 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000697_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000697_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef91c705229285b21383c4479991defb8cd82066 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000697_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.082976 0.174678 0.091662 0.094686 +1 0.082976 0.000001 0.188399 0.015953 0.018978 +2 0.174678 0.188399 0.000001 0.197085 0.200110 +3 0.091662 0.015953 0.197085 0.000001 0.003024 +4 0.094686 0.018978 0.200110 0.003024 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000699_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000699_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b62453dd28b0837c138346a3b48afbd12f4f043c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000699_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.518319 0.434005 0.518207 0.502860 +1 0.518319 0.000001 0.537778 0.029785 0.015459 +2 0.434005 0.537778 0.000001 0.537667 0.522320 +3 0.518207 0.029785 0.537667 0.000001 0.015347 +4 0.502860 0.015459 0.522320 0.015347 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000703_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000703_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d21371a0427607dda27d0cce378b3924a6011948 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000703_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.046606 0.000001 0.000001 +1 0.000001 0.000001 0.046606 0.000001 0.000001 +2 0.046606 0.046606 0.000001 0.046606 0.046606 +3 0.000001 0.000001 0.046606 0.000001 0.000001 +4 0.000001 0.000001 0.046606 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b9601b0737e36cf7f06121f6a35c82beb4e8be3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.580187 0.978856 0.561021 0.524150 +1 0.580187 0.000001 1.126541 0.026388 0.070759 +2 0.978856 1.126541 0.000001 1.107375 1.070504 +3 0.561021 0.026388 1.107375 0.000001 0.051593 +4 0.524150 0.070759 1.070504 0.051593 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d841a28eb01fda233bcdee75751ad91d6fe1a60d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000709_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29376250 Before NNI: tree length is 0.29376250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000710_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000710_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf048c5bf09739209fb2fe2e10fc98739e7fedb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000710_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10995911 Before NNI: tree length is 0.10995912 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6c44759cb0aa8ac83ad3497668277d3b1f2566bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000711_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04399628 Before NNI: tree length is 0.04399625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000713_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000713_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21c9b70a15437be70cd3e6e154e82b2c1f16ddc5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000713_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31186100 Before NNI: tree length is 0.31186100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..940e1f85c54e5df69943982e44fa5689043f2aa0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000715_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.101140 0.205121 0.101367 0.109807 +1 0.101140 0.000001 0.191018 0.000227 0.008667 +2 0.205121 0.191018 0.000001 0.191245 0.199685 +3 0.101367 0.000227 0.191245 0.000001 0.008441 +4 0.109807 0.008667 0.199685 0.008441 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f91ad266f71662641b4ceb9944176efab46da51d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000717_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08859575 Before NNI: tree length is 0.08859575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000718_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000718_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f93ac021eab97469aa2c95bf192a5069303ff14a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000718_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.158959 0.192118 0.157797 0.162851 +1 0.158959 0.000001 0.205155 0.006762 0.020361 +2 0.192118 0.205155 0.000001 0.203994 0.209048 +3 0.157797 0.006762 0.203994 0.000001 0.019199 +4 0.162851 0.020361 0.209048 0.019199 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..934a64cf819e31538faecc889910954162013b43 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000725_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.155738 0.222754 0.155738 0.170254 +1 0.155738 0.000001 0.232689 0.000001 0.020748 +2 0.222754 0.232689 0.000001 0.232689 0.247205 +3 0.155738 0.000001 0.232689 0.000001 0.020748 +4 0.170254 0.020748 0.247205 0.020748 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..513dc1891aedf532511f6ce8549f008e3aa11400 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.121882 0.252699 0.124253 0.117234 +1 0.121882 0.000001 0.288101 0.021643 0.014625 +2 0.252699 0.288101 0.000001 0.290472 0.283454 +3 0.124253 0.021643 0.290472 0.000001 0.013704 +4 0.117234 0.014625 0.283454 0.013704 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7e83d4f1ea3784103958e793863f6f01af3ed8db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000726_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34669090 Before NNI: tree length is 0.34669088 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..543c6cfd97c0f735d68886e0a2b6a35d3a92d4e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.178697 0.510321 0.167993 0.167993 +1 0.178697 0.000001 0.496015 0.025080 0.025080 +2 0.510321 0.496015 0.000001 0.485311 0.485311 +3 0.167993 0.025080 0.485311 0.000001 0.000001 +4 0.167993 0.025080 0.485311 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..16f5595ebf0f9bbda495e196fd582b58f109f052 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000727_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59970500 Before NNI: tree length is 0.59970500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000735_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000735_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18e666dcadf94ace5183a008da2741342e722ae9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000735_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38063500 Before NNI: tree length is 0.38063500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0a4f43aa3c97f69046bd6ebd0383565e887a94b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000736_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.429316 0.561845 0.429316 0.429316 +1 0.429316 0.000001 0.545296 0.000001 0.000001 +2 0.561845 0.545296 0.000001 0.545296 0.545296 +3 0.429316 0.000001 0.545296 0.000001 0.000001 +4 0.429316 0.000001 0.545296 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e49b3237560efd700751ec70d69ebd2d0df16a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39367700 Before NNI: tree length is 0.39367700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000741_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000741_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ede5712f22a4304db4190a88d61606edad326996 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000741_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.141884 0.373343 0.141884 0.164540 +1 0.141884 0.000001 0.372323 0.000001 0.036634 +2 0.373343 0.372323 0.000001 0.372323 0.394979 +3 0.141884 0.000001 0.372323 0.000001 0.036634 +4 0.164540 0.036634 0.394979 0.036634 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000744_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000744_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e910540745d46c871146ea24c07808c867d15ff4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000744_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.142146 0.262359 0.142146 0.142146 +1 0.142146 0.000001 0.287688 0.000001 0.000001 +2 0.262359 0.287688 0.000001 0.287688 0.287688 +3 0.142146 0.000001 0.287688 0.000001 0.000001 +4 0.142146 0.000001 0.287688 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b79857c9d78aca21fcdb1b5718368efa2dc77e03 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000745_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56567350 Before NNI: tree length is 0.56567350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000753_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000753_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7db7c29600cbf92cd69423d421bd85377cc70173 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000753_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.93094350 Before NNI: tree length is 0.93094350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000755_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000755_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2373993a3f00b112cc11a947cb72a9ea713fd78d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000755_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.104347 0.186246 0.102817 0.097054 +1 0.104347 0.000001 0.227518 0.017495 0.027826 +2 0.186246 0.227518 0.000001 0.225988 0.220225 +3 0.102817 0.017495 0.225988 0.000001 0.026295 +4 0.097054 0.027826 0.220225 0.026295 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000758_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000758_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7ab70873aa1fc3a6d793cdb86841acd0b68535a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000758_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42549136 Before NNI: tree length is 0.42549138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fb2b4c9df3bd481a9a610ef84dd55440b9080ae2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026869 0.068996 0.022717 0.022717 +1 0.026869 0.000001 0.083183 0.006349 0.006349 +2 0.068996 0.083183 0.000001 0.079030 0.079030 +3 0.022717 0.006349 0.079030 0.000001 0.000001 +4 0.022717 0.006349 0.079030 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..96bffcfe1964423cde09f761002158c105c08251 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000761_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09062268 Before NNI: tree length is 0.09062275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..82e3e7d422f334ff2e7eaf629c9ad407150d0ba1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036907 0.087278 0.035602 0.034297 +1 0.036907 0.000001 0.114035 0.001305 0.002609 +2 0.087278 0.114035 0.000001 0.112731 0.111426 +3 0.035602 0.001305 0.112731 0.000001 0.001305 +4 0.034297 0.002609 0.111426 0.001305 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1412134190573e67895e41048510f4d6d7f8d9d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000762_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11911009 Before NNI: tree length is 0.11911012 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..746cb901b6b6d3ebae6124c46459881de4c7bdcb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022061 0.040968 0.022061 0.022061 +1 0.022061 0.000001 0.035924 0.000001 0.000001 +2 0.040968 0.035924 0.000001 0.035924 0.035924 +3 0.022061 0.000001 0.035924 0.000001 0.000001 +4 0.022061 0.000001 0.035924 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75a3f98652ebe71d61f29ce62b07548f0421f0ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000763_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04947750 Before NNI: tree length is 0.04947750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000765_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000765_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6bb2a31c7cc144f38cbf2c84cfb58f7a0adac762 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000765_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012498 0.008333 0.012498 0.012498 +1 0.012498 0.000001 0.012498 0.004141 0.004141 +2 0.008333 0.012498 0.000001 0.012498 0.012498 +3 0.012498 0.004141 0.012498 0.000001 0.000001 +4 0.012498 0.004141 0.012498 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000766_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000766_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..44021c2883535a307ddda7317b8f5ec66da780fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000766_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00654800 Before NNI: tree length is 0.00654800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999997 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dcbfe56dbe56f228237df923cded6f2721558234 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000767_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043879 0.046985 0.045032 0.043879 +1 0.043879 0.000001 0.053869 0.001475 0.000001 +2 0.046985 0.053869 0.000001 0.055022 0.053869 +3 0.045032 0.001475 0.055022 0.000001 0.001475 +4 0.043879 0.000001 0.053869 0.001475 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000768_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000768_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4aa40d393428e9047ecdcda3aca7a8b8c514d2a6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000768_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014325 0.021380 0.017632 0.014230 +1 0.014325 0.000001 0.024934 0.003306 0.000095 +2 0.021380 0.024934 0.000001 0.028240 0.024839 +3 0.017632 0.003306 0.028240 0.000001 0.003402 +4 0.014230 0.000095 0.024839 0.003402 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..959f072717e7fe31107f0d890facbd211d263c8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000769_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.80692630 Before NNI: tree length is 0.80692625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000771_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000771_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..599985b3e3ea3a1afb38757b1a759122baffb83f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000771_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00000250 Before NNI: tree length is 0.00000250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : -4460149039706124200828622340096.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000772_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000772_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e45dd6799fa7123af26975c95006a1736d15081 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000772_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021401 0.034639 0.032555 0.021431 +1 0.021401 0.000001 0.031671 0.011154 0.000030 +2 0.034639 0.031671 0.000001 0.042826 0.031702 +3 0.032555 0.011154 0.042826 0.000001 0.011124 +4 0.021431 0.000030 0.031702 0.011124 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000773_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000773_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5ecc3ad91ccd969cb38855744f0fcfcaa76d1a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000773_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007685 0.030732 0.007685 0.007685 +1 0.007685 0.000001 0.038417 0.000001 0.000001 +2 0.030732 0.038417 0.000001 0.038417 0.038417 +3 0.007685 0.000001 0.038417 0.000001 0.000001 +4 0.007685 0.000001 0.038417 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df2f2a81e00b434a790318a347f51d360167b447 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.079356 0.000001 0.000001 +1 0.000001 0.000001 0.079356 0.000001 0.000001 +2 0.079356 0.079356 0.000001 0.079356 0.079356 +3 0.000001 0.000001 0.079356 0.000001 0.000001 +4 0.000001 0.000001 0.079356 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000775_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000775_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2e09fe78eca982310e3698769d02f54dac753fe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000775_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01271750 Before NNI: tree length is 0.01271750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999999 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000776_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000776_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a8253e5be5521c6cf9f9dd23d22cd1d658ddf4b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000776_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00522350 Before NNI: tree length is 0.00522350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999997 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000778_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000778_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8404e455a9f7390ea81c3ac38e8bbe63653da8ce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000778_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049930 0.055827 0.036568 0.036568 +1 0.049930 0.000001 0.082947 0.018121 0.018121 +2 0.055827 0.082947 0.000001 0.069584 0.069584 +3 0.036568 0.018121 0.069584 0.000001 0.000001 +4 0.036568 0.018121 0.069584 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000783_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000783_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cc093f856a9fb08837fe26f4c67f7886d41d546d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000783_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039512 0.051655 0.039512 0.039512 +1 0.039512 0.000001 0.056091 0.000001 0.000001 +2 0.051655 0.056091 0.000001 0.056091 0.056091 +3 0.039512 0.000001 0.056091 0.000001 0.000001 +4 0.039512 0.000001 0.056091 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000789_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000789_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23a9cc24e17ab75af0e34891cb0f77f20f8bf5ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000789_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10857850 Before NNI: tree length is 0.10857850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000790_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000790_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f923b4639522522c3d22c1b128e061b5ea8586d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000790_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015884 0.084146 0.015884 0.015884 +1 0.015884 0.000001 0.088131 0.000001 0.000001 +2 0.084146 0.088131 0.000001 0.088131 0.088131 +3 0.015884 0.000001 0.088131 0.000001 0.000001 +4 0.015884 0.000001 0.088131 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000792_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000792_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ccfc2b9ed359e84a5c645d144d9a4ca4b1ac0a20 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000792_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18917985 Before NNI: tree length is 0.18917987 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000799_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000799_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0d618951119b8e44e0b2c1557ea77c11744b3b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000799_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15764700 Before NNI: tree length is 0.15764700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bae1c25787c7307e5f8838c4f3ea853069800634 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045863 0.123271 0.048697 0.044030 +1 0.045863 0.000001 0.125373 0.002930 0.002348 +2 0.123271 0.125373 0.000001 0.128207 0.123540 +3 0.048697 0.002930 0.128207 0.000001 0.005182 +4 0.044030 0.002348 0.123540 0.005182 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..49c5681a5cc7ff20847aa3a37e1ddda29e88c14a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000804_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15039300 Before NNI: tree length is 0.15039300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7a9ccb97edc6b2d350b506d6d9c604734ea40c65 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000805_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.391098 0.976010 0.391098 0.391098 +1 0.391098 0.000001 1.066906 0.000001 0.000001 +2 0.976010 1.066906 0.000001 1.066906 1.066906 +3 0.391098 0.000001 1.066906 0.000001 0.000001 +4 0.391098 0.000001 1.066906 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000811_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000811_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..623b615f5b3971f309f64906724949e4ba4ba49e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000811_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25678569 Before NNI: tree length is 0.25678575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f1443942b31c4ff4fd077662fb3cab84d592467 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.266901 0.511726 0.267368 0.254541 +1 0.266901 0.000001 0.495804 0.018396 0.025227 +2 0.511726 0.495804 0.000001 0.496272 0.483445 +3 0.267368 0.018396 0.496272 0.000001 0.025695 +4 0.254541 0.025227 0.483445 0.025695 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8053d968d32aa7d35dacba35eac63bd81c501289 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000813_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65308110 Before NNI: tree length is 0.65308113 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b743547256ce11fbde1d7efbad4d20e628c345c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51362050 Before NNI: tree length is 0.51362050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7a659b6666f66439ad0212d24fd2c24336f230a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28469050 Before NNI: tree length is 0.28469050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000822_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000822_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..006a831bc867425c96f8d46da230d37376adece4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000822_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086357 0.162645 0.078550 0.078773 +1 0.086357 0.000001 0.173818 0.015440 0.015663 +2 0.162645 0.173818 