diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6da90d0c1c1d6080206fee9369d3669c5260b81 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000002_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01185158 Before NNI: tree length is 0.01289563 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.67535562 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbbf1ab0d27cd23ebe533b4410012b1ceda33a51 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003934 1.017795 0.003944 0.003573 +1 0.003934 0.000001 1.021834 0.000010 0.000010 +2 1.017795 1.021834 0.000001 1.021843 1.021473 +3 0.003944 0.000010 1.021843 0.000001 0.000010 +4 0.003573 0.000010 1.021473 0.000010 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..872a943f2a51a37b0d599534c4b9bf5bd1bf19ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.171446 0.652536 1.472841 1.472714 +1 1.171446 0.000001 1.192253 0.016522 0.006381 +2 0.652536 1.192253 0.000001 1.493648 1.493521 +3 1.472841 0.016522 1.493648 0.000001 0.010141 +4 1.472714 0.006381 1.493521 0.010141 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..82325834aa239216bfa15e96f367ca88db7568bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53949550 Before NNI: tree length is 0.53949550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.67772178 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b248356e6aebfe4b5ea8589a68810c5cc0b883a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000014_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20770083 Before NNI: tree length is 0.20554287 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.58131314 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1c46b3b5323d68b34c2100991b19737e0b0548c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000017_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.018828 0.759249 1.027331 1.021223 +1 1.018828 0.000001 1.332099 0.010081 0.016322 +2 0.759249 1.332099 0.000001 1.340602 1.334494 +3 1.027331 0.010081 1.340602 0.000001 0.006241 +4 1.021223 0.016322 1.334494 0.006241 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000019_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fdcc1952bfa1c55e74e9c76f6aaeb2c65a2a3433 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21929113 Before NNI: tree length is 0.21980737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.93696507 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..67652efb7e711dd64e4818d986762e46e1f8ac03 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13555542 Before NNI: tree length is 0.11741950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.27042417 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2a7e404bf0f59e1723b08d35b70d33addc2d7281 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000023_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.785654 0.541722 0.173219 0.178632 +1 0.785654 0.000001 1.033124 0.027040 0.011176 +2 0.541722 1.033124 0.000001 0.535400 0.540813 +3 0.173219 0.027040 0.535400 0.000001 0.017275 +4 0.178632 0.011176 0.540813 0.017275 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a03c6248a4a9ef1e3267a46c14717adc75e6957 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.772929 0.764995 0.769622 0.894707 +1 0.772929 0.000001 0.874068 0.017091 0.308374 +2 0.764995 0.874068 0.000001 0.870760 0.995845 +3 0.769622 0.017091 0.870760 0.000001 0.280338 +4 0.894707 0.308374 0.995845 0.280338 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eb34161112e3d7893d9b05ec0360d304a944ca1f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.418135 0.885723 0.417412 0.420999 +1 0.418135 0.000001 0.925916 0.017508 0.003829 +2 0.885723 0.925916 0.000001 0.925193 0.928780 +3 0.417412 0.017508 0.925193 0.000001 0.020372 +4 0.420999 0.003829 0.928780 0.020372 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a07fae96357265a7543dd8a25367e29f34bd490f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025657 0.382509 0.024680 0.026153 +1 0.025657 0.000001 0.359083 0.004083 0.028635 +2 0.382509 0.359083 0.000001 0.360934 0.385486 +3 0.024680 0.004083 0.360934 0.000001 0.027658 +4 0.026153 0.028635 0.385486 0.027658 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..745faa0a954db0ec5cc6146d944636dc4be9adc8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39974262 Before NNI: tree length is 0.39974262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000029_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..118b6184a50d6bafd1b2ee81ad8009e96f244ff1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55495933 Before NNI: tree length is 0.55495925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.57127693 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000045_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000045_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a73576d35b2341f07e43acadf8550c0ccbe2ebb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000045_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013044 2.552770 0.004653 0.101135 +1 0.013044 0.000001 2.539727 0.010642 0.106076 +2 2.552770 2.539727 0.000001 2.550368 1.311741 +3 0.004653 0.010642 2.550368 0.000001 0.098733 +4 0.101135 0.106076 1.311741 0.098733 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..61daaa10fd0f242337f0ba61c1da13ecc6186547 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000049_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.146767 0.147573 0.146558 0.145467 +1 0.146767 0.000001 0.136225 0.014730 0.010087 +2 0.147573 0.136225 0.000001 0.136015 0.134924 +3 0.146558 0.014730 0.136015 0.000001 0.013429 +4 0.145467 0.010087 0.134924 0.013429 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000050_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000050_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb35e5758ccc98cd65f4ced464273aa2abb0821d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000050_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20151291 Before NNI: tree length is 0.20151288 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5be62615a838e9caa9003e873e300577d62ec36b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015414 1.809867 0.004325 0.009925 +1 0.015414 0.000001 1.805175 0.015054 0.020654 +2 1.809867 1.805175 0.000001 0.271309 1.815107 +3 0.004325 0.015054 0.271309 0.000001 0.005600 +4 0.009925 0.020654 1.815107 0.005600 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..26340785d058c124815234d2f7ae80e7afc3e2b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.28072100 Before NNI: tree length is 1.28072100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000066_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bad35f1538bea3ad946fe0d2d5dd17e788393c9c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.218916 0.339775 0.213188 0.216158 +1 0.218916 0.000001 0.270454 0.024794 0.002758 +2 0.339775 0.270454 0.000001 0.264726 0.267696 +3 0.213188 0.024794 0.264726 0.000001 0.022036 +4 0.216158 0.002758 0.267696 0.022036 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23e57682034692202aa743f88af075b9e635c4f2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23133150 Before NNI: tree length is 0.23133150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..702cc9f222671323299af1593175813163ce8baf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.073818 0.233031 0.066151 0.066572 +1 0.073818 0.000001 0.221118 0.007667 0.007246 +2 0.233031 0.221118 0.000001 0.213452 0.213872 +3 0.066151 0.007667 0.213452 0.000001 0.000420 +4 0.066572 0.007246 0.213872 0.000420 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed8d54785ce8c5bdfa1150c6cefd0ad8807cf8e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26398345 Before NNI: tree length is 0.26398350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad78ae65b3b92e7ec098d0a9fe6fd795b26018c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10773950 Before NNI: tree length is 0.10773950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea0a5f8b9b52c11cd23912b82f592fbdbeb61b61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.93500350 Before NNI: tree length is 1.93500350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f4262db94656955a36c336464d1f7eb172f9cab --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.09283350 Before NNI: tree length is 1.09283350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7fe76de38ddbd040f7f6ea4f329ed34e9c1bedd6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000080_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.230853 0.224586 0.252054 0.233992 +1 0.230853 0.000001 0.254435 0.035774 0.039012 +2 0.224586 0.254435 0.000001 0.275636 0.257574 +3 0.252054 0.035774 0.275636 0.000001 0.060214 +4 0.233992 0.039012 0.257574 0.060214 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000081_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..238d205f76f74613b9c4cc84e6c23e820f80a7eb --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024347 0.418268 0.029887 0.024347 +1 0.024347 0.000001 0.404926 0.010363 0.000001 +2 0.418268 0.404926 0.000001 0.410465 0.404926 +3 0.029887 0.010363 0.410465 0.000001 0.010363 +4 0.024347 0.000001 0.404926 0.010363 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c2b90f1a0f81cf4585a983de73c64f7b1d8e5a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35758064 Before NNI: tree length is 0.35758062 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000086_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6e16424066912f5d716fea6fd358dd6a4f6ca8ae --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.354261 0.677430 0.345101 0.344587 +1 0.354261 0.000001 0.550555 0.046843 0.031659 +2 0.677430 0.550555 0.000001 0.541395 0.540881 +3 0.345101 0.046843 0.541395 0.000001 0.037168 +4 0.344587 0.031659 0.540881 0.037168 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0e9e4aa7abf2f269db6229cc906aa66db1935f64 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.194118 0.007310 0.185132 0.233608 +1 0.194118 0.000001 0.195555 0.017497 0.221382 +2 0.007310 0.195555 0.000001 0.186569 0.235045 +3 0.185132 0.017497 0.186569 0.000001 0.212395 +4 0.233608 0.221382 0.235045 0.212395 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50ccbb32ab7050b4e9e496538b98a5136daf9c51 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52807225 Before NNI: tree length is 0.52807225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000095_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..12edc1ea7420fb438e9594dff2cc0762da9ae48e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.417561 0.711238 1.154604 0.419442 +1 0.417561 0.000001 0.677750 1.121116 0.016950 +2 0.711238 0.677750 0.000001 1.273487 0.679631 +3 1.154604 1.121116 1.273487 0.000001 1.122996 +4 0.419442 0.016950 0.679631 1.122996 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..03cb94675ec1cdae1e93df60b9bd82efa0911e26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000100_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.307708 0.819085 0.307708 0.307708 +1 0.307708 0.000001 0.837435 0.000001 0.000001 +2 0.819085 0.837435 0.000001 0.837435 0.837435 +3 0.307708 0.000001 0.837435 0.000001 0.000001 +4 0.307708 0.000001 0.837435 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e7601b76990e5e500f7fec563b36ded053533b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.343525 0.346665 0.340455 0.340620 +1 0.343525 0.000001 0.058480 0.024947 0.020893 +2 0.346665 0.058480 0.000001 0.055410 0.055575 +3 0.340455 0.024947 0.055410 0.000001 0.022042 +4 0.340620 0.020893 0.055575 0.022042 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a833e59301d4a1c8915c1b7b1f1e2572a91183f3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39426750 Before NNI: tree length is 0.39426750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ca189f0aaab87e224f922a9282251fc12aa693bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036785 0.029765 0.053416 0.038522 +1 0.036785 0.000001 0.018469 0.031906 0.037868 +2 0.029765 0.018469 0.000001 0.035099 0.030848 +3 0.053416 0.031906 0.035099 0.000001 0.054499 +4 0.038522 0.037868 0.030848 0.054499 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5a45e7c5ac63872f59a1ad587112f86349d9ab1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30231217 Before NNI: tree length is 0.30231225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7433c76ec53269ba3382950e4ba59ec41c3ef7ab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27058081 Before NNI: tree length is 0.27058075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..417b7dfcbb4a9c253dec9e31b9aff9c43cb73793 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000118_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28581579 Before NNI: tree length is 0.28581575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000121_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000121_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2e9ed57ca208896a867399561c64747465bf55bd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000121_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.226401 0.289038 0.234220 0.228147 +1 0.226401 0.000001 0.338002 0.027716 0.038711 +2 0.289038 0.338002 0.000001 0.345821 0.339748 +3 0.234220 0.027716 0.345821 0.000001 0.046530 +4 0.228147 0.038711 0.339748 0.046530 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000122_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0eeb401ee2588439f5308882111dce0dd0bdbabd --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54066920 Before NNI: tree length is 0.54066925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..37f7a40a8c6130e33561909caed6954cd2ab5f71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000123_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.221096 0.344100 0.212467 0.215142 +1 0.221096 0.000001 0.342274 0.013635 0.012476 +2 0.344100 0.342274 0.000001 0.333644 0.336319 +3 0.212467 0.013635 0.333644 0.000001 0.007680 +4 0.215142 0.012476 0.336319 0.007680 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..668254c0d16460d61458044861782796d0248616 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.056250 0.013124 0.023889 0.091341 +1 0.056250 0.000001 0.053023 0.072481 0.139933 +2 0.013124 0.053023 0.000001 0.029355 0.096807 +3 0.023889 0.072481 0.029355 0.000001 0.067452 +4 0.091341 0.139933 0.096807 0.067452 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000127_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000127_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c9233d4b5ede4092e8a9741457e5403fe47bb281 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000127_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020840 0.056607 0.023030 0.027687 +1 0.020840 0.000001 0.056540 0.006557 0.014788 +2 0.056607 0.056540 0.000001 0.058730 0.063387 +3 0.023030 0.006557 0.058730 0.000001 0.016978 +4 0.027687 0.014788 0.063387 0.016978 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fa2f7f91ed3bf170e8a3b115570d2e41b26947a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.089136 0.057076 0.039918 0.082460 +1 0.089136 0.000001 0.057024 0.076756 0.042734 +2 0.057076 0.057024 0.000001 0.044696 0.050348 +3 0.039918 0.076756 0.044696 0.000001 0.070080 +4 0.082460 0.042734 0.050348 0.070080 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f46c4b6766b335aa9be9b121e18cc8591ee9d3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13341600 Before NNI: tree length is 0.13341600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000129_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000129_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..481a01a1e230fe8ee90589b261685b08daa93b58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000129_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05093258 Before NNI: tree length is 0.05093263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af8c8b17191fc66a48e2e91177b613ba33b052ac --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023543 0.899687 0.033722 0.030037 +1 0.023543 0.000001 0.206304 0.021171 0.017486 +2 0.899687 0.206304 0.000001 0.909296 0.905610 +3 0.033722 0.021171 0.909296 0.000001 0.017795 +4 0.030037 0.017486 0.905610 0.017795 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3e0c82f6d7f4f5d1f0a8fab2511dc342ca9755a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39040308 Before NNI: tree length is 0.39040312 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99752435 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000138_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000138_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c0b6c2566c5d6d8759425effe6d84aa73b265c33 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000138_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.089054 0.171370 0.084821 0.090021 +1 0.089054 0.000001 0.180971 0.007608 0.003887 +2 0.171370 0.180971 0.000001 0.176738 0.181938 +3 0.084821 0.007608 0.176738 0.000001 0.008576 +4 0.090021 0.003887 0.181938 0.008576 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c5df40655711b46e02082630d26ded4b1c4138c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32009171 Before NNI: tree length is 0.32009175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000151_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e00b7383e200d9a049bde71947bc5b0df8691173 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.17722573 Before NNI: tree length is 1.17722575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0a7ee3ccd8ae8f98130d5ad0e83b7d67a9ae6c5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27231450 Before NNI: tree length is 0.27231450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..519db9ba1a02f47d22257c2274316fab896fa19b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.151310 0.290713 0.148333 0.148795 +1 0.151310 0.000001 0.285108 0.028096 0.028559 +2 0.290713 0.285108 0.000001 0.282131 0.282594 +3 0.148333 0.028096 0.282131 0.000001 0.006508 +4 0.148795 0.028559 0.282594 0.006508 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d375e60b69eb995692ab76832c25a8a1fd5d3919 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37961039 Before NNI: tree length is 0.37961037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000165_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000165_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04ef0fe360568b0b27c11116cf3ccd3a59a17a86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000165_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.05333025 Before NNI: tree length is 1.05333025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000167_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cab4531222313cd55c2e476cbb2de0d2115117e5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13827750 Before NNI: tree length is 0.13827750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8d975d8ec197f0a5a208b34d23bcafd68a890ae9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000168_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.539292 0.481546 0.454220 0.490445 +1 0.539292 0.000001 0.166867 0.086231 0.050006 +2 0.481546 0.166867 0.000001 0.253098 0.216874 +3 0.454220 0.086231 0.253098 0.000001 0.036225 +4 0.490445 0.050006 0.216874 0.036225 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c91eb555140d54cfc43c557883ef763885e5a236 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000170_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08685950 Before NNI: tree length is 0.08685950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..446688b044452d39a090f1176789797b9fcb4df7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000174_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30566788 Before NNI: tree length is 0.30566787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..033fe075d863779b5913f36e85f0172b380c9927 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.079418 0.129761 0.079338 0.082699 +1 0.079418 0.000001 0.118358 0.000080 0.003281 +2 0.129761 0.118358 0.000001 0.118277 0.121639 +3 0.079338 0.000080 0.118277 0.000001 0.003361 +4 0.082699 0.003281 0.121639 0.003361 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e6c2e7ac0a33914e93e77bdaa89513103aaf8ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16704928 Before NNI: tree length is 0.16704925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc610f89ab7aba112ef5554d3c1c3c703e41b75a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15747970 Before NNI: tree length is 0.15747975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000181_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000181_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..95d37166b468d9a5f0afee80ea7d38ab96b5f1d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000181_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81486650 Before NNI: tree length is 0.81486650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000182_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..381c9cf210e5ecefe635879ec5bb898b09ae8e0b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10624850 Before NNI: tree length is 0.10624850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c36d788ff1b0e85ccb6671931c7ada8d5164be03 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000185_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.123746 0.301767 0.118417 0.109799 +1 0.123746 0.000001 0.336059 0.032161 0.023543 +2 0.301767 0.336059 0.000001 0.330731 0.322112 +3 0.118417 0.032161 0.330731 0.000001 0.010734 +4 0.109799 0.023543 0.322112 0.010734 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000186_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000186_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b764897a5729535515854e3614665797789ea1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000186_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73969050 Before NNI: tree length is 0.73969050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..476c0234af7aee3f35f3c158075182d1909c51de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.242294 0.343450 0.242420 0.243573 +1 0.242294 0.000001 0.336739 0.022180 0.023332 +2 0.343450 0.336739 0.000001 0.336865 0.338018 +3 0.242420 0.022180 0.336865 0.000001 0.001182 +4 0.243573 0.023332 0.338018 0.001182 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000193_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000193_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdfcc7848cf1a03b550f3549610167b97f4072fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000193_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.50936375 Before NNI: tree length is 0.50936375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d34857c005650bd8f1db0e4e2ea40de56a04082 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56233114 Before NNI: tree length is 0.56233113 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..928e756e246c87192175e1acc7cad457262793d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000198_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084615 0.186859 0.088609 0.087468 +1 0.084615 0.000001 0.166713 0.006700 0.007004 +2 0.186859 0.166713 0.000001 0.170707 0.169566 +3 0.088609 0.006700 0.170707 0.000001 0.010998 +4 0.087468 0.007004 0.169566 0.010998 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..30240d25c007ef099b3f57470dbcb6da5ae9dc67 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000202_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15027050 Before NNI: tree length is 0.15027050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000209_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12c0e8e653132d3224329ae131197aadcbfb62d2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48817047 Before NNI: tree length is 1.48817050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..67594bbfbdbd2be75ec7e2194ec8d0af7c0e22a8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.136976 0.127504 0.117091 0.122786 +1 0.136976 0.000001 0.176652 0.030927 0.026255 +2 0.127504 0.176652 0.000001 0.156767 0.162462 +3 0.117091 0.030927 0.156767 0.000001 0.016736 +4 0.122786 0.026255 0.162462 0.016736 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5dd538929d72016236df750ab6c3c428c730064 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000219_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23211925 Before NNI: tree length is 0.23211925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72b4d9e60e733c375e1d04bb94f94d6b92c681a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000222_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28340389 Before NNI: tree length is 0.28340387 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000229_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000229_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3aaf89ad345d8aff1c289a0ff8c2f2bd7ec72977 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000229_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.158345 0.247877 0.136963 0.136236 +1 0.158345 0.000001 0.307073 0.021382 0.022109 +2 0.247877 0.307073 0.000001 0.285691 0.284964 +3 0.136963 0.021382 0.285691 0.000001 0.000727 +4 0.136236 0.022109 0.284964 0.000727 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eb75d31f86ae6de8bf412db45769de44cdfe8455 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.426257 0.748346 0.424163 0.421007 +1 0.426257 0.000001 0.382041 0.002626 0.008192 +2 0.748346 0.382041 0.000001 0.379947 0.376790 +3 0.424163 0.002626 0.379947 0.000001 0.006098 +4 0.421007 0.008192 0.376790 0.006098 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000232_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000232_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a251da504e486b413f48247cb3b5c5a4b32ba6a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000232_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.84167769 Before NNI: tree length is 0.84167775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1ebd3ae5be9dcb44a03b6be7b88d31863421d0ac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.449851 0.808879 0.458666 0.438453 +1 0.449851 0.000001 0.798593 0.085450 0.065237 +2 0.808879 0.798593 0.000001 0.807408 0.787195 +3 0.458666 0.085450 0.807408 0.000001 0.030550 +4 0.438453 0.065237 0.787195 0.030550 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..72761d6be730cff7c2a239723369627eaf9451cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000234_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08096250 Before NNI: tree length is 1.08096250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fffd6854c9055cfe38e642fe9dd6335f793e14f7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59668518 Before NNI: tree length is 0.59668525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000238_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000238_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cfebbcfee628ed5d36f9bec5cfe273205463bf8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000238_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36951950 Before NNI: tree length is 0.36951950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b1ac33baa640615f570a6aa034e8cada2641bb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.482303 1.271304 0.457275 0.476363 +1 0.482303 0.000001 1.289377 0.069430 0.046819 +2 1.271304 1.289377 0.000001 1.264348 1.283436 +3 0.457275 0.069430 1.264348 0.000001 0.063490 +4 0.476363 0.046819 1.283436 0.063490 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..05bf2bbd663b869672ee278895bbcea3e5624d7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.56413215 Before NNI: tree length is 