0.000001 0.166011 0.166234 +3 0.078550 0.015440 0.166011 0.000001 0.006960 +4 0.078773 0.015663 0.166234 0.006960 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000824_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000824_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..696b0cb6e04314ba86e9d650c4c4006b539e7e56 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000824_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.566421 1.039561 0.557128 0.561454 +1 0.566421 0.000001 0.609263 0.027583 0.039096 +2 1.039561 0.609263 0.000001 0.599970 0.604296 +3 0.557128 0.027583 0.599970 0.000001 0.029803 +4 0.561454 0.039096 0.604296 0.029803 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b845b4346acaaf6e2889863878f5fadc406cfb66 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008135 0.013631 0.000023 0.000046 +1 0.008135 0.000001 0.021766 0.008159 0.008182 +2 0.013631 0.021766 0.000001 0.013608 0.013584 +3 0.000023 0.008159 0.013608 0.000001 0.000023 +4 0.000046 0.008182 0.013584 0.000023 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000830_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000830_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..825d9fbfb4777d6bc5a86f5def7c8a575216b86e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000830_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24307772 Before NNI: tree length is 0.24307775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000836_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000836_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f313a5746283c95a04167d46cb4c3e5db94a8349 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000836_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39778390 Before NNI: tree length is 0.39778388 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d6b59faeecfc64c1d40d560d089e8af67cb47c5d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000843_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.207269 0.655118 0.216886 0.212022 +1 0.207269 0.000001 0.666488 0.022366 0.009261 +2 0.655118 0.666488 0.000001 0.676105 0.671241 +3 0.216886 0.022366 0.676105 0.000001 0.027120 +4 0.212022 0.009261 0.671241 0.027120 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000845_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000845_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..508d92b185f28739ed8482391d99cc92c6e79163 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000845_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.52018125 Before NNI: tree length is 1.52018125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000846_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000846_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb5cc2bc8e249ed839d7ff7d5e837e99e6daed28 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000846_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055342 0.069598 0.055342 0.059486 +1 0.055342 0.000001 0.070025 0.000001 0.004190 +2 0.069598 0.070025 0.000001 0.070025 0.074170 +3 0.055342 0.000001 0.070025 0.000001 0.004190 +4 0.059486 0.004190 0.074170 0.004190 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..588f984b5562ef43d8b8cb0309aa94f3958df1e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.178065 0.439299 0.186163 0.173717 +1 0.178065 0.000001 0.445124 0.008318 0.051918 +2 0.439299 0.445124 0.000001 0.453223 0.440777 +3 0.186163 0.008318 0.453223 0.000001 0.060016 +4 0.173717 0.051918 0.440777 0.060016 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e2482616508ad940893836facef409925224add --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000847_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56323735 Before NNI: tree length is 0.56323738 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000848_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000848_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..066820801316125736c7682830e32a1cacd7b86e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000848_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.316003 0.302376 0.335385 0.316003 +1 0.316003 0.000001 0.193062 0.027316 0.000001 +2 0.302376 0.193062 0.000001 0.212445 0.193062 +3 0.335385 0.027316 0.212445 0.000001 0.027316 +4 0.316003 0.000001 0.193062 0.027316 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000849_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000849_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c0fc8427552a59f26835d704c447d26f99a85a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000849_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44314250 Before NNI: tree length is 0.44314250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bcf6f898aab374dc9e758a6fd196fbe665a6c3f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.238648 0.197545 0.209488 0.245259 +1 0.238648 0.000001 0.129294 0.078629 0.031313 +2 0.197545 0.129294 0.000001 0.100134 0.135906 +3 0.209488 0.078629 0.100134 0.000001 0.085241 +4 0.245259 0.031313 0.135906 0.085241 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000857_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000857_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8547c4957eb3ccf5bf5781a262ee56b2a6f8324b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000857_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039593 0.043014 0.040855 0.030810 +1 0.039593 0.000001 0.019365 0.021496 0.011451 +2 0.043014 0.019365 0.000001 0.024917 0.014871 +3 0.040855 0.021496 0.024917 0.000001 0.010046 +4 0.030810 0.011451 0.014871 0.010046 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000858_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000858_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ec9be68c734f62cd4bcfd52e36c332dbc8078f8c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000858_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.128003 0.131857 0.121992 0.132954 +1 0.128003 0.000001 0.043508 0.022027 0.032989 +2 0.131857 0.043508 0.000001 0.037497 0.048458 +3 0.121992 0.022027 0.037497 0.000001 0.016066 +4 0.132954 0.032989 0.048458 0.016066 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000859_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000859_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..541482c439c7c4c9b267f38538eab576dcf27e0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000859_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.067249 0.080411 0.074944 0.067283 +1 0.067249 0.000001 0.018691 0.007695 0.000034 +2 0.080411 0.018691 0.000001 0.026386 0.018724 +3 0.074944 0.007695 0.026386 0.000001 0.007662 +4 0.067283 0.000034 0.018724 0.007662 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7287768a1bef53efac73af06292f329a026d4f74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000860_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.096044 0.092298 0.092739 0.096044 +1 0.096044 0.000001 0.024270 0.003782 0.000001 +2 0.092298 0.024270 0.000001 0.020964 0.024270 +3 0.092739 0.003782 0.020964 0.000001 0.003782 +4 0.096044 0.000001 0.024270 0.003782 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000862_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000862_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0dec4dc6e46dc1cbd2306716b3ff8a8cc940e13e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000862_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015255 0.003670 0.017588 0.020348 +1 0.015255 0.000001 0.014321 0.004145 0.006905 +2 0.003670 0.014321 0.000001 0.016654 0.019414 +3 0.017588 0.004145 0.016654 0.000001 0.007367 +4 0.020348 0.006905 0.019414 0.007367 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000863_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000863_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a24d5001312ebb21d78ffbc1c6c0c754b6db2d2d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000863_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.031693 0.969055 1.031693 1.006718 +1 1.031693 0.000001 0.062638 0.000001 0.032885 +2 0.969055 0.062638 0.000001 0.062638 0.037663 +3 1.031693 0.000001 0.062638 0.000001 0.032885 +4 1.006718 0.032885 0.037663 0.032885 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000864_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000864_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..94320370e8cdcee7d38ff60355062af8388dde64 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000864_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.103347 0.121811 0.103347 0.106031 +1 0.103347 0.000001 0.124877 0.000001 0.012097 +2 0.121811 0.124877 0.000001 0.124877 0.127561 +3 0.103347 0.000001 0.124877 0.000001 0.012097 +4 0.106031 0.012097 0.127561 0.012097 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b1278fa2cf75fbc1d1ba4822548d75a34211e79 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000865_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38245550 Before NNI: tree length is 0.38245550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000866_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000866_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb05c4e85cfcee899a85dbec20be37c75b09f687 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000866_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46376850 Before NNI: tree length is 0.46376850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000867_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000867_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e89651bc0b682b1178095785a38f62a5f1178a96 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000867_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.280187 0.355127 0.278580 0.280187 +1 0.280187 0.000001 0.242399 0.005671 0.000001 +2 0.355127 0.242399 0.000001 0.240792 0.242399 +3 0.278580 0.005671 0.240792 0.000001 0.005671 +4 0.280187 0.000001 0.242399 0.005671 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..124dd0492ee8f7dc60f47cbef4aaa21480c3d3d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71687938 Before NNI: tree length is 0.71687937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000873_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000873_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a70866745acdcba6e71aca2a516f89c845e16bf3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000873_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30122550 Before NNI: tree length is 0.30122550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..28ac39902f00a9a4a6c5a8eba68431cc03005371 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.221424 0.260164 0.225316 0.222344 +1 0.221424 0.000001 0.311130 0.008641 0.005668 +2 0.260164 0.311130 0.000001 0.315021 0.312049 +3 0.225316 0.008641 0.315021 0.000001 0.002972 +4 0.222344 0.005668 0.312049 0.002972 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..312c5adbad6e67c850c333e7cd371fd4f4dd7016 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000874_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40262497 Before NNI: tree length is 0.40262500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000875_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000875_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..069ef8cce0f488278532b206cc244edb7bf36a7b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000875_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.89873515 Before NNI: tree length is 0.89873512 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bdfec7500779eb9b82ea60b92db86d07ef990fc0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.291694 0.380064 0.292157 0.295685 +1 0.291694 0.000001 0.356236 0.003003 0.009553 +2 0.380064 0.356236 0.000001 0.356699 0.360227 +3 0.292157 0.003003 0.356699 0.000001 0.010016 +4 0.295685 0.009553 0.360227 0.010016 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..117eafa6fdf175033dcf981c93cabf09d893a87d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000876_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52250200 Before NNI: tree length is 0.52250200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d02a9f712d5df948c76a0ded23135270d588a4d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.092257 0.152885 0.092094 0.098298 +1 0.092257 0.000001 0.171445 0.008503 0.007585 +2 0.152885 0.171445 0.000001 0.171281 0.177486 +3 0.092094 0.008503 0.171281 0.000001 0.014544 +4 0.098298 0.007585 0.177486 0.014544 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbfc99a4ebeaa6f9800aa799ade8fecb98177e6f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.233414 0.890310 0.240919 0.236201 +1 0.233414 0.000001 0.871248 0.050952 0.008646 +2 0.890310 0.871248 0.000001 0.878752 0.874035 +3 0.240919 0.050952 0.878752 0.000001 0.053739 +4 0.236201 0.008646 0.874035 0.053739 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba609bc666621e9cd5fc3956268c92b5329625da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000880_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.03243081 Before NNI: tree length is 1.03243075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5f72913feffbee7e76fab36c96c8e17b1affcbcf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054457 0.266461 0.054457 0.060999 +1 0.054457 0.000001 0.275856 0.000001 0.050147 +2 0.266461 0.275856 0.000001 0.275856 0.282398 +3 0.054457 0.000001 0.275856 0.000001 0.050147 +4 0.060999 0.050147 0.282398 0.050147 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000883_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000883_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4bb3170c65685f50a49bd87af473996de32e6bc0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000883_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38692575 Before NNI: tree length is 0.38692575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000888_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000888_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e39e8c0d560e6c9b15f9fd67974a1ce06094667c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000888_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09469350 Before NNI: tree length is 0.09469350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000889_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000889_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..149cf44a81a7e22e72224efe84d3eca6c8d7c2d2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000889_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21697200 Before NNI: tree length is 0.21697200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1b7b21b3db6eeb1c76825a26ce831bfa7b09d40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000890_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23906190 Before NNI: tree length is 0.23906187 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..41dc7b4f983183702ef32f46ea2af8ae03166ea0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025264 0.138683 0.026851 0.026851 +1 0.025264 0.000001 0.136856 0.009592 0.009592 +2 0.138683 0.136856 0.000001 0.138442 0.138442 +3 0.026851 0.009592 0.138442 0.000001 0.000001 +4 0.026851 0.009592 0.138442 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd8efb7f3a59295a7caa53d6f930e630d7e77cef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.219987 0.382936 0.203730 0.201354 +1 0.219987 0.000001 0.386227 0.063673 0.029723 +2 0.382936 0.386227 0.000001 0.369970 0.367594 +3 0.203730 0.063673 0.369970 0.000001 0.045040 +4 0.201354 0.029723 0.367594 0.045040 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4080b44d6c608f77776f5d4c113589d7cb12e24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000895_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52382800 Before NNI: tree length is 0.52382800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000896_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000896_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b84c7e619a00ed3c31725331b596ec53a858ad6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000896_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.98840600 Before NNI: tree length is 0.98840600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000898_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000898_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..89769d6d9c1818774d79769998da490cd6420bb7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000898_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.26389466 Before NNI: tree length is 1.26389463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f7a4e68a471ab368bf3f273faad42c7a3d6e40f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000899_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.630409 1.213859 0.687915 0.696795 +1 0.630409 0.000001 0.583450 0.057507 0.066387 +2 1.213859 0.583450 0.000001 0.592776 0.572499 +3 0.687915 0.057507 0.592776 0.000001 0.075712 +4 0.696795 0.066387 0.572499 0.075712 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e00d0e251d6814b4a2ebcbbff937b9b558c99c2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30009229 Before NNI: tree length is 0.30009225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000901_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000901_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be4ead3af29bf84e9318bb7165112e0f89867049 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000901_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60590471 Before NNI: tree length is 0.60590475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000904_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000904_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c21ba362690effac64d9c532bcad9c0565f9598 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000904_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60236215 Before NNI: tree length is 0.60236212 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000912_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000912_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0b213bbb2f06df943e5d6b4d5603e9bacd48be2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000912_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37257550 Before NNI: tree length is 0.37257550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..12bd917ae55d0540f2de624bfe791a2ac0d7cc43 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097285 0.544738 0.097285 0.104265 +1 0.097285 0.000001 0.560128 0.000001 0.036259 +2 0.544738 0.560128 0.000001 0.560128 0.567108 +3 0.097285 0.000001 0.560128 0.000001 0.036259 +4 0.104265 0.036259 0.567108 0.036259 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000919_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000919_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a5036ad77958b353f613e5f3d350a0e583decde --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000919_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049120 0.347732 0.047960 0.041334 +1 0.049120 0.000001 0.323203 0.035269 0.028643 +2 0.347732 0.323203 0.000001 0.333881 0.327255 +3 0.047960 0.035269 0.333881 0.000001 0.020655 +4 0.041334 0.028643 0.327255 0.020655 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000922_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000922_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b879c8cc0b263beb78921eedac780bf0d38bb280 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000922_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.092579 0.236420 0.092959 0.089788 +1 0.092579 0.000001 0.248467 0.017211 0.016414 +2 0.236420 0.248467 0.000001 0.248848 0.245676 +3 0.092959 0.017211 0.248848 0.000001 0.016795 +4 0.089788 0.016414 0.245676 0.016795 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000923_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000923_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6c669cc6da7476413db09ecf01583bf4e8eb52b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000923_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.331980 0.580079 0.332126 0.311969 +1 0.331980 0.000001 0.719992 0.018471 0.039218 +2 0.580079 0.719992 0.000001 0.720138 0.699981 +3 0.332126 0.018471 0.720138 0.000001 0.039364 +4 0.311969 0.039218 0.699981 0.039364 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000925_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000925_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..685e813f3c32cdc2d2ef9bf11acafaf00e634ccb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000925_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.144802 0.374460 0.142951 0.144202 +1 0.144802 0.000001 0.358319 0.016896 0.018147 +2 0.374460 0.358319 0.000001 0.356467 0.357718 +3 0.142951 0.016896 0.356467 0.000001 0.005698 +4 0.144202 0.018147 0.357718 0.005698 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bd7e443613f00708798234f20ccf1abff4f490e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.202257 0.574661 0.202139 0.197730 +1 0.202257 0.000001 0.492277 0.037423 0.033015 +2 0.574661 0.492277 0.000001 0.492160 0.487751 +3 0.202139 0.037423 0.492160 0.000001 0.020858 +4 0.197730 0.033015 0.487751 0.020858 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..32754740e89ddaeec5343e0e8d34579416683846 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.159811 0.566862 0.158453 0.158215 +1 0.159811 0.000001 0.575547 0.001533 0.018043 +2 0.566862 0.575547 0.000001 0.574189 0.573951 +3 0.158453 0.001533 0.574189 0.000001 0.016685 +4 0.158215 0.018043 0.573951 0.016685 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000932_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000932_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dfbf8010537106d4541ff72f86a24355381189f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000932_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.106017 0.251668 0.101439 0.103572 +1 0.106017 0.000001 0.246441 0.005647 0.010586 +2 0.251668 0.246441 0.000001 0.241862 0.243995 +3 0.101439 0.005647 0.241862 0.000001 0.006007 +4 0.103572 0.010586 0.243995 0.006007 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c28e87d6de1c1280ac8b6132f53b6260886548fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.68184400 Before NNI: tree length is 0.68184400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7f33235d77102caae180ad9d573cab95b69d5b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47063150 Before NNI: tree length is 0.47063150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3fba1d19c509fed4f5d533e66abb1baa8523faab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.075275 0.156337 0.073172 0.069556 +1 0.075275 0.000001 0.153783 0.002613 0.010607 +2 0.156337 0.153783 0.000001 0.151680 0.148064 +3 0.073172 0.002613 0.151680 0.000001 0.008504 +4 0.069556 0.010607 0.148064 0.008504 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9900e3e8094f5b6808f299113c36f4ed0604dd2b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000944_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19539650 Before NNI: tree length is 0.19539650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba17389e100a00aada66d31b1acc1ad15bdfac78 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000946_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49612875 Before NNI: tree length is 0.49612875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000949_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000949_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d74baf606ed70d083e5f2b4547feeb5dc46c2130 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000949_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79388400 Before NNI: tree length is 0.79388400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000956_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000956_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5bf390c2cc3425e9ae11736610785d25538a0214 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000956_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.225470 0.577521 0.216811 0.218330 +1 0.225470 0.000001 0.506846 0.019564 0.007426 +2 0.577521 0.506846 0.000001 0.498188 0.499707 +3 0.216811 0.019564 0.498188 0.000001 0.012425 +4 0.218330 0.007426 0.499707 0.012425 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000958_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000958_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3dfc27d2e3ff56e7779c98087d355e1acfe03f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000958_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.151448 0.358198 0.151448 0.151448 +1 0.151448 0.000001 0.338605 0.000001 0.000001 +2 0.358198 0.338605 0.000001 0.338605 0.338605 +3 0.151448 0.000001 0.338605 0.000001 0.000001 +4 0.151448 0.000001 0.338605 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d5b86180035f91c516c64b5d706473b0c5b87215 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081374 0.136993 0.066805 0.081374 +1 0.081374 0.000001 0.153367 0.083179 0.000001 +2 0.136993 0.153367 0.000001 0.112613 0.153367 +3 0.066805 0.083179 0.112613 0.000001 0.083179 +4 0.081374 0.000001 0.153367 0.083179 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..489242b79e31ac67f91a6d3ecf91910d5f50c9e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000961_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20708000 Before NNI: tree length is 0.20708000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..feb786e947bca9ec8c2c725a57bc238f60b49aa4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.83115000 Before NNI: tree length is 0.83115000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000966_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000966_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2164352c4e01849dbd390cb7ec0f5f1b492bf68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000966_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69834120 Before NNI: tree length is 0.69834125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000972_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000972_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78b62d935594e3e9739646957cd6a052d020e32a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000972_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.813047 1.640820 0.813047 0.738824 +1 0.813047 0.000001 1.752828 0.000001 0.089914 +2 1.640820 1.752828 0.000001 1.752828 1.678606 +3 0.813047 0.000001 1.752828 0.000001 0.089914 +4 0.738824 0.089914 1.678606 0.089914 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000974_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000974_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..911c133b1c27c7c253102097879687bc79503792 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000974_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.162890 0.327254 0.165053 0.162861 +1 0.162890 0.000001 0.313653 0.012588 0.002340 +2 0.327254 0.313653 0.000001 0.315815 0.313623 +3 0.165053 0.012588 0.315815 0.000001 0.012558 +4 0.162861 0.002340 0.313623 0.012558 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d4d51b81a3af2054f526f2af1c53fe3ba208f5c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000977_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.107611 0.213730 0.104817 0.106531 +1 0.107611 0.000001 0.195689 0.002794 0.008071 +2 0.213730 0.195689 0.000001 0.192895 0.194609 +3 0.104817 0.002794 0.192895 0.000001 0.005276 +4 0.106531 0.008071 0.194609 0.005276 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000978_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000978_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c25628479a2c602e9f7dfaedada618e4320ea62f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000978_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.173308 0.294372 0.171846 0.171113 +1 0.173308 0.000001 0.286289 0.004304 0.010281 +2 0.294372 0.286289 0.000001 0.284826 0.284094 +3 0.171846 0.004304 0.284826 0.000001 0.008818 +4 0.171113 0.010281 0.284094 0.008818 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000980_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000980_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a11b4d49c39bbc211a020f07f138e54d083bbf1c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000980_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.078640 0.255978 0.078640 0.078640 +1 0.078640 0.000001 0.245504 0.000001 0.000001 +2 0.255978 0.245504 0.000001 0.245504 0.245504 +3 0.078640 0.000001 0.245504 0.000001 0.000001 +4 0.078640 0.000001 0.245504 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de94424c8aef74270005f87404b483f6cfc0137b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000982_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027665 0.046608 0.024781 0.024693 +1 0.027665 0.000001 0.041887 0.008261 0.003070 +2 0.046608 0.041887 0.000001 0.039003 0.038915 +3 0.024781 0.008261 0.039003 0.000001 0.005289 +4 0.024693 0.003070 0.038915 0.005289 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000985_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000985_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..455073b1e08b735c0447fa27c3dba9c0e2f84694 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000985_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086467 0.189980 0.089612 0.088401 +1 0.086467 0.000001 0.169307 0.009926 0.001934 +2 0.189980 0.169307 0.000001 0.172452 0.171241 +3 0.089612 0.009926 0.172452 0.000001 0.011861 +4 0.088401 0.001934 0.171241 0.011861 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8622bfd4d82fb024479317c5d40b3ac52629b218 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000987_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.245195 0.401304 0.227982 0.227982 +1 0.245195 0.000001 0.449408 0.030681 0.030681 +2 0.401304 0.449408 0.000001 0.432195 0.432195 +3 0.227982 0.030681 0.432195 0.000001 0.000001 +4 0.227982 0.030681 0.432195 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000990_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000990_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f11379f8f5273c268e0f526b0199e113de980a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000990_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33854975 Before NNI: tree length is 0.33854975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..86c08571f5bfd8f7a792aa03d913c7f39088315f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097464 0.229913 0.081824 0.101001 +1 0.097464 0.000001 0.228704 0.036660 0.014753 +2 0.229913 0.228704 0.000001 0.213064 0.232241 +3 0.081824 0.036660 0.213064 0.000001 0.040197 +4 0.101001 0.014753 0.232241 0.040197 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..20289234268b748f7408572395dcfdd3cd2f6f37 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000991_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29769550 Before NNI: tree length is 0.29769550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000995_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000995_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..43dd43cf279a7a0f4852743d35d75d54e2d2c457 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000995_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057541 0.076172 0.057672 0.060309 +1 0.057541 0.000001 0.093108 0.005875 0.004501 +2 0.076172 0.093108 0.000001 0.093240 0.095876 +3 0.057672 0.005875 0.093240 0.000001 0.008644 +4 0.060309 0.004501 0.095876 0.008644 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001001_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001001_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6c899fecd42ff20e5fc187d13bde6b64db8a20fe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001001_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.85186971 Before NNI: tree length is 1.85186975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001003_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001003_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3dfe32a9f37c0ac8402229d4fd295ed61d98cfb3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001003_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24311457 Before NNI: tree length is 0.24311450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001005_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001005_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..52e5ac38aab8c92004d5fa2ee990bb7ad29885a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001005_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.209154 0.582046 0.212831 0.217099 +1 0.209154 0.000001 0.552528 0.029173 0.033441 +2 0.582046 0.552528 0.000001 0.556205 0.560473 +3 0.212831 0.029173 0.556205 0.000001 0.005331 +4 0.217099 0.033441 0.560473 0.005331 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001010_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001010_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e586356b3db614107ecc624604120e083fd2718c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001010_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37109535 Before NNI: tree length is 0.37109538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001011_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001011_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0c5a26197d31685a80cea2cca0ea7ec5706915d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001011_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.269572 0.441533 0.268449 0.269572 +1 0.269572 0.000001 0.490335 0.006704 0.000001 +2 0.441533 0.490335 0.000001 0.489211 0.490335 +3 0.268449 0.006704 0.489211 0.000001 0.006704 +4 0.269572 0.000001 0.490335 0.006704 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001012_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001012_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dabfe4f935195907a53023d63c74a021c652877a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001012_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097614 0.181216 0.114763 0.100603 +1 0.097614 0.000001 0.150835 0.052466 0.009680 +2 0.181216 0.150835 0.000001 0.167983 0.153823 +3 0.114763 0.052466 0.167983 0.000001 0.055454 +4 0.100603 0.009680 0.153823 0.055454 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..60037527202050c8721410ccd60ff343ae74306c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019847 0.126232 0.020089 0.019847 +1 0.019847 0.000001 0.120708 0.002132 0.000001 +2 0.126232 0.120708 0.000001 0.120950 0.120708 +3 0.020089 0.002132 0.120950 0.000001 0.002132 +4 0.019847 0.000001 0.120708 0.002132 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7dbc1fa35358033e4814e54a9da1495e0e82f94c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001013_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13458100 Before NNI: tree length is 0.13458100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001014_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001014_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e57fb73fe2059fbfde67a99a2b9a940a9a772a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001014_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.78199855 Before NNI: tree length is 0.78199850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001018_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001018_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..793768a031b14f177554cd43caaf046e5d9ad862 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001018_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.09719350 Before NNI: tree length is 1.09719350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5de70d1b14707a4000131abfae8e90da5df7b59b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001024_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.391844 0.434113 0.389649 0.388978 +1 0.391844 0.000001 0.173889 0.009785 0.003191 +2 0.434113 0.173889 0.000001 0.171695 0.171023 +3 0.389649 0.009785 0.171695 0.000001 0.006919 +4 0.388978 0.003191 0.171023 0.006919 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001025_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001025_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6a96b0670295e5923e85360564b9bd3ea188d13 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001025_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25239553 Before NNI: tree length is 0.25239550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fe63fb1376ffc2f560942ee1097e4f8e13e9f82f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001037_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.122384 0.208249 0.129104 0.119713 +1 0.122384 0.000001 0.141839 0.009464 0.012867 +2 0.208249 0.141839 0.000001 0.148560 0.139169 +3 0.129104 0.009464 0.148560 0.000001 0.019588 +4 0.119713 0.012867 0.139169 0.019588 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9a4fcfa725b9790247339f219fc720e8da26424 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33065425 Before NNI: tree length is 0.33065425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001043_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001043_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4225a28c87662628ad836601fdc8d01811989f0e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001043_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044924 0.105361 0.030639 0.042717 +1 0.044924 0.000001 0.120339 0.017541 0.008848 +2 0.105361 0.120339 0.000001 0.106054 0.118132 +3 0.030639 0.017541 0.106054 0.000001 0.015334 +4 0.042717 0.008848 0.118132 0.015334 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..349c554913881c9ac31d1d1be7e71b08ff0abd4c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.107418 0.319430 0.109798 0.099787 +1 0.107418 0.000001 0.319833 0.030713 0.020702 +2 0.319430 0.319833 0.000001 0.322212 0.312202 +3 0.109798 0.030713 0.322212 0.000001 0.014863 +4 0.099787 0.020702 0.312202 0.014863 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..836aaba1360bab77c9650b82b779c96d17d5dab1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001048_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016819 0.086872 0.018315 0.016819 +1 0.016819 0.000001 0.075277 0.003713 0.000001 +2 0.086872 0.075277 0.000001 0.076772 0.075277 +3 0.018315 0.003713 0.076772 0.000001 0.003713 +4 0.016819 0.000001 0.075277 0.003713 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..63973a1421e8c97f8936cd5e696df7c7efbd6a74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002221 0.168911 0.007476 0.000067 +1 0.002221 0.000001 0.171132 0.009580 0.002288 +2 0.168911 0.171132 0.000001 0.176387 0.168845 +3 0.007476 0.009580 0.176387 0.000001 0.007543 +4 0.000067 0.002288 0.168845 0.007543 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b3d30da8221932c7c2e9030f0f705a0be608afa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001049_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17855000 Before NNI: tree length is 0.17855000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001058_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001058_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..67fa871f7c81791db00048eb515743db5caa8970 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001058_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068754 0.224024 0.067570 0.080841 +1 0.068754 0.000001 0.249119 0.001184 0.012087 +2 0.224024 0.249119 0.000001 0.247935 0.261206 +3 0.067570 0.001184 0.247935 0.000001 0.013272 +4 0.080841 0.012087 0.261206 0.013272 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001062_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001062_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b13298a180edefd95ab57fbfa317223ac8862fcc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001062_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26965860 Before NNI: tree length is 0.26965863 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001063_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001063_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3484432aa4cb977c2b4aa1ed278ab2a0fc974d70 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001063_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22233675 Before NNI: tree length is 0.22233675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63878dc23454b1a58527112d9c107b06f90cfc68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23659825 Before NNI: tree length is 0.23659825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9901464275c05fce1230e0c6f7382ab124dc8b51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001073_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56383350 Before NNI: tree length is 0.56383350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3cd04b3892f3696f3d07997ded4aea708ce6ab98 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.336440 0.786279 0.336440 0.336440 +1 0.336440 0.000001 0.640004 0.000001 0.000001 +2 0.786279 0.640004 0.000001 0.640004 0.640004 +3 0.336440 0.000001 0.640004 0.000001 0.000001 +4 0.336440 0.000001 0.640004 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..44978f816cc4f1e779f58df5edf81ed054417fdd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001074_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.88136250 Before NNI: tree length is 0.88136250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001077_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001077_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c542d1603fcde404d7fa25bca29262ea5efaa6d7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001077_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45379720 Before NNI: tree length is 0.45379725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001078_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001078_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2e752f53368003ba6c80533fa82fc2786e7c9d89 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001078_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.164294 0.388696 0.164294 0.164294 +1 0.164294 0.000001 0.409891 0.000001 0.000001 +2 0.388696 0.409891 0.000001 0.409891 0.409891 +3 0.164294 0.000001 0.409891 0.000001 0.000001 +4 0.164294 0.000001 0.409891 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2cf7250914626cab02d778722eee7e99870581c6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060974 0.211953 0.060974 0.060974 +1 0.060974 0.000001 0.206022 0.000001 0.000001 +2 0.211953 0.206022 0.000001 0.206022 0.206022 +3 0.060974 0.000001 0.206022 0.000001 0.000001 +4 0.060974 0.000001 0.206022 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..16352e17cbbb6da6f845b8aac25694afbcda8615 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001079_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23947550 Before NNI: tree length is 0.23947550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..224385f33b82347383be0f35d9c0d907c1d62b5f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.212029 0.282521 0.206834 0.205150 +1 0.212029 0.000001 0.331633 0.010081 0.007746 +2 0.282521 0.331633 0.000001 0.326438 0.324755 +3 0.206834 0.010081 0.326438 0.000001 0.003203 +4 0.205150 0.007746 0.324755 0.003203 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ac8f2e8841ac80ab91a11ed4ef5e456e62e3090 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001087_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41596839 Before NNI: tree length is 0.41596837 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001089_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001089_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7dbaf77749ec3f13d720088a6d816417b7733ab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001089_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.279206 0.511134 0.271890 0.272487 +1 0.279206 0.000001 0.497574 0.007317 0.006719 +2 0.511134 0.497574 0.000001 0.490257 0.490854 +3 0.271890 0.007317 0.490257 0.000001 0.000597 +4 0.272487 0.006719 0.490854 0.000597 