1.56413213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000244_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000244_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2685c57aab798724b567d2e2c9f89006150e56b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000244_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.071855 0.148036 0.071855 0.072537 +1 0.071855 0.000001 0.142096 0.000001 0.006804 +2 0.148036 0.142096 0.000001 0.142096 0.142778 +3 0.071855 0.000001 0.142096 0.000001 0.006804 +4 0.072537 0.006804 0.142778 0.006804 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21cb2940ad33816b544f2406fcd8a8225b8c9bf9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26182537 Before NNI: tree length is 0.26182538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..058dc422f3cfe739743d8b0cd6b9cdc5097660be --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.192344 0.205919 0.175253 0.181690 +1 0.192344 0.000001 0.072654 0.034112 0.039562 +2 0.205919 0.072654 0.000001 0.055563 0.062001 +3 0.175253 0.034112 0.055563 0.000001 0.023459 +4 0.181690 0.039562 0.062001 0.023459 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b44d78a8d51d54d5273ef1d466dc7bf1b249819c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031958 0.116539 0.031958 0.029423 +1 0.031958 0.000001 0.130195 0.000001 0.003093 +2 0.116539 0.130195 0.000001 0.130195 0.127661 +3 0.031958 0.000001 0.130195 0.000001 0.003093 +4 0.029423 0.003093 0.127661 0.003093 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..31d44a8c2caeb8ff8f028c20f21c10923d94d146 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13962568 Before NNI: tree length is 0.13962575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ac78c11a2c9fc33bb44f4e91a2631105b8b97eb4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.433892 0.363524 0.522821 0.400004 +1 0.433892 0.000001 0.313605 0.214979 0.061275 +2 0.363524 0.313605 0.000001 0.402533 0.279717 +3 0.522821 0.214979 0.402533 0.000001 0.181091 +4 0.400004 0.061275 0.279717 0.181091 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42a66db5063adeefb91293f740d2b6a7e467130e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72115772 Before NNI: tree length is 0.72115775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000252_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba9977d998ea0ae758f5b8ef55c9e033b6ae62b8 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.28721200 Before NNI: tree length is 1.28721200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bed72a0231f2ad30d080f150e45b575f88f055a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.053004 0.123030 0.061369 0.052379 +1 0.053004 0.000001 0.070026 0.010553 0.000625 +2 0.123030 0.070026 0.000001 0.080579 0.070651 +3 0.061369 0.010553 0.080579 0.000001 0.009928 +4 0.052379 0.000625 0.070651 0.009928 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f2cc042a37d38179fcf6d6f6a42dd7d3ff3a24c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000255_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13248900 Before NNI: tree length is 0.13248900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000256_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000256_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c197440da89650702c5454315f48783abd499629 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.072230 0.119309 0.069283 0.070469 +1 0.072230 0.000001 0.099564 0.002948 0.011550 +2 0.119309 0.099564 0.000001 0.096616 0.097803 +3 0.069283 0.002948 0.096616 0.000001 0.008602 +4 0.070469 0.011550 0.097803 0.008602 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75bf363c2b994ab13daefd3b5665a1cd8655f5e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24646500 Before NNI: tree length is 0.24646500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4a75595cb954be7455a94b65f3dafb9626d57c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000267_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09960125 Before NNI: tree length is 0.09960125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78cc5a547892744fe2641f8d3accc5753c95bc08 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022947 0.064937 0.023656 0.018287 +1 0.022947 0.000001 0.067601 0.004541 0.026339 +2 0.064937 0.067601 0.000001 0.068310 0.068328 +3 0.023656 0.004541 0.068310 0.000001 0.027048 +4 0.018287 0.026339 0.068328 0.027048 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..afc56e1d047488152c488db3c5c48a62c4855669 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09120675 Before NNI: tree length is 0.09120675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000273_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fde50bacbf626650f420fb7ce4179840b825e6d7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036438 0.127660 0.044024 0.042032 +1 0.036438 0.000001 0.124456 0.031210 0.029218 +2 0.127660 0.124456 0.000001 0.132041 0.130049 +3 0.044024 0.031210 0.132041 0.000001 0.017941 +4 0.042032 0.029218 0.130049 0.017941 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9ded2480ad2b896138d45e580a9f2b48aa6a231a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019378 0.455546 0.012853 0.013659 +1 0.019378 0.000001 0.461504 0.014245 0.009029 +2 0.455546 0.461504 0.000001 0.454980 0.455785 +3 0.012853 0.014245 0.454980 0.000001 0.008526 +4 0.013659 0.009029 0.455785 0.008526 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a133633937cdf314b74c0f96b9c026a484b332ae --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063759 0.694980 0.080314 0.080314 +1 0.063759 0.000001 0.728163 0.043256 0.043256 +2 0.694980 0.728163 0.000001 0.744718 0.744718 +3 0.080314 0.043256 0.744718 0.000001 0.000001 +4 0.080314 0.043256 0.744718 0.000001 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d138925f902779d3202402ebb00e86f1229d4562 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38630475 Before NNI: tree length is 0.38630475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000281_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8dcfb5785ed464db661e3a1148b63b493f930c7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16930600 Before NNI: tree length is 0.16930600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..da99d4653a7826d42b0a78738f214d7745528fb9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061837 0.105597 0.065821 0.057314 +1 0.061837 0.000001 0.100390 0.013687 0.013475 +2 0.105597 0.100390 0.000001 0.104375 0.095868 +3 0.065821 0.013687 0.104375 0.000001 0.017460 +4 0.057314 0.013475 0.095868 0.017460 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a481f1499fbdebaaffae866dd798ea669493df1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14722411 Before NNI: tree length is 0.14722413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..23c8f92cf194c53e5cc4681a3b516fb1397bf137 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.172098 0.507628 0.172098 0.172098 +1 0.172098 0.000001 0.513469 0.000001 0.000001 +2 0.507628 0.513469 0.000001 0.513469 0.513469 +3 0.172098 0.000001 0.513469 0.000001 0.000001 +4 0.172098 0.000001 0.513469 0.000001 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cbb61b1bbc4b4963849e9d5a30304d743e09350 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26335425 Before NNI: tree length is 0.26335425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e84f4cd58617b6adad4a3e9e279e7fcfefc78f7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.098097 0.283985 0.117984 0.097750 +1 0.098097 0.000001 0.285773 0.019887 0.000347 +2 0.283985 0.285773 0.000001 0.305660 0.285426 +3 0.117984 0.019887 0.305660 0.000001 0.020234 +4 0.097750 0.000347 0.285426 0.020234 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ddf155e94563301fff25fcd4e93b4eef96657abf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.116825 0.152698 0.127966 0.114201 +1 0.116825 0.000001 0.176495 0.011141 0.005598 +2 0.152698 0.176495 0.000001 0.187635 0.173871 +3 0.127966 0.011141 0.187635 0.000001 0.016739 +4 0.114201 0.005598 0.173871 0.016739 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb37f76acbb1e7cf80db1874339d23b81234635f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23563685 Before NNI: tree length is 0.23563687 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000305_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000305_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..311a876c524404cd4c7d9310dafa86068e1bb584 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000305_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24007114 Before NNI: tree length is 0.24007112 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dc5eac0e27fe0d5eaa9d10bc782888b50266d720 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000306_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.102943 0.228180 0.103708 0.103708 +1 0.102943 0.000001 0.225357 0.002448 0.002448 +2 0.228180 0.225357 0.000001 0.226123 0.226123 +3 0.103708 0.002448 0.226123 0.000001 0.000001 +4 0.103708 0.002448 0.226123 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..735a9fee78b296b622139bda624bfb675b0e3085 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000307_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66916465 Before NNI: tree length is 0.66916462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a22102764b20924668faa81f4a57cee34ac8808c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000308_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30733973 Before NNI: tree length is 0.30733975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000309_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000309_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..89e6a29497e4f84e444f9430494ed8113428e6bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000309_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.128921 0.182084 0.128921 0.128921 +1 0.128921 0.000001 0.223443 0.000001 0.000001 +2 0.182084 0.223443 0.000001 0.223443 0.223443 +3 0.128921 0.000001 0.223443 0.000001 0.000001 +4 0.128921 0.000001 0.223443 0.000001 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000310_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..33cf4a8c92eb276552b7b8f1f525522733de6129 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.127433 0.425851 0.127433 0.127433 +1 0.127433 0.000001 0.431662 0.000001 0.000001 +2 0.425851 0.431662 0.000001 0.431662 0.431662 +3 0.127433 0.000001 0.431662 0.000001 0.000001 +4 0.127433 0.000001 0.431662 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000321_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000321_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2d0a366b1d7ffad2053a6d08bc0b08d582522038 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000321_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026688 0.081968 0.026203 0.025176 +1 0.026688 0.000001 0.079625 0.003992 0.001549 +2 0.081968 0.079625 0.000001 0.079140 0.078112 +3 0.026203 0.003992 0.079140 0.000001 0.002479 +4 0.025176 0.001549 0.078112 0.002479 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d52453975022df10aa3d3c17d46e944ac490a62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14544375 Before NNI: tree length is 0.14544375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55dffbdaa802206d64c0c39cf3f6f2f5987467d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.173677 0.203072 0.175363 0.178515 +1 0.173677 0.000001 0.175308 0.013786 0.016938 +2 0.203072 0.175308 0.000001 0.176994 0.180146 +3 0.175363 0.013786 0.176994 0.000001 0.004823 +4 0.178515 0.016938 0.180146 0.004823 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8250fb96cd890ad18f5bd5b28af8bc19aa0bce5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28775200 Before NNI: tree length is 0.28775200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7b39467fc3c00c53e0a47caf7e98fd6fb7ee525 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032685 0.026377 0.031091 0.032685 +1 0.032685 0.000001 0.024773 0.029488 0.000001 +2 0.026377 0.024773 0.000001 0.015409 0.024773 +3 0.031091 0.029488 0.015409 0.000001 0.029488 +4 0.032685 0.000001 0.024773 0.029488 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f2b856bf5405f8e8feca435728f248376681d37 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.205092 0.387471 0.187222 0.189667 +1 0.205092 0.000001 0.418710 0.031063 0.069617 +2 0.387471 0.418710 0.000001 0.400840 0.403286 +3 0.187222 0.031063 0.400840 0.000001 0.051747 +4 0.189667 0.069617 0.403286 0.051747 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e5d6155f8f5096a381fec01ded06a77e14b8065 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57564162 Before NNI: tree length is 0.57564162 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2b9ed80873ed8addecd9653a1b3f17befd3d3a62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.201302 0.219866 0.199017 0.199017 +1 0.201302 0.000001 0.221073 0.011671 0.011671 +2 0.219866 0.221073 0.000001 0.218788 0.218788 +3 0.199017 0.011671 0.218788 0.000001 0.000001 +4 0.199017 0.011671 0.218788 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..54fbca58eac66cc6a8a6be2a03d1824eec1c9127 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000338_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.118215 0.353688 0.123831 0.123831 +1 0.118215 0.000001 0.378879 0.006051 0.006051 +2 0.353688 0.378879 0.000001 0.384496 0.384496 +3 0.123831 0.006051 0.384496 0.000001 0.000001 +4 0.123831 0.006051 0.384496 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8a834c7fd17bf743bea60437f78dd5beaed81c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.051643 0.245145 0.063328 0.062651 +1 0.051643 0.000001 0.237014 0.018748 0.018072 +2 0.245145 0.237014 0.000001 0.248698 0.248022 +3 0.063328 0.018748 0.248698 0.000001 0.020493 +4 0.062651 0.018072 0.248022 0.020493 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8d9297e42e1dd0a3b9e8376eb0dae2ac7dc5bec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29202559 