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001103_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001103_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f41bb690974e8c669e282832be8856bf6d1c5f6c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001103_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.236261 0.443435 0.234541 0.220189 +1 0.236261 0.000001 0.430625 0.039172 0.024819 +2 0.443435 0.430625 0.000001 0.428905 0.414552 +3 0.234541 0.039172 0.428905 0.000001 0.015803 +4 0.220189 0.024819 0.414552 0.015803 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..34f2e7d830cdec566b8ede487266e9e7b3706f1b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12717636 Before NNI: tree length is 0.12717638 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001105_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001105_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eea0c92165e8014db2ef5f757aa5bf49647e07f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001105_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35088000 Before NNI: tree length is 0.35088000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d595cb0b574b4957ad7d43d25d1f81d6a60122dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04957550 Before NNI: tree length is 1.04957550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9edcb87fa6f97284806fa3e8b4f08870b0e1b2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01099600 Before NNI: tree length is 0.01099600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999998 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001113_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001113_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..57616a55a1be1546b591048ce83e321890673fde --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001113_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.61011141 Before NNI: tree length is 0.61011150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c0c9070a5107cf2678b1c29aca5f96e1c0273fe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11703250 Before NNI: tree length is 0.11703250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001119_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001119_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..545c49099eb380d1ffc2b140fc58379814804328 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001119_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22757000 Before NNI: tree length is 0.22757000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f6ae5ae11e2ea41b2390164ddfdd8d8da367672 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001120_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047912 0.219735 0.047912 0.052580 +1 0.047912 0.000001 0.198989 0.000001 0.008004 +2 0.219735 0.198989 0.000001 0.198989 0.203657 +3 0.047912 0.000001 0.198989 0.000001 0.008004 +4 0.052580 0.008004 0.203657 0.008004 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001121_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001121_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ec45e35fd097eb4e7d1a692ce0f3cdb6af74327 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001121_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56570950 Before NNI: tree length is 0.56570950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001124_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001124_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..69d4af4cafcced4ec8e41e2c8c2996917f51a23f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001124_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46056090 Before NNI: tree length is 0.46056087 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2e699786086a4271338a8e6bc40ad2266e90ba2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001134_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49139300 Before NNI: tree length is 0.49139300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..961897d11c365f97304912da6fefe1c410ac689f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86954611 Before NNI: tree length is 0.86954613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001140_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001140_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b18d5a281f4a0844950c5da1fe76cda228f9f599 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001140_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10521460 Before NNI: tree length is 0.10521463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f0ce15a073e9abce97fd437d2c559e774bc34045 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001141_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.108011 0.472566 0.107480 0.113959 +1 0.108011 0.000001 0.473894 0.000531 0.005948 +2 0.472566 0.473894 0.000001 0.473363 0.479842 +3 0.107480 0.000531 0.473363 0.000001 0.006479 +4 0.113959 0.005948 0.479842 0.006479 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb6c7ea30120da2a541685267e20ee5cc282c3fe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.103842 0.184333 0.111004 0.110155 +1 0.103842 0.000001 0.141693 0.010928 0.010080 +2 0.184333 0.141693 0.000001 0.148855 0.148007 +3 0.111004 0.010928 0.148855 0.000001 0.013983 +4 0.110155 0.010080 0.148007 0.013983 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f8a42c6c9e5de3b21bfe22f86be65373d7d9cd71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001142_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23054638 Before NNI: tree length is 0.23054637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001143_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001143_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f67bb77ec43297c922d3eefc95b545f96c3b301 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001143_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25904300 Before NNI: tree length is 0.25904300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001147_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001147_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f72104d529ef1363e22781a26e262c55a668c04d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001147_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.078436 0.141601 0.078436 0.078436 +1 0.078436 0.000001 0.125266 0.000001 0.000001 +2 0.141601 0.125266 0.000001 0.125266 0.125266 +3 0.078436 0.000001 0.125266 0.000001 0.000001 +4 0.078436 0.000001 0.125266 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001148_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001148_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..18d6763d2509de7f4750def13899b9863c219978 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001148_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.127888 0.308067 0.132006 0.127888 +1 0.127888 0.000001 0.324020 0.008086 0.000001 +2 0.308067 0.324020 0.000001 0.328139 0.324020 +3 0.132006 0.008086 0.328139 0.000001 0.008086 +4 0.127888 0.000001 0.324020 0.008086 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e584763fe4393e83db8ec27fe56164f8d300d9a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001150_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12576285 Before NNI: tree length is 0.12576288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b6a1edd2efbd3fe59eb55a4b542ed8e2812ed09f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.312656 0.434261 0.309181 0.312656 +1 0.312656 0.000001 0.175024 0.021991 0.000001 +2 0.434261 0.175024 0.000001 0.171549 0.175024 +3 0.309181 0.021991 0.171549 0.000001 0.021991 +4 0.312656 0.000001 0.175024 0.021991 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..745f4695056beade8c0d7a158a91fca42ecf65b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001151_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47022900 Before NNI: tree length is 0.47022900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001152_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001152_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..965b92318ce6d124e265dc0d18032bbb965266af --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001152_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81788050 Before NNI: tree length is 0.81788050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c413d330880b287251b3890cbc11bf521debb94 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.103848 0.158577 0.076327 0.109117 +1 0.103848 0.000001 0.208450 0.069311 0.015859 +2 0.158577 0.208450 0.000001 0.180928 0.213719 +3 0.076327 0.069311 0.180928 0.000001 0.074579 +4 0.109117 0.015859 0.213719 0.074579 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b4b4b69a3debec8b460ad831c4396469be7879a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001159_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26689603 Before NNI: tree length is 0.26689600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001174_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001174_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a89018548ea8a0c9b764dd3db5868d710b611be --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001174_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.71874500 Before NNI: tree length is 0.71874500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001176_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001176_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a3627d5ed663d16ed7b89407902d9747adeeaf6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001176_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53361750 Before NNI: tree length is 0.53361750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3e3bbd4927c5a0413dc8e646949e97f71627d2a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.199900 0.562910 0.198738 0.198658 +1 0.199900 0.000001 0.537069 0.019902 0.009682 +2 0.562910 0.537069 0.000001 0.535907 0.535827 +3 0.198738 0.019902 0.535907 0.000001 0.018659 +4 0.198658 0.009682 0.535827 0.018659 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..18771599d8e44801bebe065d4521a76000f31643 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001178_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66352925 Before NNI: tree length is 0.66352925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..584ecd64d7096457c32eff528057f0a877c5bd52 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001180_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.095297 0.214873 0.083391 0.085983 +1 0.095297 0.000001 0.203352 0.014200 0.013099 +2 0.214873 0.203352 0.000001 0.191447 0.194039 +3 0.083391 0.014200 0.191447 0.000001 0.004887 +4 0.085983 0.013099 0.194039 0.004887 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6aa9cf0435979be55cd62b1f450acc0f3d929bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33193025 Before NNI: tree length is 0.33193025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001184_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001184_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..88b8a33a41696330cb3dff1864eb4d886e286253 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001184_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29584975 Before NNI: tree length is 0.29584975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001188_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001188_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69c4f31564abba8e550af810d26abd919e9c5abe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001188_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.316997 0.360629 0.308994 0.317267 +1 0.316997 0.000001 0.362861 0.035467 0.052127 +2 0.360629 0.362861 0.000001 0.354858 0.363130 +3 0.308994 0.035467 0.354858 0.000001 0.044123 +4 0.317267 0.052127 0.363130 0.044123 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..21ad49e67aa46c4c2c2e2f42ce5cbc2ac9ed6de7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.108770 0.104008 0.108770 0.108770 +1 0.108770 0.000001 0.143171 0.000001 0.000001 +2 0.104008 0.143171 0.000001 0.143171 0.143171 +3 0.108770 0.000001 0.143171 0.000001 0.000001 +4 0.108770 0.000001 0.143171 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72d42a33ca6b7035cc563a5b0cff62b0d07df02d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14519450 Before NNI: tree length is 0.14519450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001199_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001199_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..385ec987f3d5104a54cfbc9d67cc4c46d89d6349 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001199_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.127181 0.240631 0.125662 0.125694 +1 0.127181 0.000001 0.249675 0.001520 0.001487 +2 0.240631 0.249675 0.000001 0.248156 0.248188 +3 0.125662 0.001520 0.248156 0.000001 0.000032 +4 0.125694 0.001487 0.248188 0.000032 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6c1102a0ed00c97dc8c1c161ad6f2e96e3152d49 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025311 0.108359 0.025311 0.025311 +1 0.025311 0.000001 0.106602 0.000001 0.000001 +2 0.108359 0.106602 0.000001 0.106602 0.106602 +3 0.025311 0.000001 0.106602 0.000001 0.000001 +4 0.025311 0.000001 0.106602 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9dde7b9595363ed15c48727dbb584e7530fea1a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001201_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12013700 Before NNI: tree length is 0.12013700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001205_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001205_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f6516a6c861f77c7df9dd1aac6d69519acb7e2d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001205_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.304065 0.327514 0.305578 0.305578 +1 0.304065 0.000001 0.179378 0.005814 0.005814 +2 0.327514 0.179378 0.000001 0.180891 0.180891 +3 0.305578 0.005814 0.180891 0.000001 0.000001 +4 0.305578 0.005814 0.180891 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001212_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001212_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d768b81e971e19198ffea71c38242c0f6c8adb3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001212_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.216137 0.354914 0.215201 0.215201 +1 0.216137 0.000001 0.336502 0.012523 0.012523 +2 0.354914 0.336502 0.000001 0.335566 0.335566 +3 0.215201 0.012523 0.335566 0.000001 0.000001 +4 0.215201 0.012523 0.335566 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6e5adfa0f69cd561eebdd89e1dca019df88e268 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44293980 Before NNI: tree length is 0.44293975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9abafe06dbc2b79abd62a6b92671ad61c6494256 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001224_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39264900 Before NNI: tree length is 0.39264900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001229_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001229_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ac5657ede9f3ea3bd6d4615b8552d7f6f0b7106 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001229_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.094518 0.179617 0.073919 0.093712 +1 0.094518 0.000001 0.194194 0.025069 0.002009 +2 0.179617 0.194194 0.000001 0.173596 0.193388 +3 0.073919 0.025069 0.173596 0.000001 0.024263 +4 0.093712 0.002009 0.193388 0.024263 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6880cecd81e8377addfbe0b1227a0276afa9137d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063590 0.131738 0.063852 0.062052 +1 0.063590 0.000001 0.131509 0.007471 0.001539 +2 0.131738 0.131509 0.000001 0.131770 0.129970 +3 0.063852 0.007471 0.131770 0.000001 0.005933 +4 0.062052 0.001539 0.129970 0.005933 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d205a260bfd06a1e3173cea7a9d7df4c5d8b4c47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001230_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16728515 Before NNI: tree length is 0.16728513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001231_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001231_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fac47c4093f63706968b45f489123294f2321abd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001231_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05727850 Before NNI: tree length is 0.05727850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b32dbf8138634f9ad1e1528dd325204a2393c687 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.114304 0.238251 0.114304 0.114304 +1 0.114304 0.000001 0.239705 0.000001 0.000001 +2 0.238251 0.239705 0.000001 0.239705 0.239705 +3 0.114304 0.000001 0.239705 0.000001 0.000001 +4 0.114304 0.000001 0.239705 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..308248a880a064a45335f48c92a4b01a9785a02d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001234_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29613100 Before NNI: tree length is 0.29613100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..09e4807e06594bfd45cb56fcb90acc48e1f017fd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001237_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024342 0.233857 0.017714 0.017714 +1 0.024342 0.000001 0.221753 0.011998 0.011998 +2 0.233857 0.221753 0.000001 0.221513 0.221513 +3 0.017714 0.011998 0.221513 0.000001 0.000001 +4 0.017714 0.011998 0.221513 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001240_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001240_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bdfd41f42b0cda387d7b61a2d3409209356bcdac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001240_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.664973 1.249622 0.645460 0.645460 +1 0.664973 0.000001 1.218217 0.032073 0.032073 +2 1.249622 1.218217 0.000001 1.198704 1.198704 +3 0.645460 0.032073 1.198704 0.000001 0.000001 +4 0.645460 0.032073 1.198704 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4d97b349027145da5e726ddd44891cbaca5cf0fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031820 0.073405 0.033084 0.033084 +1 0.031820 0.000001 0.064194 0.008118 0.008118 +2 0.073405 0.064194 0.000001 0.065458 0.065458 +3 0.033084 0.008118 0.065458 0.000001 0.000001 +4 0.033084 0.008118 0.065458 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001245_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001245_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9fd0d7d65e91d5bb2a85e9b4c8f899a7eee8b7b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001245_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.02230886 Before NNI: tree length is 1.02230887 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b243369343e92888ef1e52181e153e24bc51060 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014463 0.044158 0.014463 0.014463 +1 0.014463 0.000001 0.039377 0.000001 0.000001 +2 0.044158 0.039377 0.000001 0.039377 0.039377 +3 0.014463 0.000001 0.039377 0.000001 0.000001 +4 0.014463 0.000001 0.039377 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..76d4be355a8632f76e5bd79f80cb563724e9267f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.139603 0.176656 0.139603 0.139603 +1 0.139603 0.000001 0.189726 0.000001 0.000001 +2 0.176656 0.189726 0.000001 0.189726 0.189726 +3 0.139603 0.000001 0.189726 0.000001 0.000001 +4 0.139603 0.000001 0.189726 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001252_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001252_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..56c3b6f04a8fcceb0de1c81f9feb479a17befc46 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001252_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43878850 Before NNI: tree length is 0.43878850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001253_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001253_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8cc31ec71a1afb67a1fa8ae444af1f8a705b494d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001253_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.328900 0.528667 0.328900 0.328900 +1 0.328900 0.000001 0.543478 0.000001 0.000001 +2 0.528667 0.543478 0.000001 0.543478 0.543478 +3 0.328900 0.000001 0.543478 0.000001 0.000001 +4 0.328900 0.000001 0.543478 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001254_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001254_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ace44599d21aa6e0d619a13ac81cc4fddf64086a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001254_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76443225 Before NNI: tree length is 0.76443225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001257_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001257_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5df29e5e8581f89a66ee8786624e6e03b2291844 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001257_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37094225 Before NNI: tree length is 0.37094225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f087dff68a2ffa168ad80213e504112bfc182cf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001259_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.340908 0.357853 0.331046 0.331046 +1 0.340908 0.000001 0.196611 0.016285 0.016285 +2 0.357853 0.196611 0.000001 0.186750 0.186750 +3 0.331046 0.016285 0.186750 0.000001 0.000001 +4 0.331046 0.016285 0.186750 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9266336f6c2503831efa50cef8c980410079fc6a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33093750 Before NNI: tree length is 0.33093750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001263_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001263_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..558d9d7dcf68ad91dccb2153288bfe09fe6a21d9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001263_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67323929 Before NNI: tree length is 