Before NNI: tree length is 0.29202562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..50bd97f05a7532a164641ffed474a04ae10e71e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054140 0.144644 0.054695 0.055785 +1 0.054140 0.000001 0.164269 0.001123 0.003842 +2 0.144644 0.164269 0.000001 0.164824 0.165913 +3 0.054695 0.001123 0.164824 0.000001 0.004396 +4 0.055785 0.003842 0.165913 0.004396 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000344_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000344_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..541784175363929a0d49f5b6c781eac3f14b9500 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000344_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09076150 Before NNI: tree length is 0.09076150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef871ba989b262d88ded8beed7187ba876c84237 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.184710 0.190269 0.181078 0.192632 +1 0.184710 0.000001 0.150051 0.010816 0.007922 +2 0.190269 0.150051 0.000001 0.146419 0.157972 +3 0.181078 0.010816 0.146419 0.000001 0.018737 +4 0.192632 0.007922 0.157972 0.018737 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cfacc827d52294652c310aa43e1c4444b6314f12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000349_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27402863 Before NNI: tree length is 0.27402862 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf06fd46079c7fb65c50e55030b961ff772e5f1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000352_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09971900 Before NNI: tree length is 0.09971900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000353_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000353_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b292203c9881d32a17a6e6f6584643045801c1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000353_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54283400 Before NNI: tree length is 0.54283400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000355_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000355_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..677fb922999e798c2f105b646d2dc31eb5de5a41 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000355_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59769700 Before NNI: tree length is 0.59769700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000361_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000361_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..de6145ca59d8ed9b9d9878babb1294ca2fd6e279 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000361_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.39801217 Before NNI: tree length is 2.39801225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..94604aee41dc44ba2bc27362698114d288542bc9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084090 0.137007 0.081133 0.082540 +1 0.084090 0.000001 0.157818 0.013628 0.015035 +2 0.137007 0.157818 0.000001 0.154861 0.156268 +3 0.081133 0.013628 0.154861 0.000001 0.001407 +4 0.082540 0.015035 0.156268 0.001407 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000366_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed5627e8b2fef212335112d633bc880ea8ca6a2b --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.344869 0.403809 0.382348 0.325933 +1 0.344869 0.000001 0.451354 0.055986 0.022054 +2 0.403809 0.451354 0.000001 0.488833 0.432419 +3 0.382348 0.055986 0.488833 0.000001 0.059533 +4 0.325933 0.022054 0.432419 0.059533 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ed40c4d3e4c0f4e2a9bcda8267f7b99f35a8cf79 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.115620 0.136750 0.121043 0.121349 +1 0.115620 0.000001 0.098252 0.005423 0.008183 +2 0.136750 0.098252 0.000001 0.103674 0.103981 +3 0.121043 0.005423 0.103674 0.000001 0.013605 +4 0.121349 0.008183 0.103981 0.013605 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000368_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000368_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..135266be9f99181e95cb62cedb3e1809ddb05425 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000368_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.122437 0.139603 0.118700 0.115409 +1 0.122437 0.000001 0.122348 0.007004 0.015226 +2 0.139603 0.122348 0.000001 0.118611 0.115321 +3 0.118700 0.007004 0.118611 0.000001 0.011488 +4 0.115409 0.015226 0.115321 0.011488 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..59fc6645e853f197e1359be5667f53e51f2f07e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000370_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17314318 Before NNI: tree length is 0.17314325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..eaa61a3ca901cdb5a8f48a048780e3ce2f9dee05 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029552 0.369112 0.029374 0.031010 +1 0.029552 0.000001 0.360649 0.000179 0.017480 +2 0.369112 0.360649 0.000001 0.360470 0.362106 +3 0.029374 0.000179 0.360470 0.000001 0.017301 +4 0.031010 0.017480 0.362106 0.017301 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d428ed624a51ab63842a0897c5db75d3ed1557c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000374_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38912533 Before NNI: tree length is 0.38912537 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000375_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000375_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d54cd4d69a063b6aa68be728b8e372eb8edbd398 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000375_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53910150 Before NNI: tree length is 0.53910150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3e3162f019bd17a8640b80980d6e0cfb181b3b3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.552350 0.893928 0.550537 0.554343 +1 0.552350 0.000001 0.809117 0.102124 0.074584 +2 0.893928 0.809117 0.000001 0.807304 0.811110 +3 0.550537 0.102124 0.807304 0.000001 0.104117 +4 0.554343 0.074584 0.811110 0.104117 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000377_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000377_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6169aa19cbd78f1d18896c1bd30e32b19d685401 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000377_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21393914 Before NNI: tree length is 0.21393913 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..acfb6f2493ae1beaef70fa25618e335b2edd64a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.148921 0.331095 0.143116 0.137344 +1 0.148921 0.000001 0.322991 0.013038 0.011577 +2 0.331095 0.322991 0.000001 0.317185 0.311414 +3 0.143116 0.013038 0.317185 0.000001 0.005772 +4 0.137344 0.011577 0.311414 0.005772 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e87a1f4103d53c33350085f4736034fc8529a9a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.69583613 Before NNI: tree length is 0.69583613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7edbbe29657e4af3145510887b31da2afa7430a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000380_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061023 0.047100 0.061023 0.061023 +1 0.061023 0.000001 0.053956 0.000001 0.000001 +2 0.047100 0.053956 0.000001 0.053956 0.053956 +3 0.061023 0.000001 0.053956 0.000001 0.000001 +4 0.061023 0.000001 0.053956 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000387_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000387_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af68a995d89efc560db93a7543059de3e9dec87b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000387_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.87951118 Before NNI: tree length is 0.87951125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000389_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000389_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71cf0da97cb3f848c9f7a7e18c10ac53fc45da92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000389_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.079854 0.141647 0.077755 0.076872 +1 0.079854 0.000001 0.133963 0.008779 0.007897 +2 0.141647 0.133963 0.000001 0.131864 0.130981 +3 0.077755 0.008779 0.131864 0.000001 0.001460 +4 0.076872 0.007897 0.130981 0.001460 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1ff54e53d41def924e708d99da3cbc361921322 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.074951 0.121732 0.072411 0.072411 +1 0.074951 0.000001 0.131963 0.005704 0.005704 +2 0.121732 0.131963 0.000001 0.129423 0.129423 +3 0.072411 0.005704 0.129423 0.000001 0.000001 +4 0.072411 0.005704 0.129423 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fa911243fb6fe2fc46f2bc06de38c89b55344c58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000401_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.067818 0.139808 0.071139 0.063892 +1 0.067818 0.000001 0.148616 0.019965 0.007696 +2 0.139808 0.148616 0.000001 0.151936 0.144690 +3 0.071139 0.019965 0.151936 0.000001 0.016039 +4 0.063892 0.007696 0.144690 0.016039 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..37cb5fb5849f94f837010efeaeca54b63b09aaa4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.807535 1.350010 0.797179 0.807689 +1 0.807535 0.000001 0.787707 0.146278 0.156788 +2 1.350010 0.787707 0.000001 0.777350 0.787861 +3 0.797179 0.146278 0.777350 0.000001 0.076076 +4 0.807689 0.156788 0.787861 0.076076 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f81fd4b7583fc646c64b08c93c2801d6a8b9d04 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55984323 Before NNI: tree length is 0.55984325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000408_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000408_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..28f11188231bb98224e9ee962ee575b202790b8e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000408_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.612885 0.817200 0.598397 0.656137 +1 0.612885 0.000001 0.788007 0.119922 0.177662 +2 0.817200 0.788007 0.000001 0.773519 0.831259 +3 0.598397 0.119922 0.773519 0.000001 0.099696 +4 0.656137 0.177662 0.831259 0.099696 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..169e2d092a446f1c2aa24e7fe26685f0f2c88869 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.84479900 Before NNI: tree length is 1.84479900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bc81b2d9e99d4ee17c7d2d06e13d471a7aa31e76 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.006849 0.000001 0.000001 +1 0.000001 0.000001 0.006849 0.000001 0.000001 +2 0.006849 0.006849 0.000001 0.006849 0.006849 +3 0.000001 0.000001 0.006849 0.000001 0.000001 +4 0.000001 0.000001 0.006849 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e555d372d99ac10d177de6040e851d005a5635b2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.00685050 Before NNI: tree length is 0.00685050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999998 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..33344919c848a280890b99f8b177066c94ed4284 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30803219 Before NNI: tree length is 0.30803225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74b870439a91c7aeec0661a794e65566bfe06880 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000417_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.039324 0.404833 0.038895 0.043729 +1 0.039324 0.000001 0.389305 0.002517 0.007351 +2 0.404833 0.389305 0.000001 0.388877 0.393711 +3 0.038895 0.002517 0.388877 0.000001 0.005642 +4 0.043729 0.007351 0.393711 0.005642 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000419_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000419_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e2e181131f6256acea4f1262d1b9cc86de41f7d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000419_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016539 0.028106 0.016052 0.017019 +1 0.016539 0.000001 0.021356 0.002274 0.006563 +2 0.028106 0.021356 0.000001 0.020870 0.021836 +3 0.016052 0.002274 0.020870 0.000001 0.006076 +4 0.017019 0.006563 0.021836 0.006076 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..61a0234bb890f926bf42bc28ae95f47b2d1811f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048299 0.365169 0.058501 0.047092 +1 0.048299 0.000001 0.331637 0.026642 0.015234 +2 0.365169 0.331637 0.000001 0.343513 0.332104 +3 0.058501 0.026642 0.343513 0.000001 0.022248 +4 0.047092 0.015234 0.332104 0.022248 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b454032623d18f6d85d33ff59ada869066d4a7f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029296 0.021120 0.021138 0.021120 +1 0.029296 0.000001 0.017546 0.008158 0.008176 +2 0.021120 0.017546 0.000001 0.009388 0.009370 +3 0.021138 0.008158 0.009388 0.000001 0.000018 +4 0.021120 0.008176 0.009370 0.000018 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c03ab1eda7ce5ff575c63aa9cae684f5818431a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000425_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03398100 Before NNI: tree length is 0.03398100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000427_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000427_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..462e3fb50431b53942eb5df5ca0a51fbd1e5fbdc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000427_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.525414 0.553402 0.525414 0.525414 +1 0.525414 0.000001 0.617375 0.000001 0.000001 +2 0.553402 0.617375 0.000001 0.617375 0.617375 +3 0.525414 0.000001 0.617375 0.000001 0.000001 +4 0.525414 0.000001 0.617375 0.000001 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000429_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b13d6ae761eee508d44e98b49fbc8caa0e5b9c80 