0.67323925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ceceb39058c032823929dd97a67a44158907eb8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001266_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.215848 0.378102 0.218073 0.218073 +1 0.215848 0.000001 0.380343 0.007663 0.007663 +2 0.378102 0.380343 0.000001 0.382569 0.382569 +3 0.218073 0.007663 0.382569 0.000001 0.000001 +4 0.218073 0.007663 0.382569 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001268_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001268_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbe279627b2cec77bad8ef3475c5865656d99a4e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001268_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14131000 Before NNI: tree length is 0.14131000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001271_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001271_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ec1449fde98a417b10862f4f246f217999ccce7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001271_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.444118 0.542675 0.435610 0.452906 +1 0.444118 0.000001 0.399548 0.032955 0.032459 +2 0.542675 0.399548 0.000001 0.391041 0.408337 +3 0.435610 0.032955 0.391041 0.000001 0.041744 +4 0.452906 0.032459 0.408337 0.041744 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be9d90da77e1ee7a2803cb64cd245e568abf35a4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.098868 0.232939 0.107809 0.097722 +1 0.098868 0.000001 0.201408 0.009434 0.016962 +2 0.232939 0.201408 0.000001 0.210349 0.200263 +3 0.107809 0.009434 0.210349 0.000001 0.025903 +4 0.097722 0.016962 0.200263 0.025903 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f61dc49ba02ec9f3b31e14f726a7731bf026a44a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001273_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28370321 Before NNI: tree length is 0.28370325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001274_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001274_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..791ba5baff607f1fc2dbd1c2487e210dbc6fea44 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001274_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.169415 0.291490 0.160058 0.165629 +1 0.169415 0.000001 0.297202 0.027393 0.016142 +2 0.291490 0.297202 0.000001 0.287845 0.293416 +3 0.160058 0.027393 0.287845 0.000001 0.023608 +4 0.165629 0.016142 0.293416 0.023608 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001279_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001279_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe78181ca26b1ac7f865a95a6517c3c667e73f95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001279_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21900486 Before NNI: tree length is 0.21900487 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001282_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001282_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..22a2fa4676890865813c379d97871c70dbe8667e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001282_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38934140 Before NNI: tree length is 0.38934138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b90231888d54f5e9cdb108ea41347d3befe471f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51050565 Before NNI: tree length is 0.51050562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c523d9440cf5fc23fb1fdd9194206409dbf2f397 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001287_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.238614 0.279694 0.238964 0.207592 +1 0.238614 0.000001 0.412078 0.014079 0.042664 +2 0.279694 0.412078 0.000001 0.412428 0.381055 +3 0.238964 0.014079 0.412428 0.000001 0.043014 +4 0.207592 0.042664 0.381055 0.043014 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5176eedc648812aadc8d234c08ca68b0d9901a66 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05589266 Before NNI: tree length is 0.05589263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e679718c46b152ca5beda20a13ff1e9c08d27b2c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001289_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026219 0.013275 0.017299 0.018899 +1 0.026219 0.000001 0.013907 0.008920 0.018922 +2 0.013275 0.013907 0.000001 0.004987 0.006587 +3 0.017299 0.008920 0.004987 0.000001 0.010003 +4 0.018899 0.018922 0.006587 0.010003 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ee2ba8e950dd8e459141eefa14b253ac8a0c896c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.231232 0.344872 0.217938 0.283643 +1 0.231232 0.000001 0.380123 0.013294 0.052438 +2 0.344872 0.380123 0.000001 0.366829 0.432534 +3 0.217938 0.013294 0.366829 0.000001 0.065705 +4 0.283643 0.052438 0.432534 0.065705 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001301_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001301_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f636282752e4fcd5d2e24e04cc080c7e6427811 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001301_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.086923 0.200794 0.086392 0.093369 +1 0.086923 0.000001 0.152181 0.009465 0.010849 +2 0.200794 0.152181 0.000001 0.151650 0.158627 +3 0.086392 0.009465 0.151650 0.000001 0.015910 +4 0.093369 0.010849 0.158627 0.015910 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001307_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001307_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b2783f17d38b0e3a3e5c9260a6a775ff3d66268 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001307_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47477900 Before NNI: tree length is 0.47477900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..20cbf984f7785a416fc41fd49dc7466347bf9c93 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001308_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33698050 Before NNI: tree length is 0.33698050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001312_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001312_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5c9d680e3a1d36d2a0ce6b0b04ba9cb705e31d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001312_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021109 0.045409 0.021109 0.021109 +1 0.021109 0.000001 0.045281 0.000001 0.000001 +2 0.045409 0.045281 0.000001 0.045281 0.045281 +3 0.021109 0.000001 0.045281 0.000001 0.000001 +4 0.021109 0.000001 0.045281 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001316_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001316_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f92afd4ed40603eae10d3b4d7251edb58dbdc8b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001316_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.288065 0.353524 0.285299 0.287459 +1 0.288065 0.000001 0.187325 0.003107 0.007973 +2 0.353524 0.187325 0.000001 0.184559 0.186719 +3 0.285299 0.003107 0.184559 0.000001 0.005207 +4 0.287459 0.007973 0.186719 0.005207 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001319_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001319_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2c11e8d908da6718513589f5159e59a78f057389 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001319_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.051321 0.040485 0.061760 0.060426 +1 0.051321 0.000001 0.030198 0.018651 0.017318 +2 0.040485 0.030198 0.000001 0.040636 0.039303 +3 0.061760 0.018651 0.040636 0.000001 0.005510 +4 0.060426 0.017318 0.039303 0.005510 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001320_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001320_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fdf8b667cbe2a68497d3d4ff1564f4823f4a4676 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001320_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040728 0.028227 0.041189 0.040728 +1 0.040728 0.000001 0.035815 0.003224 0.000001 +2 0.028227 0.035815 0.000001 0.036277 0.035815 +3 0.041189 0.003224 0.036277 0.000001 0.003224 +4 0.040728 0.000001 0.035815 0.003224 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001322_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001322_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6bdc99bc1d2e8d637926656ba029f34ef4caf0b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001322_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01199083 Before NNI: tree length is 0.01199088 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999998 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001324_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001324_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0beb45cbf96747f8829be2c4b608963aa58e5bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001324_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44583700 Before NNI: tree length is 0.44583700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001325_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001325_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0612b558745332cf44156e912741b57a8cfa9ae7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001325_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07586150 Before NNI: tree length is 0.07586150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001329_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001329_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f087291a29fa9ee551876a89848a32b14bfad456 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001329_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.426048 0.163365 0.426048 0.426048 +1 0.426048 0.000001 0.407252 0.000001 0.000001 +2 0.163365 0.407252 0.000001 0.407252 0.407252 +3 0.426048 0.000001 0.407252 0.000001 0.000001 +4 0.426048 0.000001 0.407252 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001332_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001332_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..76eec10ca0b8b3ebed7dc46b5cc71192742c01d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001332_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007985 0.084409 0.014731 0.014731 +1 0.007985 0.000001 0.080943 0.006745 0.006745 +2 0.084409 0.080943 0.000001 0.087689 0.087689 +3 0.014731 0.006745 0.087689 0.000001 0.000001 +4 0.014731 0.006745 0.087689 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001335_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001335_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32b099f4b3dac39245e78519ea6e61570d94f991 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001335_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48976271 Before NNI: tree length is 0.48976275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001336_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001336_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7ae6c0e6c6957d06a68193ac36e43650fada6701 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001336_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.102140 0.200701 0.097566 0.091386 +1 0.102140 0.000001 0.218258 0.025771 0.027125 +2 0.200701 0.218258 0.000001 0.213684 0.207504 +3 0.097566 0.025771 0.213684 0.000001 0.022551 +4 0.091386 0.027125 0.207504 0.022551 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..746e824c883cceb36220d8c28192dc81dd7a8196 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022416 0.092898 0.019836 0.020749 +1 0.022416 0.000001 0.084501 0.002726 0.003638 +2 0.092898 0.084501 0.000001 0.081921 0.082833 +3 0.019836 0.002726 0.081921 0.000001 0.000913 +4 0.020749 0.003638 0.082833 0.000913 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..03ffc044c9f0652681abd512b7da7f8b80905f87 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.439717 0.488804 0.422454 0.434973 +1 0.439717 0.000001 0.442317 0.084151 0.033269 +2 0.488804 0.442317 0.000001 0.425053 0.437573 +3 0.422454 0.084151 0.425053 0.000001 0.079407 +4 0.434973 0.033269 0.437573 0.079407 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..24643fec83aabbb0036ea63cf87c82395a1598b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001340_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73312525 Before NNI: tree length is 0.73312525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001342_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001342_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c827d6fbd551cdca47101017c4b1b886b716fb8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001342_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.457553 0.572132 0.454830 0.467561 +1 0.457553 0.000001 0.289687 0.013890 0.018622 +2 0.572132 0.289687 0.000001 0.286964 0.299696 +3 0.454830 0.013890 0.286964 0.000001 0.023898 +4 0.467561 0.018622 0.299696 0.023898 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78dbd115f4ed51a2c818a5fa732ac086002bb374 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.110856 0.129782 0.104744 0.111739 +1 0.110856 0.000001 0.043832 0.007194 0.014190 +2 0.129782 0.043832 0.000001 0.037720 0.044715 +3 0.104744 0.007194 0.037720 0.000001 0.006996 +4 0.111739 0.014190 0.044715 0.006996 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001349_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001349_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..722b5fd3a01a5c9b3c02b3fd8019175e578680e0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001349_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.92847926 Before NNI: tree length is 0.92847925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001350_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001350_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb678d33061a7f77e58eb1cfb18bd7d522031f25 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001350_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.237608 0.330483 0.239630 0.243100 +1 0.237608 0.000001 0.343243 0.042035 0.030740 +2 0.330483 0.343243 0.000001 0.345266 0.348736 +3 0.239630 0.042035 0.345266 0.000001 0.047528 +4 0.243100 0.030740 0.348736 0.047528 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8335cd8f20c5e7e96e4d378a39baa92b1174d907 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040758 0.127517 0.043548 0.043296 +1 0.040758 0.000001 0.131063 0.005985 0.008171 +2 0.127517 0.131063 0.000001 0.133852 0.133600 +3 0.043548 0.005985 0.133852 0.000001 0.010961 +4 0.043296 0.008171 0.133600 0.010961 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d0cb283b5e36632aad959eeb0d6f5a127f79097 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001357_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15941066 Before NNI: tree length is 0.15941062 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e9151faad21cd9176fa7eedf041d4b8766ec9a8f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.292340 0.439586 0.285645 0.282052 +1 0.292340 0.000001 0.544079 0.090480 0.045773 +2 0.439586 0.544079 0.000001 0.537383 0.533790 +3 0.285645 0.090480 0.537383 0.000001 0.080191 +4 0.282052 0.045773 0.533790 0.080191 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ce4cd222a0fdfb928b90f5115031d64ce03f24ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001362_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69763690 Before NNI: tree length is 0.69763688 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001363_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001363_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4361938d8e9bfd02b2b89f58d07056a0e314bd2c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001363_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79809131 Before NNI: tree length is 0.79809125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..40061c1d73f5ea49f03dc53de15654bb275d4cb7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.316152 0.851890 0.316152 0.316152 +1 0.316152 0.000001 0.736065 0.000001 0.000001 +2 0.851890 0.736065 0.000001 0.736065 0.736065 +3 0.316152 0.000001 0.736065 0.000001 0.000001 +4 0.316152 0.000001 0.736065 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c46c72fb96ec7d177fc02501a91e53ee6564874d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001378_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.95205450 Before NNI: tree length is 0.95205450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b0f3d5d53137305c11760135402817ef544471c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48410950 Before NNI: tree length is 0.48410950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001383_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001383_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bdc82464ab8bae6bd9dfe62e0ab84bd2007664c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001383_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10216900 Before NNI: tree length is 0.10216900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001384_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001384_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6713ab1986982d9d73d6aad1d9d9e1e8d0b8492e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001384_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.078044 0.125577 0.059762 0.059762 +1 0.078044 0.000001 0.092483 0.020285 0.020285 +2 0.125577 0.092483 0.000001 0.074201 0.074201 +3 0.059762 0.020285 0.074201 0.000001 0.000001 +4 0.059762 0.020285 0.074201 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3198a43580fa8771ca9bd7e1136c8cba7a317e30 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001386_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.287637 0.206645 0.205918 +1 0.000001 0.000001 0.287637 0.206645 0.205918 +2 0.287637 0.287637 0.000001 0.246827 0.246100 +3 0.206645 0.206645 0.246827 0.000001 0.027097 +4 0.205918 0.205918 0.246100 0.027097 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001388_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001388_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1d11876532a0792844e346b79332804573702d7d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001388_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.281996 0.252369 0.111228 0.098683 +1 0.281996 0.000001 0.179881 0.299207 0.300177 +2 0.252369 0.179881 0.000001 0.269579 0.270550 +3 0.111228 0.299207 0.269579 0.000001 0.129409 +4 0.098683 0.300177 0.270550 0.129409 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..05093016e5363468f3e6743a70e3ef22e1b0d7dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001389_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.358256 0.954963 0.358405 1.241401 +1 0.358256 0.000001 0.926929 0.010069 1.213367 +2 0.954963 0.926929 0.000001 0.927079 1.305983 +3 0.358405 0.010069 0.927079 0.000001 1.213517 +4 1.241401 1.213367 1.305983 1.213517 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001392_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001392_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f4b30829326fc5720de3bf39a334c59932164ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001392_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.204739 0.206374 0.205867 0.011660 +1 0.204739 0.000001 0.229902 0.001229 0.206000 +2 0.206374 0.229902 0.000001 0.231030 0.207636 +3 0.205867 0.001229 0.231030 0.000001 0.207128 +4 0.011660 0.206000 0.207636 0.207128 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b08aea73e552bd8eb3e818d0b8f844fcd1eb721 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.092027 0.191787 0.094489 0.088959 +1 0.092027 0.000001 0.217912 0.007579 0.006771 +2 0.191787 0.217912 0.000001 0.220374 0.214844 +3 0.094489 0.007579 0.220374 0.000001 0.009234 +4 0.088959 0.006771 0.214844 0.009234 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..10931d2075328e45ee05e832d21fd4bed55b6022 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001399_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25773525 Before NNI: tree length is 0.25773525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8fe04b9ddd4c63d6329a1ca7140b5cede4836e39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.098774 0.229193 0.107147 0.097346 +1 0.098774 0.000001 0.234100 0.008373 0.003298 +2 0.229193 0.234100 0.000001 0.242474 0.232673 +3 0.107147 0.008373 0.242474 0.000001 0.011671 +4 0.097346 0.003298 0.232673 0.011671 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001403_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001403_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..facd43cd5f3f180da968b372daff8d642c37c4a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001403_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.104660 0.241749 0.103099 0.107015 +1 0.104660 0.000001 0.198141 0.015620 0.013109 +2 0.241749 0.198141 0.000001 0.196580 0.200496 +3 0.103099 0.015620 0.196580 0.000001 0.017976 +4 0.107015 0.013109 0.200496 0.017976 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b830a9379ba7a2e8c49cb82028913b5aec36246 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.273086 0.818046 0.258205 0.258591 +1 0.273086 0.000001 0.811222 0.062947 0.063333 +2 0.818046 0.811222 0.000001 0.796341 0.796726 +3 0.258205 0.062947 0.796341 0.000001 0.030160 +4 0.258591 0.063333 0.796726 0.030160 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2e90cdd8ea7250c320c2bd3bd118f250e9241dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001404_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.99048285 Before NNI: tree length is 0.99048288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ff0ba939e1afe4993489bafd6d78662aaae499a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001410_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07864564 Before NNI: tree length is 0.07864562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001411_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001411_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c92f20b0dd4a9c2b9371292acccb7eade74fb323 