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.80159150 Before NNI: tree length is 0.80159150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000431_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..347e1d87bf39aaba3da785cb5f06f58f2e0c27a5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.191270 0.160829 0.188147 0.191270 +1 0.191270 0.000001 0.146969 0.003291 0.000001 +2 0.160829 0.146969 0.000001 0.143845 0.146969 +3 0.188147 0.003291 0.143845 0.000001 0.003291 +4 0.191270 0.000001 0.146969 0.003291 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5535d318d05bf6d1f9a6ff6db5206005cff646b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.18063000 Before NNI: tree length is 1.18063000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000443_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..886c32c19e697759b4e900776bf0a7711348422b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.75646239 Before NNI: tree length is 0.75646237 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d227a6203285fc248349ebe444f1ed64e897839f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000447_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60668259 Before NNI: tree length is 0.60668262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5780304cbb31818ee213cefdf1d64a0b63cbc3e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.265134 0.512675 0.264506 0.271552 +1 0.265134 0.000001 0.537417 0.011263 0.018309 +2 0.512675 0.537417 0.000001 0.536790 0.543836 +3 0.264506 0.011263 0.536790 0.000001 0.013207 +4 0.271552 0.018309 0.543836 0.013207 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000451_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a8f268e58ee739f9fcccb559b0e6bf730d40f39f --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.174549 0.398616 0.179025 0.194658 +1 0.174549 0.000001 0.405628 0.028435 0.044068 +2 0.398616 0.405628 0.000001 0.410104 0.425737 +3 0.179025 0.028435 0.410104 0.000001 0.028845 +4 0.194658 0.044068 0.425737 0.028845 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000457_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e2110c5f8b8d2cd1f9a895caf29a77a036e4a0f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34658725 Before NNI: tree length is 0.34658725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000460_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8aa41811cda666ee3ba48a47feb790311c60156e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.82198312 Before NNI: tree length is 0.82198312 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0193bdbda4b7fbfa5626392865a3e1ed21d3dd29 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000465_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.160470 0.250146 0.164304 0.176541 +1 0.160470 0.000001 0.196701 0.012645 0.044213 +2 0.250146 0.196701 0.000001 0.200534 0.212772 +3 0.164304 0.012645 0.200534 0.000001 0.048047 +4 0.176541 0.044213 0.212772 0.048047 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000469_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000469_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f671b702d69f65e5f36f608754191957e9b33042 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000469_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.48167250 Before NNI: tree length is 1.48167250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000470_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000470_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bd679f78744c67697e90b4b5e584f5b924fc26c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000470_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77029450 Before NNI: tree length is 0.77029450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a314443b8e9f69542d1114672c784bdc6648e013 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084320 0.212651 0.219679 0.214588 +1 0.084320 0.000001 0.189342 0.196370 0.191279 +2 0.212651 0.189342 0.000001 0.016053 0.010962 +3 0.219679 0.196370 0.016053 0.000001 0.005091 +4 0.214588 0.191279 0.010962 0.005091 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b43ed764c709a710b9312778c92354971a7d0fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25469700 Before NNI: tree length is 0.25469700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea8297b3e7f098265b4e2d59d0599b75aa11b066 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000487_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47949350 Before NNI: tree length is 0.47949350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4083e5323f9a6cf93197ddc477dc885c40bded4f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000490_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063470 0.255079 0.072153 0.072153 +1 0.063470 0.000001 0.249736 0.012500 0.012500 +2 0.255079 0.249736 0.000001 0.258419 0.258419 +3 0.072153 0.012500 0.258419 0.000001 0.000001 +4 0.072153 0.012500 0.258419 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f4feb56503dc7048bb3d12c121488faf39ea5fa5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.169348 0.449988 0.201861 0.204824 +1 0.169348 0.000001 0.438715 0.068847 0.071811 +2 0.449988 0.438715 0.000001 0.471227 0.474191 +3 0.201861 0.068847 0.471227 0.000001 0.016217 +4 0.204824 0.071811 0.474191 0.016217 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ee8529c1e47ed812eddc2671d7cbeb4de6e4515 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000491_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58929560 Before NNI: tree length is 0.58929562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb67d07e9776ac79389493c8b0a3cc02aea92751 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012654 0.014276 0.010856 0.010856 +1 0.012654 0.000001 0.021667 0.002837 0.002837 +2 0.014276 0.021667 0.000001 0.019868 0.019868 +3 0.010856 0.002837 0.019868 0.000001 0.000001 +4 0.010856 0.002837 0.019868 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000501_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000501_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6dd01625af60e6e43ece1c2747118e360443e34 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000501_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.091069 0.084851 0.093054 0.093054 +1 0.091069 0.000001 0.022044 0.030247 0.030247 +2 0.084851 0.022044 0.000001 0.020462 0.020462 +3 0.093054 0.030247 0.020462 0.000001 0.000001 +4 0.093054 0.030247 0.020462 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41263ac9fc3edae8d47a6dc0299589078792dd97 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000504_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72314400 Before NNI: tree length is 0.72314400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c34427585573167653bb3a0c7d9a58f1204eb50 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.180213 0.377164 0.190041 0.174174 +1 0.180213 0.000001 0.395903 0.062093 0.029478 +2 0.377164 0.395903 0.000001 0.405731 0.389864 +3 0.190041 0.062093 0.405731 0.000001 0.056054 +4 0.174174 0.029478 0.389864 0.056054 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2331b69beb4eea938b9a50ca4e428dc7c130562f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060399 0.378444 0.070646 0.065071 +1 0.060399 0.000001 0.363884 0.028166 0.033552 +2 0.378444 0.363884 0.000001 0.374131 0.368555 +3 0.070646 0.028166 0.374131 0.000001 0.043799 +4 0.065071 0.033552 0.368555 0.043799 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4dd4e245fe68f7a277f2df59a256e2c7957087ee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000516_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.356357 1.029267 0.356357 0.363123 +1 0.356357 0.000001 1.076578 0.000001 0.021142 +2 1.029267 1.076578 0.000001 1.076578 1.083345 +3 0.356357 0.000001 1.076578 0.000001 0.021142 +4 0.363123 0.021142 1.083345 0.021142 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8ec5d2f489d4356b65f4aa01bca460439ebd9b74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020061 0.018096 0.020061 0.023863 +1 0.020061 0.000001 0.026926 0.000001 0.004506 +2 0.018096 0.026926 0.000001 0.026926 0.030728 +3 0.020061 0.000001 0.026926 0.000001 0.004506 +4 0.023863 0.004506 0.030728 0.004506 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b08daee73d0d3ce891da3dd7f94e5f645934498 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37553163 Before NNI: tree length is 0.37553162 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000531_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000531_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bccd7198f82f56e0a1fe2f14a8dcc0d836386c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000531_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44315965 Before NNI: tree length is 0.44315962 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000535_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f1cad6f33f82b31e17325c2a7088ea77d00ba87 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41649350 Before NNI: tree length is 0.41649350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9582ae216699733fd055bd9091cd5bc86fb60b6f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.205063 0.415373 0.208101 0.208371 +1 0.205063 0.000001 0.428732 0.028076 0.028345 +2 0.415373 0.428732 0.000001 0.431770 0.432040 +3 0.208101 0.028076 0.431770 0.000001 0.025295 +4 0.208371 0.028345 0.432040 0.025295 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f181c9ae9f5f57f7aba9ad7ae5a0a4177ed3de6a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47706263 Before NNI: tree length is 0.47706263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9962546b213f4cd32eb41fd1482515e83f6eb69b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.230970 0.230866 0.237852 0.237852 +1 0.230970 0.000001 0.023649 0.030634 0.030634 +2 0.230866 0.023649 0.000001 0.018131 0.018131 +3 0.237852 0.030634 0.018131 0.000001 0.000001 +4 0.237852 0.030634 0.018131 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a13c51112e2a7148c02a500f5e102b81d76dc7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000540_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.046954 0.024881 0.046954 0.053822 +1 0.046954 0.000001 0.048089 0.000001 0.015518 +2 0.024881 0.048089 0.000001 0.048089 0.054957 +3 0.046954 0.000001 0.048089 0.000001 0.015518 +4 0.053822 0.015518 0.054957 0.015518 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cccb2590bc4a89b584927e7201c03954ace89f12 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055632 0.830210 0.055632 0.055632 +1 0.055632 0.000001 0.849719 0.000001 0.000001 +2 0.830210 0.849719 0.000001 0.849719 0.849719 +3 0.055632 0.000001 0.849719 0.000001 0.000001 +4 0.055632 0.000001 0.849719 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c80e35eecd1c5713ca44edfdf3558dd6c1e5562c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 1.086355 1.494951 1.132311 1.175324 +1 1.086355 0.000001 2.018619 0.071524 0.114537 +2 1.494951 2.018619 0.000001 2.064575 2.107588 +3 1.132311 0.071524 2.064575 0.000001 0.105007 +4 1.175324 0.114537 2.107588 0.105007 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000548_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000548_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a905c42cd4fa93854bdb4967ef6d4b96549a0856 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000548_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56996467 Before NNI: tree length is 0.56996475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000549_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..aa942f5d029a8417b98d4a75544b2276b5552460 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.049017 0.134453 0.050940 0.050382 +1 0.049017 0.000001 0.103290 0.007349 0.005785 +2 0.134453 0.103290 0.000001 0.105213 0.104655 +3 0.050940 0.007349 0.105213 0.000001 0.008714 +4 0.050382 0.005785 0.104655 0.008714 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000554_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000554_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2d908b2c4df1056c3cd522d986f4304666bf7014 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000554_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048659 0.048601 0.047966 0.045749 +1 0.048659 0.000001 0.008523 0.003919 0.009039 +2 0.048601 0.008523 0.000001 0.007829 0.008981 +3 0.047966 0.003919 0.007829 0.000001 0.008346 +4 0.045749 0.009039 0.008981 0.008346 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0c20a8a1be098dbf402f72d98b0373a71b9ff510 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.129219 0.176508 0.128512 0.128512 +1 0.129219 0.000001 0.161062 0.007088 0.007088 +2 0.176508 0.161062 0.000001 0.160354 0.160354 +3 0.128512 0.007088 0.160354 0.000001 0.000001 +4 0.128512 0.007088 0.160354 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fea1382e8c062acaea613428ab5be2ba5a31f2c7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000555_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23658523 Before NNI: tree length is 0.23658525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000558_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000558_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..217920e3954d8de37ec58e77bd92476dfb135e3b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000558_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22002800 Before NNI: tree length is 0.22002800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000559_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000559_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d3687494172bbecec28b90734f7084186e7f0097 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.051404 0.063259 0.051404 0.051404 +1 0.051404 0.000001 0.086716 0.000001 0.000001 +2 0.063259 0.086716 0.000001 0.086716 0.086716 +3 0.051404 0.000001 0.086716 0.000001 0.000001 +4 0.051404 0.000001 0.086716 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1cf85b0abb072c0dbd8062d93fa16a1ea351e11e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.178310 0.455606 0.178310 0.178310 +1 0.178310 0.000001 0.489194 0.000001 0.000001 +2 0.455606 0.489194 0.000001 0.489194 0.489194 +3 0.178310 0.000001 0.489194 0.000001 0.000001 +4 0.178310 0.000001 0.489194 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..200fdce784aa63755e9b4b0fbdfa679d99a3e883 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56155600 Before NNI: tree length is 0.56155600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000573_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000573_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..daf4afaccdb48c549c11dc7f8a7708cd38cb0d9b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000573_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30769435 Before NNI: tree length is 0.30769438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000575_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000575_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a9f088c19b8621fc89d95e969dd191607b03130d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000575_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033870 0.131557 0.032548 0.027726 +1 0.033870 0.000001 0.137989 0.011153 0.011814 +2 0.131557 0.137989 0.000001 0.136666 0.131844 +3 0.032548 0.011153 0.136666 0.000001 0.010492 +4 0.027726 0.011814 0.131844 0.010492 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000576_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000576_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a19501682d4f5dba9b3b1c4cf1f30a7061159ed6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000576_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.026706 0.005766 0.005337 +1 0.000001 0.000001 0.026706 0.005766 0.005337 +2 0.026706 0.026706 0.000001 0.032125 0.031696 +3 0.005766 0.005766 0.032125 0.000001 0.005115 +4 0.005337 0.005337 0.031696 0.005115 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000578_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000578_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c63346cb9f69afb55b6e9f43dd32fd16466f6cf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000578_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58296792 Before NNI: tree length is 0.58296800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2a458e3b7393e421ec2426fc6766412bb6ec5316 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.259040 0.259623 0.259790 0.262355 +1 0.259040 0.000001 0.024321 0.012483 0.011684 +2 0.259623 0.024321 0.000001 0.025072 0.027636 +3 0.259790 0.012483 0.025072 0.000001 0.015798 +4 0.262355 0.011684 0.027636 0.015798 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2ca2cd7bee739367e1171f76179ed9e99420bcb9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.461713 0.457415 0.457415 0.460398 +1 0.461713 0.000001 0.006818 0.006818 0.014090 +2 0.457415 0.006818 0.000001 0.000001 0.009792 +3 0.457415 0.006818 0.000001 0.000001 0.009792 +4 0.460398 0.014090 0.009792 0.009792 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000584_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f3ed77d9a5d1434ea24ed03b15dbd1b1ab97116 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42967950 Before NNI: tree length is 0.42967950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d5d112844c436e45f6581ea7193b4df4518b87f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000588_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49844078 Before NNI: tree length is 0.49844075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000589_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2403f3ef1ca4d2aa41b0e590114a7607af466e4c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.99646990 Before NNI: tree length is 0.99646987 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000596_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b28221f5452bbbe23d76bf863e1730530dd78570 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11118689 Before NNI: tree length is 0.11118687 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000597_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000597_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2bc568e147bb801ad9a25cfd26ec323b2e2c8ce0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000597_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032340 0.050011 0.032325 0.032325 +1 0.032340 0.000001 0.034229 0.016543 0.016543 +2 0.050011 0.034229 0.000001 0.029503 0.029503 +3 0.032325 0.016543 0.029503 0.000001 0.000001 +4 0.032325 0.016543 0.029503 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f04b0f4464c6dcd692ced331deba964392424612 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.585537 0.763458 0.617643 0.585537 +1 0.585537 0.000001 0.492320 0.035748 0.000001 +2 0.763458 0.492320 0.000001 0.524426 0.492320 +3 0.617643 0.035748 0.524426 0.000001 0.035748 +4 0.585537 0.000001 0.492320 0.035748 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..085073469b17a00e5460f124684ef00e387b350a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000602_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.295003 0.311219 0.291892 0.293352 +1 0.295003 0.000001 0.275582 0.003837 0.008282 +2 0.311219 0.275582 0.000001 0.272470 0.273930 +3 0.291892 0.003837 0.272470 0.000001 0.005171 +4 0.293352 0.008282 0.273930 0.005171 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0cc0ca4e1d2fcf6ef4cd4789ede7254df62379fc --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.283384 0.256311 0.283384 0.283384 +1 0.283384 0.000001 0.049608 0.000001 0.000001 +2 0.256311 0.049608 0.000001 0.049608 0.049608 +3 0.283384 0.000001 0.049608 0.000001 0.000001 +4 0.283384 0.000001 0.049608 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0e70970e809d89d508629437d7f37d711ae53ca0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000620_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.056384 0.000001 0.000001 +1 0.000001 0.000001 0.056384 0.000001 0.000001 +2 0.056384 0.056384 0.000001 0.056384 0.056384 +3 0.000001 0.000001 0.056384 0.000001 0.000001 +4 0.000001 0.000001 0.056384 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000621_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000621_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6962859eefa242cfe3a6ddede14996cb76c3f2df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000621_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03576300 Before NNI: tree length is 0.03576300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6af0065efcd2aac9b0fc30722cd986b57f4bfe44 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.979689 1.516786 1.006853 0.967890 +1 0.979689 0.000001 0.613213 0.127090 0.021711 +2 1.516786 0.613213 0.000001 0.664187 0.601414 +3 1.006853 0.127090 0.664187 0.000001 0.115291 +4 0.967890 0.021711 0.601414 0.115291 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3d664e5c6f55e737a8427c6047a5fbe083624b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33371741 Before NNI: tree length is 0.33371737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a855d6bb1ff3c3f14fa76a8ede5fcf16e10ab9a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.087234 0.183630 0.087605 0.087234 +1 0.087234 0.000001 0.195353 0.006116 0.000001 +2 0.183630 0.195353 0.000001 0.195723 0.195353 +3 0.087605 0.006116 0.195723 0.000001 0.006116 +4 0.087234 0.000001 0.195353 0.006116 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..821930a0354d8fe7ee3add0733b3ff93f36e7c84 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23635230 Before NNI: tree length is 0.23635225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e1099484115351c596aaaf0770b11e3fd0741e57 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.088092 0.324207 0.078029 0.088092 +1 0.088092 0.000001 0.370147 0.023670 0.000001 +2 0.324207 0.370147 0.000001 0.360083 0.370147 +3 0.078029 0.023670 0.360083 0.000001 0.023670 +4 0.088092 0.000001 0.370147 0.023670 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..355a51b47b65323e1858f32fdca8d493e505171e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39802682 Before NNI: tree length is 0.39802675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..81479de54055ab0d8223aaebe5bccb9c417a0a3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000641_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51718541 Before NNI: tree length is 0.51718537 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..16c4752c0966a9d80a932d6af72defd3cfd35a21 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034608 0.394507 0.044882 0.048156 +1 0.034608 0.000001 0.391324 0.028480 0.015941 +2 0.394507 0.391324 0.000001 0.401597 0.404872 +3 0.044882 0.028480 0.401597 0.000001 0.042028 +4 0.048156 0.015941 0.404872 0.042028 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4867446b7c75364788d4758db2d157d02b28c980 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.155243 0.618740 0.155243 0.017570 +1 0.155243 0.000001 0.606101 0.000001 0.164761 +2 0.618740 0.606101 0.000001 0.606101 0.628259 +3 0.155243 0.000001 0.606101 0.000001 0.164761 +4 0.017570 0.164761 0.628259 0.164761 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf57a4f6a8e3ae315f05b75cbf9e23158c80864f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000647_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.06514184 Before NNI: tree length is 1.06514188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000649_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d8a18f37b02ae14eb23c58e8c6e448fd26ca106f --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.05844300 Before NNI: tree length is 1.05844300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000653_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000653_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..71fad68e47df0d1a72dd8ef9a2bb2423d9f90911 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000653_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21769150 Before NNI: tree length is 0.21769150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000656_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000656_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..98cfef4fb9215a60c1af3d8dba07dcf10187d810 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000656_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64638256 Before NNI: tree length is 0.64638250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..975550881deb4f9be4616b4975f84ffdf9ea4a0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000662_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28837350 Before NNI: tree length is 0.28837350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000666_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000666_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c8034d47587ab84864d6fe8e05a2b6da86df999 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000666_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.296991 0.656515 0.298819 0.296991 +1 0.296991 0.000001 0.602410 0.032993 0.000001 +2 0.656515 0.602410 0.000001 0.604239 0.602410 +3 0.298819 0.032993 0.604239 0.000001 0.032993 +4 0.296991 0.000001 0.602410 0.032993 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000668_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..684a3c01981f67ca237b346b66e847bdf082aa32 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49314876 Before NNI: tree length is 0.49314875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e602ff115e7f7cc7c160bf24c2555acf3210e4f2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58443700 Before NNI: tree length is 0.58443700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36c58af986c9be7f5ab8684fc7c909f4152db526 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.123565 0.324451 0.124535 0.124763 +1 0.123565 0.000001 0.335902 0.007990 0.002635 +2 0.324451 0.335902 0.000001 0.336873 0.337101 +3 0.124535 0.007990 0.336873 0.000001 0.009189 +4 0.124763 0.002635 0.337101 0.009189 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5d521c80e34ca408a3321e2e5ec8df64a48aa50 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000671_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39835610 Before NNI: tree length is 0.39835613 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd50564fc3782f022e3b1064abbdbc2c372e0c0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000672_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.355990 0.684168 0.374933 0.365346 +1 0.355990 0.000001 0.678744 0.018943 0.060492 +2 0.684168 0.678744 0.000001 0.697687 0.688101 +3 0.374933 0.018943 0.697687 0.000001 0.079435 +4 0.365346 0.060492 0.688101 0.079435 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000673_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000673_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7d1bf7384971b7fac6cab0063db8b0ed6f4fdd6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000673_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.087241 0.444500 0.087241 0.087241 +1 0.087241 0.000001 0.425071 0.000001 0.000001 +2 0.444500 0.425071 0.000001 0.425071 0.425071 +3 0.087241 0.000001 0.425071 0.000001 0.000001 +4 0.087241 0.000001 0.425071 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..41b33d903f21bb6f73324e62601835d94af8a7be --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.087419 0.351487 0.091848 0.087937 +1 0.087419 0.000001 0.355019 0.007416 0.013731 +2 0.351487 0.355019 0.000001 0.359448 0.355537 +3 0.091848 0.007416 0.359448 0.000001 0.018160 +4 0.087937 0.013731 0.355537 0.018160 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc01843633dc456c9a1745c342e8359e44535b0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000679_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77016850 Before NNI: tree length is 0.77016850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000680_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000680_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c21448a8d045c48893b839ba997560d1e8d9676c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000680_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007134 0.069011 0.007134 0.007134 +1 0.007134 0.000001 0.067872 0.000001 0.000001 +2 0.069011 0.067872 0.000001 0.067872 0.067872 +3 0.007134 0.000001 0.067872 0.000001 0.000001 +4 0.007134 0.000001 0.067872 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ff67d56889769121b4ff840c58aa124cacc1aaa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14256450 Before NNI: tree length is 0.14256450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ee50db0a6c93a5401fe6d66c02e9d38b523f2ac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000686_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64144603 Before NNI: tree length is 0.64144600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2a34ed0549991074105c9bb9e24554102fb7cef2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.261896 0.540657 0.251259 0.257226 +1 0.261896 0.000001 0.613110 0.029287 0.049501 +2 0.540657 0.613110 0.000001 0.602473 0.608440 +3 0.251259 0.029287 0.602473 0.000001 0.038864 +4 0.257226 0.049501 0.608440 0.038864 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000691_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000691_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad68f69960a1b587d78a22f970a77bfa157bab1d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000691_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.54694325 Before NNI: tree length is 1.54694325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c64291e0e236ae532e1e18e58ff8457f33e396ba --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.158368 0.519226 0.126767 0.158368 +1 0.158368 0.000001 0.530564 0.059456 0.000001 +2 0.519226 0.530564 0.000001 0.498963 0.530564 +3 0.126767 0.059456 0.498963 0.000001 0.059456 +4 0.158368 0.000001 0.530564 0.059456 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000700_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000700_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe96a464df7cbe8a54680d7bdd6d095d9cbb0c82 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000700_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13106411 Before NNI: tree length is 0.13106413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000705_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..486b6e60830454ffc7a4af53361965f7a9eb1a59 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.35376400 Before NNI: tree length is 1.35376400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000706_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000706_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af067328bc7ba3d2e618480bc92549830ac86a60 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000706_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37368778 Before NNI: tree length is 0.37368775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3042a1eca1451509ef4a5504190202f9804f473 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.379816 0.453821 0.006933 0.350537 +1 0.379816 0.000001 0.387289 0.386749 0.094113 +2 0.453821 0.387289 0.000001 0.460753 0.358009 +3 0.006933 0.386749 0.460753 0.000001 0.357469 +4 0.350537 0.094113 0.358009 0.357469 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b669c4440229e929743523b898945b3949d1914 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000716_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17066021 Before NNI: tree length is 0.17066025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df3a3ec9ea25f11a38df69e9db7314c5823bf9d9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.238623 0.862951 0.234430 0.239228 +1 0.238623 0.000001 0.800647 0.016173 0.002808 +2 0.862951 0.800647 0.000001 0.796455 0.801253 +3 0.234430 0.016173 0.796455 0.000001 0.016778 +4 0.239228 0.002808 0.801253 0.016778 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ac8f200a2d6a8adc9654e1b802fd3056dff8cc38 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.253895 0.410569 0.239061 0.244458 +1 0.253895 0.000001 0.435782 0.024716 0.030114 +2 0.410569 0.435782 0.000001 0.420947 0.426345 +3 0.239061 0.024716 0.420947 0.000001 0.008280 +4 0.244458 0.030114 0.426345 0.008280 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdd2d9607003fe1bed36ba7f80c60fc12f093ed4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000720_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56190261 Before NNI: tree length is 0.56190263 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a6ac8685964f1295afa91cb7c6228ad97fa9df55 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.111843 0.214361 0.113084 0.113617 +1 0.111843 0.000001 0.216955 0.009936 0.010469 +2 0.214361 0.216955 0.000001 0.218195 0.218729 +3 0.113084 0.009936 0.218195 0.000001 0.002746 +4 0.113617 0.010469 0.218729 0.002746 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..13a7823b4ef3f3b6d0632969371c32d9d4dd3372 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34332887 Before NNI: tree length is 0.34332887 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000723_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000723_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..39def95c5c0da7cfd97451cd388fac405d94f5ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000723_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18778800 Before NNI: tree length is 0.18778800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000728_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000728_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32c68828ee15b96e82777b8f534339cd4f93d9b0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000728_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10680700 Before NNI: tree length is 0.10680700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0ba84c237c81a9a4a3afc9fd1cd029ed562e187 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48548285 Before NNI: tree length is 0.48548287 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..235fb208aaffb0ff3d93f5f99622371dba49888e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000731_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.115097 0.271364 0.113928 0.115736 +1 0.115097 0.000001 0.279837 0.006508 0.012880 +2 0.271364 0.279837 0.000001 0.278667 0.280476 +3 0.113928 0.006508 0.278667 0.000001 0.011711 +4 0.115736 0.012880 0.280476 0.011711 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000737_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000737_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c1d70d3842b21901de5ca3a6ccf47a6f187b39e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000737_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084049 0.233501 0.084049 0.074248 +1 0.084049 0.000001 0.215517 0.000001 0.009801 +2 0.233501 0.215517 0.000001 0.215517 0.205716 +3 0.084049 0.000001 0.215517 0.000001 0.009801 +4 0.074248 0.009801 0.205716 0.009801 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e4096b4b807b1e7f38c0d40eb68ff98f683a3b3 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.120475 0.309902 0.120150 0.135113 +1 0.120475 0.000001 0.327701 0.000325 0.014638 +2 0.309902 0.327701 0.000001 0.327376 0.342339 +3 0.120150 0.000325 0.327376 0.000001 0.014963 +4 0.135113 0.014638 0.342339 0.014963 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d52c026746d9e1d82aaaeef1001d316b1169087c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35836800 Before NNI: tree length is 0.35836800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000743_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000743_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a99226fa233dc618b3e55ad08081fced5c0f97e3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000743_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035038 0.103418 0.035038 0.035038 +1 0.035038 0.000001 0.086712 0.000001 0.000001 +2 0.103418 0.086712 0.000001 0.086712 0.086712 +3 0.035038 0.000001 0.086712 0.000001 0.000001 +4 0.035038 0.000001 0.086712 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000746_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000746_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d86d097700c361e4d42063ae8b2cc8a73ce4414a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000746_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.64662950 Before NNI: tree length is 0.64662950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a2254df3c50dbc3f96ff40c7664de3dff8ecb04 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000747_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57169975 Before NNI: tree length is 0.57169975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000748_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000748_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4c8e2352e7f221a3c099f3c2193fb029a9597ae3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000748_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.038370 0.098906 0.038370 0.038370 +1 0.038370 0.000001 0.137276 0.000001 0.000001 +2 0.098906 0.137276 0.000001 0.137276 0.137276 +3 0.038370 0.000001 0.137276 0.000001 0.000001 +4 0.038370 0.000001 0.137276 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc2210f58f18a903df4478747c509d790c7510e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27724400 Before NNI: tree length is 0.27724400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000750_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000750_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63b3756c23d7ad1c619f39eb05d4d9b72b6a5f62 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000750_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41191100 Before NNI: tree length is 0.41191100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58807ed171d778c69892e77e71b1201338a3d700 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000754_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.268142 0.352648 0.257321 0.268709 +1 0.268142 0.000001 0.343239 0.040903 0.024464 +2 0.352648 0.343239 0.000001 0.332418 0.343807 +3 0.257321 0.040903 0.332418 0.000001 0.041470 +4 0.268709 0.024464 0.343807 0.041470 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000756_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000756_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af7c64b75bfd707c404a1c30b7fcb1d61edb490d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000756_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.125258 0.176009 0.120516 0.118562 +1 0.125258 0.000001 0.145192 0.005864 0.017148 +2 0.176009 0.145192 0.000001 0.140449 0.138496 +3 0.120516 0.005864 0.140449 0.000001 0.012406 +4 0.118562 0.017148 0.138496 0.012406 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e89ef55b22c3dfe343672ec7a8b0106b81b6110 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11389325 Before NNI: tree length is 0.11389325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..113e0bce7adf3057553ba056587faf8449a59b5f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.024369 0.054111 0.024678 0.024369 +1 0.024369 0.000001 0.050709 0.001988 0.000001 +2 0.054111 0.050709 0.000001 0.051017 0.050709 +3 0.024678 0.001988 0.051017 0.000001 0.001988 +4 0.024369 0.000001 0.050709 0.001988 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000765_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d28c2f2d4b1143fdedc9469ba40f8562954794e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01873550 Before NNI: tree length is 0.01873550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999999 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000770_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000770_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d19e18e307390703d62d67ebee5629e7837af17e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000770_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.264852 0.387367 0.261497 0.264852 +1 0.264852 0.000001 0.454450 0.016448 0.000001 +2 0.387367 0.454450 0.000001 0.451095 0.454450 +3 0.261497 0.016448 0.451095 0.000001 0.016448 +4 0.264852 0.000001 0.454450 0.016448 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000774_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed7536fd8cb55e71bf0be113369c9508bf9e5f91 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07935750 Before NNI: tree length is 0.07935750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9e958cc222f5276a5d59aff67ac7587d0e4fcf4c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000777_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.024369 0.000001 0.000001 +1 0.000001 0.000001 0.024369 0.000001 0.000001 +2 0.024369 0.024369 0.000001 0.024369 0.024369 +3 0.000001 0.000001 0.024369 0.000001 0.000001 +4 0.000001 0.000001 0.024369 0.000001 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000778_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b271777d7ed8dd46a511a716d040ed681d859871 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09673170 Before NNI: tree length is 0.09673175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000784_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000784_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c3f8ddb78df46c0071d3e65c0456d8ef01bcc26 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000784_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022986 0.028591 0.022986 0.022986 +1 0.022986 0.000001 0.027128 0.000001 0.000001 +2 0.028591 0.027128 0.000001 0.027128 0.027128 +3 0.022986 0.000001 0.027128 