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001411_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20126500 Before NNI: tree length is 0.20126500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001415_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001415_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5e56406a59209938d2fbbf79f9c813bea2ab186c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001415_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.260105 0.521732 0.258420 0.245403 +1 0.260105 0.000001 0.561199 0.026869 0.024979 +2 0.521732 0.561199 0.000001 0.559516 0.546497 +3 0.258420 0.026869 0.559516 0.000001 0.023296 +4 0.245403 0.024979 0.546497 0.023296 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001418_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001418_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..15d90cbd755796130195fe81f18ac841d0f1b979 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001418_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043570 0.074253 0.048504 0.048504 +1 0.043570 0.000001 0.072458 0.011268 0.011268 +2 0.074253 0.072458 0.000001 0.077392 0.077392 +3 0.048504 0.011268 0.077392 0.000001 0.000001 +4 0.048504 0.011268 0.077392 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001420_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001420_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c37c32115188e8fddca3f32b1eb14bf17801dfee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001420_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22117225 Before NNI: tree length is 0.22117225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001422_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001422_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6c9c1214b6a0c42b3e292391a919f398c3eb8c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001422_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23852400 Before NNI: tree length is 0.23852400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..013a3f1824371d3485ea7ce8546e17ad14ffa1c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001424_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.058983 0.201473 0.055247 0.055247 +1 0.058983 0.000001 0.207461 0.005192 0.005192 +2 0.201473 0.207461 0.000001 0.203726 0.203726 +3 0.055247 0.005192 0.203726 0.000001 0.000001 +4 0.055247 0.005192 0.203726 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001425_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001425_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..020b1ff713ba0712993f610413f15e26eaa6a2ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001425_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06898350 Before NNI: tree length is 0.06898350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e94f7dbcec00d3e9e25d407eb9855d5d21b1658 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.080037 0.000001 0.006329 +1 0.000001 0.000001 0.080037 0.000001 0.006329 +2 0.080037 0.080037 0.000001 0.080037 0.085144 +3 0.000001 0.000001 0.080037 0.000001 0.006329 +4 0.006329 0.006329 0.085144 0.006329 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ce9ab927868511a6cc05424fa23772a2d645a5c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001426_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08575600 Before NNI: tree length is 0.08575600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001427_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001427_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..753c7dd6f2ce42a17417ae840cf1700fba95d16d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001427_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17650300 Before NNI: tree length is 0.17650300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1dc1e6e18cba890412ed80a1b84aa30ceee73665 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061658 0.124654 0.061250 0.064666 +1 0.061658 0.000001 0.151802 0.000409 0.003008 +2 0.124654 0.151802 0.000001 0.151394 0.154810 +3 0.061250 0.000409 0.151394 0.000001 0.003417 +4 0.064666 0.003008 0.154810 0.003417 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a198254bc3b78056774d307a81a772667cbb485e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001430_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17206550 Before NNI: tree length is 0.17206550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ecc6b2017b3b6fde96692b8308b7c80c2a9f943a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.232611 0.466689 0.232611 0.225743 +1 0.232611 0.000001 0.477195 0.000001 0.020978 +2 0.466689 0.477195 0.000001 0.477195 0.470327 +3 0.232611 0.000001 0.477195 0.000001 0.020978 +4 0.225743 0.020978 0.470327 0.020978 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1973298b27df688e3a9887fb468679cbb50ba5fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001431_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59530300 Before NNI: tree length is 0.59530300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001432_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001432_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..feb93e0b86833a1698c659b0c21c9dbd2a7120c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001432_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23666479 Before NNI: tree length is 0.23666475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001433_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001433_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b63972caa8d22830303e607856ed60c3a3f910a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001433_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44459450 Before NNI: tree length is 0.44459450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001434_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001434_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81047d7f3eae9058928ec000bd4ace19ecffa5f1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001434_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04490000 Before NNI: tree length is 1.04490000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001435_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001435_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef9f6d29aa00eeb0f9ae60f81a4378dd1d5b58c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001435_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.364182 0.242025 0.363968 0.362977 +1 0.364182 0.000001 0.338667 0.008880 0.002486 +2 0.242025 0.338667 0.000001 0.338453 0.337462 +3 0.363968 0.008880 0.338453 0.000001 0.007675 +4 0.362977 0.002486 0.337462 0.007675 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001439_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001439_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab2c7ac3e362001a372dd98cee755b903b89f39c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001439_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18366585 Before NNI: tree length is 0.18366588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001446_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001446_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..840add6c6af27fe42498d4217ec13f4b0d1f3869 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001446_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15675661 Before NNI: tree length is 0.15675663 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001450_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001450_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b095d4c701395d0ce60b972c12d6c80529848209 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001450_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.221408 0.335335 0.220432 0.215434 +1 0.221408 0.000001 0.359973 0.025757 0.020759 +2 0.335335 0.359973 0.000001 0.358998 0.354000 +3 0.220432 0.025757 0.358998 0.000001 0.010274 +4 0.215434 0.020759 0.354000 0.010274 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001451_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001451_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..61df86354a058e27c6f2f19dace4c6bfb25c09a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001451_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69791154 Before NNI: tree length is 0.69791150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001453_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001453_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..762be894445fff8cb768c3c0991c7dd9416879a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001453_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13279950 Before NNI: tree length is 0.13279950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001454_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001454_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4642318749b61ca79d7bfffff575521a10e49926 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001454_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.745777 0.784061 1.724717 1.756810 +1 1.745777 0.000001 1.740017 0.096925 0.073226 +2 0.784061 1.740017 0.000001 1.718958 1.751051 +3 1.724717 0.096925 1.718958 0.000001 0.107958 +4 1.756810 0.073226 1.751051 0.107958 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001455_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001455_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bac9295a6fa578b0202dce0bbace6401892c5db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001455_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.39806590 Before NNI: tree length is 1.39806587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001463_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001463_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d2283bdb7ac1542a38e439b21c3053cf269f9729 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001463_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027709 0.176772 0.027709 0.029813 +1 0.027709 0.000001 0.172093 0.000001 0.002930 +2 0.176772 0.172093 0.000001 0.172093 0.174197 +3 0.027709 0.000001 0.172093 0.000001 0.002930 +4 0.029813 0.002930 0.174197 0.002930 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb515f8aad7af178276f3f57c455e9b7de3b4ff8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50362400 Before NNI: tree length is 0.50362400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b0f0dd972e12f68ec6d79c033e42557bde6163c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.209135 0.435023 0.197165 0.195526 +1 0.209135 0.000001 0.451139 0.019734 0.029167 +2 0.435023 0.451139 0.000001 0.439168 0.437529 +3 0.197165 0.019734 0.439168 0.000001 0.017197 +4 0.195526 0.029167 0.437529 0.017197 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f75d937d443514ae47c573c8727a182665cc29c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001469_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55930915 Before NNI: tree length is 0.55930912 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001470_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001470_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b998c9b0020d4878c5b83f8a228f9e3e661ad32b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001470_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.038317 0.084091 0.038317 0.038317 +1 0.038317 0.000001 0.093392 0.000001 0.000001 +2 0.084091 0.093392 0.000001 0.093392 0.093392 +3 0.038317 0.000001 0.093392 0.000001 0.000001 +4 0.038317 0.000001 0.093392 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001471_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001471_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ed3bff459dc1937fbfd11339cfc5ff2aa1dff92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001471_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23689000 Before NNI: tree length is 0.23689000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5cb61e3afc590b1465e6e951749f682db292b0f5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052017 0.225662 0.051751 0.040678 +1 0.052017 0.000001 0.232850 0.005385 0.027237 +2 0.225662 0.232850 0.000001 0.232584 0.221511 +3 0.051751 0.005385 0.232584 0.000001 0.026970 +4 0.040678 0.027237 0.221511 0.026970 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001475_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001475_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a642a94699c6f769c2c7d543a5a3b2a39ae199d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001475_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009970 0.165874 0.009970 0.009970 +1 0.009970 0.000001 0.160117 0.000001 0.000001 +2 0.165874 0.160117 0.000001 0.160117 0.160117 +3 0.009970 0.000001 0.160117 0.000001 0.000001 +4 0.009970 0.000001 0.160117 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001477_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001477_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..010b60dc5ca51774be7bc937075c1d69d91e2c3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001477_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021779 0.160998 0.022252 0.023662 +1 0.021779 0.000001 0.153215 0.002074 0.015879 +2 0.160998 0.153215 0.000001 0.153688 0.149243 +3 0.022252 0.002074 0.153688 0.000001 0.016351 +4 0.023662 0.015879 0.149243 0.016351 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001480_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001480_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2c42c840d27c9bff92edfb6f5c63f4aa82aa50d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001480_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32063045 Before NNI: tree length is 0.32063050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..383929531b014a9ed609553445378d55f6ed574a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001482_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.273976 0.287202 0.274277 0.290720 +1 0.273976 0.000001 0.260592 0.024572 0.026128 +2 0.287202 0.260592 0.000001 0.260892 0.277336 +3 0.274277 0.024572 0.260892 0.000001 0.041316 +4 0.290720 0.026128 0.277336 0.041316 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001483_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001483_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..958fc87e5f5fbb5b5b7d871e48ae31de42adbf28 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001483_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.153882 0.184731 0.156065 0.153229 +1 0.153882 0.000001 0.172350 0.011352 0.004391 +2 0.184731 0.172350 0.000001 0.174532 0.171696 +3 0.156065 0.011352 0.174532 0.000001 0.010699 +4 0.153229 0.004391 0.171696 0.010699 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa0dd06cdcb65c9a913c38f70a4907c41f514f68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001484_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28066522 Before NNI: tree length is 0.28066525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001488_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001488_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2ae7c4d0670efaffd57536e96ad97bbe6bb509c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001488_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.284331 0.278644 0.285130 0.283207 +1 0.284331 0.000001 0.294118 0.012048 0.010125 +2 0.278644 0.294118 0.000001 0.294917 0.292994 +3 0.285130 0.012048 0.294917 0.000001 0.004773 +4 0.283207 0.010125 0.292994 0.004773 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001489_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001489_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed6ef471bb37875d609769f7f7dc3c87d25308df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001489_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.80129125 Before NNI: tree length is 0.80129125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..826295e77e5e8e603477d9e9ed90bbd83f1a03cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.105536 0.264952 0.105031 0.108348 +1 0.105536 0.000001 0.273340 0.005311 0.011980 +2 0.264952 0.273340 0.000001 0.272834 0.276151 +3 0.105031 0.005311 0.272834 0.000001 0.011475 +4 0.108348 0.011980 0.276151 0.011475 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001494_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001494_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..99cff426e68a0aaf2f8b5f3aede8190dadfe2872 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001494_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060826 0.154145 0.054240 0.054464 +1 0.060826 0.000001 0.170731 0.006586 0.006361 +2 0.154145 0.170731 0.000001 0.164145 0.164369 +3 0.054240 0.006586 0.164145 0.000001 0.000224 +4 0.054464 0.006361 0.164369 0.000224 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001498_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001498_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..68a9da752f4063f7eca6a2746f8ae3a2b9fca0d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001498_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057161 0.194898 0.054539 0.051866 +1 0.057161 0.000001 0.181052 0.008565 0.009881 +2 0.194898 0.181052 0.000001 0.178430 0.175757 +3 0.054539 0.008565 0.178430 0.000001 0.007259 +4 0.051866 0.009881 0.175757 0.007259 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d11732db934c665e4f3b632d417cbf918f83a8a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012209 0.012209 0.018373 0.012209 +1 0.012209 0.000001 0.000001 0.009132 0.000001 +2 0.012209 0.000001 0.000001 0.009132 0.000001 +3 0.018373 0.009132 0.009132 0.000001 0.009132 +4 0.012209 0.000001 0.000001 0.009132 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..123d3d778abe81a08c9b35856f61f49760ccf0f2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001500_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01985800 Before NNI: tree length is 0.01985800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001509_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001509_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bb4bff6b72a5f4a4ed5b0bd743257ca7037680f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001509_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52303050 Before NNI: tree length is 0.52303050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001512_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001512_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69aaf85ac2804fd70a3b80a5c43619710947cddc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001512_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.083362 0.207782 0.087865 0.088333 +1 0.083362 0.000001 0.233531 0.009282 0.018702 +2 0.207782 0.233531 0.000001 0.238035 0.238503 +3 0.087865 0.009282 0.238035 0.000001 0.023206 +4 0.088333 0.018702 0.238503 0.023206 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001513_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001513_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b3c8c879af7b0f3aebd701440e0a26ba36f78fa8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001513_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063723 0.158294 0.063723 0.064166 +1 0.063723 0.000001 0.142057 0.000001 0.001907 +2 0.158294 0.142057 0.000001 0.142057 0.142500 +3 0.063723 0.000001 0.142057 0.000001 0.001907 +4 0.064166 0.001907 0.142500 0.001907 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001518_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001518_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c40fe7f374b536393ce66a67c123126c0989479c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001518_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53346900 Before NNI: tree length is 0.53346900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0df287c145a111a98e348a256102c18055002e5f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001521_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.116927 0.238212 0.120986 0.116271 +1 0.116927 0.000001 0.254687 0.030208 0.009186 +2 0.238212 0.254687 0.000001 0.258746 0.254031 +3 0.120986 0.030208 0.258746 0.000001 0.029551 +4 0.116271 0.009186 0.254031 0.029551 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d461d03458f3b0258570fb835bdacde3dd939df3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013578 0.057802 0.013539 0.017285 +1 0.013578 0.000001 0.047547 0.000039 0.003707 +2 0.057802 0.047547 0.000001 0.047509 0.051254 +3 0.013539 0.000039 0.047509 0.000001 0.003745 +4 0.017285 0.003707 0.051254 0.003745 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001526_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001526_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b29ed26f2939bb50829dd7978bca5552737e12a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001526_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25098450 Before NNI: tree length is 0.25098450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001528_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001528_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..542be57bd7985f618f80ea31c5982d674a499851 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001528_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.071623 0.210321 0.072090 0.077437 +1 0.071623 0.000001 0.228250 0.004217 0.009564 +2 0.210321 0.228250 0.000001 0.228717 0.234064 +3 0.072090 0.004217 0.228717 0.000001 0.007411 +4 0.077437 0.009564 0.234064 0.007411 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ca17fac1637229fb9c6b00845de3457b8a1db68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001530_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20901887 Before NNI: tree length is 0.20901887 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001531_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001531_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8403aa803113a3e6a8dd7cdffdb72303820c1c61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001531_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.572169 0.070235 0.405845 0.405845 +1 0.572169 0.000001 0.531232 0.373456 0.373456 +2 0.070235 0.531232 0.000001 0.364908 0.364908 +3 0.405845 0.373456 0.364908 0.000001 0.000001 +4 0.405845 0.373456 0.364908 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001537_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001537_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..57bf6d10dbbce521f927a5f58f615cf010c39fcf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001537_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10071040 Before NNI: tree length is 0.10071037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..676a0b56d98c17bf2b7bdb7b7487ed0ed821c96f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.224051 0.222163 0.224051 0.224051 +1 0.224051 0.000001 0.352629 0.000001 0.000001 +2 0.222163 0.352629 0.000001 0.352629 0.352629 +3 0.224051 0.000001 0.352629 0.000001 0.000001 +4 0.224051 0.000001 0.352629 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bff66d190e90be021f3d741965d9aee527bc6642 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001539_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39942250 Before NNI: tree length is 0.39942250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001542_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001542_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64dc25f38564395984581b0dd562abb6c4b81338 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001542_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58324200 Before NNI: tree length is 0.58324200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d1674fe8784b8c1eb80b742df77dead5f4484386 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001543_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015443 0.529594 0.015399 0.018389 +1 0.015443 0.000001 0.532855 0.000914 0.005973 +2 0.529594 0.532855 0.000001 0.532811 0.535801 +3 0.015399 0.000914 0.532811 0.000001 0.005929 +4 0.018389 0.005973 0.535801 0.005929 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001548_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001548_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd8fb903064015379d82916705a22986151c3867 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001548_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09374704 Before NNI: tree length is 0.09374700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5714058bd312efaa6e352e2841c884bffd8a7666 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.61369650 Before NNI: tree length is 0.61369650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001555_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001555_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64ae447862d4bef6202fae613359c5275fbeadce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001555_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29426356 Before NNI: tree length is 0.29426350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001556_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001556_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3dd47705bedbc4ad35c250c0a6f1c178b164faf2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001556_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15804300 Before NNI: tree length is 0.15804300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001557_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001557_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b999519b1fff7159e553858716a92139a8e698b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001557_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.133052 0.174789 0.128755 0.126850 +1 0.133052 0.000001 0.185397 0.011701 0.009797 +2 0.174789 0.185397 0.000001 0.181100 0.179196 +3 0.128755 0.011701 0.181100 0.000001 0.003148 +4 0.126850 0.009797 0.179196 0.003148 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001558_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001558_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1637b175e04f73bc5cfff5f682d5ae893163ad6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001558_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.053227 0.196856 0.053227 0.053227 +1 0.053227 0.000001 0.201979 0.000001 0.000001 +2 0.196856 0.201979 0.000001 0.201979 0.201979 +3 0.053227 0.000001 0.201979 0.000001 0.000001 +4 0.053227 0.000001 0.201979 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..489e30cae24f8d2dda72448d80617027e1ebe290 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001561_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.213632 0.204197 0.215306 0.211827 +1 0.213632 0.000001 0.116410 0.005068 0.003385 +2 0.204197 0.116410 0.000001 0.118084 0.114605 +3 0.215306 0.005068 0.118084 0.000001 0.005059 +4 0.211827 0.003385 0.114605 0.005059 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6604752f1a55831c8fedb3cc6852cdb612debad9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039125 0.059410 0.037605 0.037412 +1 0.039125 0.000001 0.069675 0.001520 0.001714 +2 0.059410 0.069675 0.000001 0.068155 0.067961 +3 0.037605 0.001520 0.068155 0.000001 0.000193 +4 0.037412 0.001714 0.067961 0.000193 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001564_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001564_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f976b5a24a3f39ac63da0eaf19896b6975973ff0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001564_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35358150 Before NNI: tree length is 0.35358150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..66a4b4a99e71a1af8f6f542bac1660146cd3d7db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001565_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31781800 Before NNI: tree length is 0.31781800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001566_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001566_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9fc053874aac39c743f3d0ef162641427ae445e4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001566_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033742 0.109899 0.027802 0.029324 +1 0.033742 0.000001 0.108765 0.006624 0.010044 +2 0.109899 0.108765 0.000001 0.102825 0.104347 +3 0.027802 0.006624 0.102825 0.000001 0.004104 +4 0.029324 0.010044 0.104347 0.004104 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001567_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001567_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92d56f4de3ff6bb6e9e9fdb0c508a68b65e1742c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001567_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31071669 Before NNI: tree length is 0.31071675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001572_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001572_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6f70871bf7eea08bffbd6c1ce8b87b2267e59ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001572_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44651550 Before NNI: tree length is 0.44651550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001576_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001576_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..14b08569451abf298fca8665b230146436c68907 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001576_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11156450 Before NNI: tree length is 0.11156450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001579_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001579_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5551ee1eef57828c1217280bb28efbb31aacb8bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001579_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67519800 Before NNI: tree length is 0.67519800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7b3303e30a53f39d4ac0665aff0f95077dab4f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.015280 0.994941 0.952754 1.041244 +1 1.015280 0.000001 0.189530 0.178927 0.128324 +2 0.994941 0.189530 0.000001 0.158588 0.215494 +3 0.952754 0.178927 0.158588 0.000001 0.204891 +4 1.041244 0.128324 0.215494 0.204891 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a800d3c68270335345bd3394a2fc4b447e67df16 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19715400 Before NNI: tree length is 0.19715400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001589_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001589_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4d6e860c4645818e2bcfc70149133bfe17726d0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001589_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.284202 0.478356 0.257928 0.254913 +1 0.284202 0.000001 0.431809 0.098768 0.095753 +2 0.478356 0.431809 0.000001 0.405535 0.402520 +3 0.257928 0.098768 0.405535 0.000001 0.013066 +4 0.254913 0.095753 0.402520 0.013066 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001590_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001590_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e7d6680ceae637248081d68983eccfeee05ab70 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001590_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26781175 Before NNI: tree length is 0.26781175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dd2e736e522172cbea7a3619ed17b0d6a60bf47b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001594_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.480666 0.439253 0.143794 0.147192 +1 0.480666 0.000001 0.295500 0.518078 0.521476 +2 0.439253 0.295500 0.000001 0.476664 0.480062 +3 0.143794 0.518078 0.476664 0.000001 0.025789 +4 0.147192 0.521476 0.480062 0.025789 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001597_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001597_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e23472f152111f8184bcf98d64d2b9c8467a9dcc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001597_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.291676 0.318294 0.269639 0.290946 +1 0.291676 0.000001 0.409087 0.029330 0.009322 +2 0.318294 0.409087 0.000001 0.387050 0.408357 +3 0.269639 0.029330 0.387050 0.000001 0.028601 +4 0.290946 0.009322 0.408357 0.028601 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d99af75b924b3e617791744758660547ef851a6c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001598_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.233352 0.358126 0.229935 0.225397 +1 0.233352 0.000001 0.355644 0.022845 0.014218 +2 0.358126 0.355644 0.000001 0.352226 0.347688 +3 0.229935 0.022845 0.352226 0.000001 0.014889 +4 0.225397 0.014218 0.347688 0.014889 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7caaf4fc509521b5beb9ef7cd46a511a15c388e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.095489 0.121083 0.088006 0.096977 +1 0.095489 0.000001 0.134224 0.016298 0.043340 +2 0.121083 0.134224 0.000001 0.126741 0.135712 +3 0.088006 0.016298 0.126741 0.000001 0.035857 +4 0.096977 0.043340 0.135712 0.035857 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..14139ac26582d88b68c9d409a23aff768b0cbe3f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52254963 Before NNI: tree length is 0.52254962 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001604_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001604_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1945b65337b027ec2f501ec25f2ba37325462515 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001604_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024773 0.113456 0.025877 0.024773 +1 0.024773 0.000001 0.107252 0.002095 0.000001 +2 0.113456 0.107252 0.000001 0.108356 0.107252 +3 0.025877 0.002095 0.108356 0.000001 0.002095 +4 0.024773 0.000001 0.107252 0.002095 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001605_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001605_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed01e6fcd4f1edc68f945e2bf10e71beac8a640e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001605_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21107465 Before NNI: tree length is 0.21107463 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f99e329ef3b13b2604b0a5af3bc0c490c6ebc679 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38695350 Before NNI: tree length is 0.38695350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001613_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001613_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3a9a146ad571769c3c4f644dcf770fe6a8b1d8ed --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001613_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.16955620 Before NNI: tree length is 1.16955625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001619_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001619_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed2845d3ab852b3eed5e50f15980ea30ff831c78 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001619_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.201788 0.275720 0.204320 0.201604 +1 0.201788 0.000001 0.300008 0.007490 0.004775 +2 0.275720 0.300008 0.000001 0.302541 0.299825 +3 0.204320 0.007490 0.302541 0.000001 0.004139 +4 0.201604 0.004775 0.299825 0.004139 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbeb75b843c47d6dbc22e8053196998f1ee20457 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51787665 Before NNI: tree length is 0.51787662 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001624_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001624_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b1ea79aff534c97919e7c0bab19cd4666ce74af --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001624_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.658313 0.907513 0.908707 0.584498 +1 0.658313 0.000001 1.020571 0.250394 0.073815 +2 0.907513 1.020571 0.000001 1.270965 0.946756 +3 0.908707 0.250394 1.270965 0.000001 0.324209 +4 0.584498 0.073815 0.946756 0.324209 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001625_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001625_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bda4e68ef9efa016221ab3cee36dfead7340f18b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001625_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037824 0.151653 0.039510 0.034564 +1 0.037824 0.000001 0.164122 0.009907 0.009084 +2 0.151653 0.164122 0.000001 0.165808 0.160861 +3 0.039510 0.009907 0.165808 0.000001 0.010770 +4 0.034564 0.009084 0.160861 0.010770 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001626_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001626_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1699cdc5f6264e5cffdcdedbc84df6a361069d7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001626_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.70601200 Before NNI: tree length is 0.70601200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c1b09b1dc8eee5cf4d1fc1e97dbc68db0fd87133 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.164812 0.448643 0.169498 0.172767 +1 0.164812 0.000001 0.474127 0.013962 0.021778 +2 0.448643 0.474127 0.000001 0.478814 0.482082 +3 0.169498 0.013962 0.478814 0.000001 0.026465 +4 0.172767 0.021778 0.482082 0.026465 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e1f261dbf21853b6e61998961162ea0c57ef2835 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.116476 0.108833 0.077405 0.103073 +1 0.116476 0.000001 0.110472 0.093743 0.113831 +2 0.108833 0.110472 0.000001 0.086100 0.106189 +3 0.077405 0.093743 0.086100 0.000001 0.080341 +4 0.103073 0.113831 0.106189 0.080341 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4ab2a3cd3b1cbdb7c972eceb4018806a1edb49d9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.203741 0.201622 0.205950 0.165495 +1 0.203741 0.000001 0.250753 0.131198 0.179362 +2 0.201622 0.250753 0.000001 0.252962 0.212507 +3 0.205950 0.131198 0.252962 0.000001 0.181572 +4 0.165495 0.179362 0.212507 0.181572 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fccbfdc4d8b607e7362e71b6109c18b939cf70ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001634_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049033 0.344879 0.294174 0.037121 +1 0.049033 0.000001 0.329355 0.278650 0.043495 +2 0.344879 0.329355 0.000001 0.225646 0.339340 +3 0.294174 0.278650 0.225646 0.000001 0.288636 +4 0.037121 0.043495 0.339340 0.288636 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001636_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001636_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94fc4f1646514996e117fc19341604e03620f715 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001636_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16231586 Before NNI: tree length is 0.16231587 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6165ce9ef19844d074ba71210060d152d629d1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32269075 Before NNI: tree length is 0.32269075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d91907b45546a614355d8e1ee292752ba4b276f7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001644_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097161 0.130160 0.102202 0.095345 +1 0.097161 0.000001 0.144861 0.015507 0.003715 +2 0.130160 0.144861 0.000001 0.149902 0.143044 +3 0.102202 0.015507 0.149902 0.000001 0.013690 +4 0.095345 0.003715 0.143044 0.013690 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001648_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001648_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae75d834f901a7031ca4f855c7d920b103617719 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001648_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20845750 Before NNI: tree length is 0.20845750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001652_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001652_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2407076592cea0699d0bac13934cf7b2352eb0bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001652_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.453047 0.608657 0.456021 0.453399 +1 0.453047 0.000001 0.352984 0.014302 0.011680 +2 0.608657 0.352984 0.000001 0.355958 0.353337 +3 0.456021 0.014302 0.355958 0.000001 0.008432 +4 0.453399 0.011680 0.353337 0.008432 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001653_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001653_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5be4093f0a079dd735bc0db345b34be3f2f2bd29 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001653_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.210503 0.638089 0.210618 0.206106 +1 0.210503 0.000001 0.633735 0.077134 0.026122 +2 0.638089 0.633735 0.000001 0.633849 0.629338 +3 0.210618 0.077134 0.633849 0.000001 0.072736 +4 0.206106 0.026122 0.629338 0.072736 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001660_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001660_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0d670bcc87acebff723355d85dacabcdd37fa03 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001660_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44135400 Before NNI: tree length is 0.44135400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001663_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001663_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a691a54c3ba0ca37fa6072ed405a4f123f550d7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001663_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11810800 Before NNI: tree length is 0.11810800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001665_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001665_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..93551b79107b5c6ae8a22958beeb5d04bbb3ad70 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001665_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35589550 Before NNI: tree length is 0.35589550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a105000914014ec26e0fbab28ae772ea9a70cda1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.037825 0.073470 0.037825 0.037825 +1 0.037825 0.000001 0.072403 0.000001 0.000001 +2 0.073470 0.072403 0.000001 0.072403 0.072403 +3 0.037825 0.000001 0.072403 0.000001 0.000001 +4 0.037825 0.000001 0.072403 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..549211574b05f70f99cfb683366cfaab8b600955 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001666_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09185000 Before NNI: tree length is 0.09185000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001668_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001668_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1ea01282aeb49a1c6b2b23a0c06f18f9155896b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001668_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34744988 Before NNI: tree length is 0.34744988 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cba082fa4cb712b7203eef95ecccff438e3d7fae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35485861 Before NNI: tree length is 0.35485862 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001677_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001677_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f43523388ef5e8a22b569ec7147a20cc7f619bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001677_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73838500 Before NNI: tree length is 0.73838500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ce87bbb33decc8878e8d4696fde7333dd548613 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001678_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44387975 Before NNI: tree length is 0.44387975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..623e6111eb0babb1220b54daa8b1136163b97830 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047579 0.288840 0.047719 0.051579 +1 0.047579 0.000001 0.273266 0.016013 0.019872 +2 0.288840 0.273266 0.000001 0.273405 0.277265 +3 0.047719 0.016013 0.273405 0.000001 0.005946 +4 0.051579 0.019872 0.277265 0.005946 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0924e0a3a5e33acf7f8bcd929b477b452e50395c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001681_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31782143 Before NNI: tree length is 0.31782150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001686_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001686_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad171d08cfa509c9976158e640d43289b82aa7a8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001686_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.100095 0.153109 0.102935 0.102886 +1 0.100095 0.000001 0.197100 0.011614 0.008680 +2 0.153109 0.197100 0.000001 0.199939 0.199891 +3 0.102935 0.011614 0.199939 0.000001 0.014406 +4 0.102886 0.008680 0.199891 0.014406 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..260cb8aea32db624fc7ad06bc8dbc58f49a02083 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.439237 0.396601 0.417588 0.436716 +1 0.439237 0.000001 0.326086 0.050599 0.012306 +2 0.396601 0.326086 0.000001 0.304437 0.323565 +3 0.417588 0.050599 0.304437 0.000001 0.048078 +4 0.436716 0.012306 0.323565 0.048078 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001692_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001692_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1332aa70107650ce47e0a442573f0174bd6bb00c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001692_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.102796 0.177286 0.102723 0.102723 +1 0.102796 0.000001 0.165003 0.003049 0.003049 +2 0.177286 0.165003 0.000001 0.164929 0.164929 +3 0.102723 0.003049 0.164929 0.000001 0.000001 +4 0.102723 0.003049 0.164929 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001693_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001693_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c53cd2e3ba256ebdd445e24a11d79aa76a2219d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001693_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22578150 Before NNI: tree length is 0.22578150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001695_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001695_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..297d4c0e5fb0ac44cb08047365786875dffab017 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001695_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.077212 0.188823 0.077212 0.077212 +1 0.077212 0.000001 0.205353 0.000001 0.000001 +2 0.188823 0.205353 0.000001 0.205353 0.205353 +3 0.077212 0.000001 0.205353 0.000001 0.000001 +4 0.077212 0.000001 0.205353 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7bc3a8da1aedc123f0d3a46a80ebd38d0666d989 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001696_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018059 0.032305 0.020038 0.018059 +1 0.018059 0.000001 0.030038 0.004682 0.000001 +2 0.032305 0.030038 0.000001 0.032017 0.030038 +3 0.020038 0.004682 0.032017 0.000001 0.004682 +4 0.018059 0.000001 0.030038 0.004682 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001704_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001704_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88874bf18f159f81ec895c55b9105bd78c372238 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001704_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.202742 0.422634 0.202742 0.228231 +1 0.202742 0.000001 0.409370 0.000001 0.047020 +2 0.422634 0.409370 0.000001 0.409370 0.434859 +3 0.202742 0.000001 0.409370 0.000001 0.047020 +4 0.228231 0.047020 0.434859 0.047020 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c6415b3b43b0d8f40df5a0aa428367343ef9f8fb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.127751 0.397084 0.125049 0.135889 +1 0.127751 0.000001 0.360638 0.005960 0.043342 +2 0.397084 0.360638 0.000001 0.357936 0.368775 +3 0.125049 0.005960 0.357936 0.000001 0.040641 +4 0.135889 0.043342 0.368775 0.040641 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2581b29eb3e746cede56f8d7b2b76da5c762f86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001705_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47010555 Before NNI: tree length is 0.47010550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7a9d6947cf34a9128a9dd71def49a25ebd61d991 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036056 0.039652 0.036088 0.036072 +1 0.036056 0.000001 0.003596 0.000032 0.000016 +2 0.039652 0.003596 0.000001 0.003564 0.003580 +3 0.036088 0.000032 0.003564 0.000001 0.000016 +4 0.036072 0.000016 0.003580 0.000016 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a33bd38d397a02275c69d23c2e7b12ae1305087 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001709_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03965200 Before NNI: tree length is 0.03965200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8cc610b30e55ed83af16aad7000417962c933f1e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43637642 Before NNI: tree length is 0.43637650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e4bc34bb65b81df636b1e59b1ca61c840031b83 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16325625 Before NNI: tree length is 0.16325625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3bd2abd8d63525a8051d35844829c89c032336b5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001728_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052812 0.256299 0.052812 0.052812 +1 0.052812 0.000001 0.244594 0.000001 0.000001 +2 0.256299 0.244594 0.000001 0.244594 0.244594 +3 0.052812 0.000001 0.244594 0.000001 0.000001 +4 0.052812 0.000001 0.244594 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e28e21d07f3764c8992249adfb6ac99ddf27689 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027978 0.046056 0.027978 0.028432 +1 0.027978 0.000001 0.041484 0.000001 0.012844 +2 0.046056 0.041484 0.000001 0.041484 0.041939 +3 0.027978 0.000001 0.041484 0.000001 0.012844 +4 0.028432 0.012844 0.041939 0.012844 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..07995ea39932fa0cc4bc435bf60e15509bcafe1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001733_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43104483 Before NNI: tree length is 0.43104475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001736_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001736_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5c3ac4c166ceebff5574ae963d0a4a8881269973 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001736_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12337682 Before NNI: tree length is 0.12337675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001738_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001738_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d30600dd0bcde6d62d94ec51562d4d463e262f47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001738_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14127150 Before NNI: tree length is 0.14127150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001739_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001739_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81bd115d88be15ff64999a544a36f9a23bca321e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001739_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04999800 Before NNI: tree length is 0.04999800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001740_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001740_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbfe03b4950fb65f436ac776535b76f0c604b8d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001740_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11522740 Before NNI: tree length is 0.11522737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001742_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001742_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..98ef002b28a88e07e67cbede788fec69b9f2f134 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001742_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.348866 0.393334 0.342746 0.342746 +1 0.348866 0.000001 0.428318 0.047953 0.047953 +2 0.393334 0.428318 0.000001 0.422198 0.422198 +3 0.342746 0.047953 0.422198 0.000001 0.000001 +4 0.342746 0.047953 0.422198 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001744_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001744_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..87927a6fba6b67dcee6ee72402c5ceab5fac1d8c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001744_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.612600 0.918130 0.595267 0.625837 +1 0.612600 0.000001 0.305529 0.017333 0.013237 +2 0.918130 0.305529 0.000001 0.322863 0.292293 +3 0.595267 0.017333 0.322863 0.000001 0.030570 +4 0.625837 0.013237 0.292293 0.030570 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3169b09a22124d62350295d90bbadacfb37f6923 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.450871 0.765737 0.572891 0.572891 +1 0.450871 0.000001 0.922244 0.136511 0.136511 +2 0.765737 0.922244 0.000001 1.044264 1.044264 +3 0.572891 0.136511 1.044264 0.000001 0.000001 +4 0.572891 0.136511 1.044264 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb2f78e7fa5e90e63469f2b545afa0333ae219ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001748_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.19869200 Before NNI: tree length is 1.19869200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..32af5481a4b8b2a4e20228ccc5143394bc850296 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.202855 0.433219 0.201553 0.199023 +1 0.202855 0.000001 0.448965 0.013526 0.010996 +2 0.433219 0.448965 0.000001 0.447663 0.445133 +3 0.201553 0.013526 0.447663 0.000001 0.002531 +4 0.199023 0.010996 0.445133 0.002531 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..638fb306be49afe7607e0055017de8d0c93f7507 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001751_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54863200 Before NNI: tree length is 0.54863200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..94daf95a9a6a7166158c3b6ffcd9e7c89f407d7b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.094779 0.192339 0.088804 0.088557 +1 0.094779 0.000001 0.167476 0.020407 0.016692 +2 0.192339 0.167476 0.000001 0.161502 0.161255 +3 0.088804 0.020407 0.161502 0.000001 0.014185 +4 0.088557 0.016692 0.161255 0.014185 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..461e8b74695d16a8750c88c8e2936164223568e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001754_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23974836 Before NNI: tree length is 0.23974838 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001756_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001756_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38814ee86a556578441e9d90cb7aad6bf31ecb7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001756_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77328975 Before NNI: tree length is 0.77328975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001761_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001761_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c4bbc1f2d59fd22fd448d1693190fb90d00045d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001761_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.267340 0.453665 0.254125 0.248408 +1 0.267340 0.000001 0.520745 0.022543 0.035252 +2 0.453665 0.520745 0.000001 0.507530 0.501812 +3 0.254125 0.022543 0.507530 0.000001 0.022037 +4 0.248408 0.035252 0.501812 0.022037 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001763_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001763_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75deba2c4d716db2408759294bc181d684458ced --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001763_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.04378280 Before NNI: tree length is 1.04378275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001764_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001764_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2bfa2b2387667054eb6a6b0fbe8eeb113b11f59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001764_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.00457404 Before NNI: tree length is 1.00457400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001767_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001767_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..76daa0a76f15b1a0fc159d896198bb38439e3c81 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001767_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.78154475 Before NNI: tree length is 1.78154475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..785d7553437cd27fa9ddd042cc9008518ccb0f7f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000016_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.02055800,0:0.00817400):0.00444025,1:0.00086575):0.00065475,3:0.00361925,4:-0.00000025); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000028_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000028_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..ec334ffb83ff2f372897a1c71cf25751d9c831ba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000028_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00000050,(3:-0.00000023,(2:0.16286733,0:0.01751967):0.01962859):0.00012873,4:0.00280950); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000029_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000029_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..e49ea82205465ef74edb4126035575193888aa7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000029_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((0:0.02610200,1:0.00000000):0.00066175,3:0.00000025):0.52819425,2:0.52819475,4:-0.52819375); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000030_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000030_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..82b72b0e300cc670d8916c33bbcadb60f5410bfa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000030_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.04633917,1:0.00758283):0.00165769,0:0.00147157):0.00116093,3:0.00000050,4:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..0f62e5913fc210b80367c8e4d5ef9111dd8a2303 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000032_tree_id.txt.tre @@ -0,0 +1,2 @@ +(0:0.00580575,((3:0.00000050,1:0.00000050):0.04485625,2:0.24625525):0.01823275,4:0.00437225); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000040_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000040_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..536b263d6bc64034c10e683588a307e6b9b2edd9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000040_tree_id.txt.tre @@ -0,0 +1,2 @@ +((2:0.16947283,0:-0.12337483):0.12337463,(3:0.01053275,1:0.01525825):0.18772125,4:0.19431420); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000046_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000046_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..c42f0a05d024d13ba1e9a6dafd9be6b8e5d5b9e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000046_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.01149855,(3:0.00746075,(2:0.08411200,0:0.03957100):0.03924425):0.00149275,4:0.00327645); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000049_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000049_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..6546bff4c60f7e550ac3bee80ac488ad900846e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000049_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00569398,(3:0.00726012,(2:0.06851517,0:0.07905783):0.06023987):0.00177588,4:0.00439302); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000052_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000052_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..4a5c77f333c84cac68a1ac861bf972af3fbba51b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000052_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((1:0.00425023,3:0.01004777):0.56179555,0:1.25426295):0.63787698,2:0.58953733,4:0.86043367); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000053_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000053_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..e9711fb6dc948c00b6e20a06f366a0ccaebc8592 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000053_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00959850,(3:0.01044034,(2:1.01000683,0:0.54098117):0.40820561):0.01586816,4:0.03364050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000057_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000057_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..7ed4df65906b09cc69713af164db294a01c5f276 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000057_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.18778600,0:0.23331200):0.16368300,1:0.00615800):0.00785800,3:0.00509100,4:0.00007600); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000061_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000061_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..f279bd3f083ccd5ec95c0f58145d2a11f8e2aa0e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000061_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00810525,(3:0.00368375,(2:0.26917600,0:0.06938900):0.09773925):0.00200375,4:0.00455275); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000068_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000068_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..4110e30076098f78b91e535563daf14fbf6baa59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000068_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00658704,(3:0.00615230,(2:0.02090383,0:0.18570017):0.05153493):0.00188370,4:0.00544796); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000078_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000078_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..e8dc5f307c5bbbd595c630d1ea3ce7e2f7eaa3bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000078_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.10454362,0:0.03920938):0.02084862,1:0.00590787):0.00225913,3:0.00135187,4:0.00271912); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000081_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000081_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..332a0a245899eeca8d445aebdbb94efc672dff27 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000081_tree_id.txt.tre @@ -0,0 +1,2 @@ +(1:0.00000050,(3:0.00795125,(2:0.39942325,0:0.01884475):0.00309075):0.00241125,4:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000095_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000095_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..8b1f374d0efa141e3680893ff225cb3773e7bd94 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000095_tree_id.txt.tre @@ -0,0 +1,2 @@ +((0:0.22552457,(3:0.85842639,2:0.41506061):0.07065289):0.18450191,1:0.00753467,4:0.00941533); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000100_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000100_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..f8ff90cc28259cf920d3017e8fe1d47e3b0bd50a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000100_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.67440600,0:0.14467900):0.16302850,1:0.00000050):-0.00000000,3:0.00000050,4:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000108_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000108_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..500420c43b7017896732bc839e4504d3da65c6f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000108_tree_id.txt.tre @@ -0,0 +1,2 @@ +((2:0.92573125,0:0.06688875):0.03533100,(3:0.01058525,1:0.00192775):0.00957150,4:0.01419000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000109_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000109_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..146a9641b3f17aa231f37bb22a912e00d00a514e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000109_tree_id.txt.tre @@ -0,0 +1,2 @@ +((2:0.30565150,(3:0.00675425,1:0.19523275):0.07924350):0.19050650,0:0.34486925,4:-0.00000025); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000111_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000111_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..9aa34d874b5a33de7b7ff2a0dd8ba1c5a04d778c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000111_tree_id.txt.tre @@ -0,0 +1,2 @@ +(((2:0.07827713,0:0.03121988):0.03088512,1:0.01357588):0.00493462,3:0.25135038,4:0.00067462); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000112_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000112_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..2dc6656b781ba762965fbc46056f90a49473d28d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000112_tree_id.txt.tre @@ -0,0 +1,2 @@ +((1:0.01177200,(2:0.00492500,0:0.25939500):0.00062600):0.00177917,3:0.02381517,4:-0.00000017); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000114_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000114_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..f99c9025203c9ca2ca129a0c90be24a227e0bc0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000114_tree_id.txt.tre @@ -0,0 +1,2 @@ +((2:0.31721783,1:-0.13490983):0.23543385,(3:0.00277125,0:0.10301375):0.00685375,4:0.00165599); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000117_tree_id.txt.tre b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000117_tree_id.txt.tre new file mode 100644 index 0000000000000000000000000000000000000000..a0cad14742e9c7d34095b6e580e9284647c31aea --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/SpeciesTrees_ids/OG0000117_tree_id.txt.tre @@ -0,0 +1,2 @@ +((2:0.07456650,0:0.07577850):0.14923550,(3:0.00000050,1:0.00000050):0.00100650,4:0.00119500); 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