0.000001 0.000001 +4 0.022986 0.000001 0.027128 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000785_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000785_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58725975a4e19e84454d1a89c9d616e25590d0bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000785_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03555808 Before NNI: tree length is 0.03555800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..76cd793bb30ddb28257d352e82ef208706f07e2e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000791_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061850 0.100433 0.061850 0.058299 +1 0.061850 0.000001 0.117722 0.000001 0.010419 +2 0.100433 0.117722 0.000001 0.117722 0.114171 +3 0.061850 0.000001 0.117722 0.000001 0.010419 +4 0.058299 0.010419 0.114171 0.010419 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000795_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000795_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04c47201f44c5112214932492f19f31cc20962b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000795_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02263450 Before NNI: tree length is 0.02263450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000799_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8950605e95b46d86ce758eee150b4a139370fad4 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.098510 0.114866 0.092764 0.098510 +1 0.098510 0.000001 0.101744 0.005919 0.000001 +2 0.114866 0.101744 0.000001 0.095998 0.101744 +3 0.092764 0.005919 0.095998 0.000001 0.005919 +4 0.098510 0.000001 0.101744 0.005919 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000801_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000801_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b8c43ab61e6c1d79ceb3c1a37adbacf1ff96771 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000801_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014927 0.042733 0.014987 0.020168 +1 0.014927 0.000001 0.057660 0.000060 0.005241 +2 0.042733 0.057660 0.000001 0.057720 0.062901 +3 0.014987 0.000060 0.057720 0.000001 0.005181 +4 0.020168 0.005241 0.062901 0.005181 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000806_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000806_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a20ed665ad887df9573b4f38751037ca816feb38 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000806_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52946050 Before NNI: tree length is 0.52946050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000807_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000807_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fdd0b856eb60fe57a3aa7861d593fb140acf4fd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000807_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32914500 Before NNI: tree length is 0.32914500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..90824ee5503ebe7a76d51f5d0e0239651bba3172 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068591 0.086673 0.061110 0.058960 +1 0.068591 0.000001 0.108009 0.017737 0.015587 +2 0.086673 0.108009 0.000001 0.100527 0.098377 +3 0.061110 0.017737 0.100527 0.000001 0.004144 +4 0.058960 0.015587 0.098377 0.004144 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b135a547f92a0d8053bd2245bad324c5a315036a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000810_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.86982780 Before NNI: tree length is 0.86982775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000811_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3d28a85430c4c025333eb83b616da98c4b5f02c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059540 0.227995 0.059540 0.060593 +1 0.059540 0.000001 0.221006 0.000001 0.003976 +2 0.227995 0.221006 0.000001 0.221006 0.222060 +3 0.059540 0.000001 0.221006 0.000001 0.003976 +4 0.060593 0.003976 0.222060 0.003976 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec3b9c1cfe62a4e25a923ee3020c9f27f0cb5e47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000812_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.67570075 Before NNI: tree length is 0.67570075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fc58f85a0aef6bf49a0432b3346ddbf105a56152 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.130737 0.442082 0.127981 0.147786 +1 0.130737 0.000001 0.350812 0.045577 0.043740 +2 0.442082 0.350812 0.000001 0.356922 0.367861 +3 0.127981 0.045577 0.356922 0.000001 0.062626 +4 0.147786 0.043740 0.367861 0.062626 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7c99d9a64b422cbb58bcc2440856185cd69983b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018818 0.126335 0.026651 0.022138 +1 0.018818 0.000001 0.119433 0.019749 0.009835 +2 0.126335 0.119433 0.000001 0.112064 0.122754 +3 0.026651 0.019749 0.112064 0.000001 0.023070 +4 0.022138 0.009835 0.122754 0.023070 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4c8c746553f2d69475dcb18a4c30b9a60a535c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14506075 Before NNI: tree length is 0.14506075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000819_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a215be719e0aaad4e1c6a12f8d0ba10b3826f868 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.171500 0.203606 0.168612 0.171533 +1 0.171500 0.000001 0.164495 0.018556 0.014079 +2 0.203606 0.164495 0.000001 0.161607 0.164528 +3 0.168612 0.018556 0.161607 0.000001 0.018589 +4 0.171533 0.014079 0.164528 0.018589 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a409c8b3bb79d209bd8a986270f537f8bca5f1da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.144684 0.373423 0.130397 0.130397 +1 0.144684 0.000001 0.382528 0.039273 0.039273 +2 0.373423 0.382528 0.000001 0.368241 0.368241 +3 0.130397 0.039273 0.368241 0.000001 0.000001 +4 0.130397 0.039273 0.368241 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3804eb7f2ba1d49ae7d4ecb7655af4a51513f41b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46281100 Before NNI: tree length is 0.46281100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000821_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000821_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..02b090d6d833751fb29535a38de8b70fbad3335a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000821_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18926791 Before NNI: tree length is 0.18926787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dd52f0456c4c2282d84bb266e8167a55267ac9c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.276279 0.179915 0.281137 0.274721 +1 0.276279 0.000001 0.325380 0.011606 0.010137 +2 0.179915 0.325380 0.000001 0.330238 0.323822 +3 0.281137 0.011606 0.330238 0.000001 0.014995 +4 0.274721 0.010137 0.323822 0.014995 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000825_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000825_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7e4d18a9b6b3c3a08fb7e171fd208672cefa75d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000825_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30483986 Before NNI: tree length is 0.30483987 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..73df6c18d18155fa28458df78338db4d1bb06d39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.093329 0.096031 0.084378 0.095371 +1 0.093329 0.000001 0.012329 0.013376 0.015143 +2 0.096031 0.012329 0.000001 0.016077 0.017844 +3 0.084378 0.013376 0.016077 0.000001 0.015418 +4 0.095371 0.015143 0.017844 0.015418 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b7b5718a46064427c6e149410e9f9ed8786b21d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000828_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.045883 0.054462 0.056477 0.055476 +1 0.045883 0.000001 0.008579 0.010594 0.009593 +2 0.054462 0.008579 0.000001 0.012085 0.012097 +3 0.056477 0.010594 0.012085 0.000001 0.014112 +4 0.055476 0.009593 0.012097 0.014112 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d187d2b6e3bda442cd86b17dd5d7e603da2fbcf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02176583 Before NNI: tree length is 0.02176588 + 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/OG0000832_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000832_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b19321edc0062ab8a6beced397892b90b47acafc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000832_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044747 0.101589 0.041892 0.040598 +1 0.044747 0.000001 0.119355 0.012316 0.009562 +2 0.101589 0.119355 0.000001 0.116499 0.115206 +3 0.041892 0.012316 0.116499 0.000001 0.008166 +4 0.040598 0.009562 0.115206 0.008166 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000832_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000832_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9bd2de257d9275b44e831fbadf7f8d9b36479e81 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000832_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14028206 Before NNI: tree length is 0.14028200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f897ca9d8d28210083d8ee08c7e499e10a0acee8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51853403 Before NNI: tree length is 0.51853400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000834_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000834_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0500cdae52828a76bc535d0b78be7a918411268 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000834_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46702550 Before NNI: tree length is 0.46702550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..238a50971f0b52a255260e25b106ecdf0c226033 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000837_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.695241 0.992878 0.700676 0.696191 +1 0.695241 0.000001 1.077986 0.058782 0.099446 +2 0.992878 1.077986 0.000001 1.083421 1.078936 +3 0.700676 0.058782 1.083421 0.000001 0.104881 +4 0.696191 0.099446 1.078936 0.104881 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..23af9446a3b948b86fa6013e51c8aa3f06185e7d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.165543 0.583589 0.180963 0.177109 +1 0.165543 0.000001 0.569661 0.020809 0.016955 +2 0.583589 0.569661 0.000001 0.585082 0.581228 +3 0.180963 0.020809 0.585082 0.000001 0.010914 +4 0.177109 0.016955 0.581228 0.010914 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000841_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000841_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ffd365e0ca2423518df87f0fa9f6ab250c562b48 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000841_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.20206550 Before NNI: tree length is 2.20206550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e172583969da0956eca61480f74e6222c4c25f90 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.476464 1.232908 0.521200 0.466878 +1 0.476464 0.000001 1.227513 0.073257 0.060655 +2 1.232908 1.227513 0.000001 1.272249 1.217927 +3 0.521200 0.073257 1.272249 0.000001 0.105392 +4 0.466878 0.060655 1.217927 0.105392 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f6e41903d84f35726229ae17497ada990e018a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.55297375 Before NNI: tree length is 1.55297375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c1cb09e0eaaf2bf201fc2a609aee1c17051c25ca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.672861 0.658063 0.676308 0.696722 +1 0.672861 0.000001 0.684180 0.022636 0.043049 +2 0.658063 0.684180 0.000001 0.687627 0.708040 +3 0.676308 0.022636 0.687627 0.000001 0.027923 +4 0.696722 0.043049 0.708040 0.027923 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4bf6ecf3d75a98284170133c9c11bf366cde4c0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15486786 Before NNI: tree length is 0.15486788 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c3091c50d7151f19f04b83ba7a5ab905996386e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.143232 0.355144 0.128532 0.132285 +1 0.143232 0.000001 0.365197 0.028813 0.023313 +2 0.355144 0.365197 0.000001 0.350497 0.354250 +3 0.128532 0.028813 0.350497 0.000001 0.017866 +4 0.132285 0.023313 0.354250 0.017866 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7896ea9d00cebbbc4a4d00074fceda83892f293 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.269358 0.466060 0.264497 0.260290 +1 0.269358 0.000001 0.418797 0.016228 0.019616 +2 0.466060 0.418797 0.000001 0.413937 0.409729 +3 0.264497 0.016228 0.413937 0.000001 0.014755 +4 0.260290 0.019616 0.409729 0.014755 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..87a5b85a6a4815e0a3d1e3ad2cf04dd3eb4f681d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58806513 Before NNI: tree length is 0.58806513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f20c8a4c82951ab9f24b45449a6aa66d06d056b7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32644036 Before NNI: tree length is 0.32644038 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6a2a6f9f1a744992877435f907699e8e6fb958cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054014 0.072852 0.068388 0.062761 +1 0.054014 0.000001 0.081076 0.076612 0.070986 +2 0.072852 0.081076 0.000001 0.076849 0.071223 +3 0.068388 0.076612 0.076849 0.000001 0.054698 +4 0.062761 0.070986 0.071223 0.054698 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000859_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..012e889abba89d1a524fd58b36a264df9188c625 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09087090 Before NNI: tree length is 0.09087087 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000862_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7c6859b3496a0f4175fadd2968f8a2b9152b7a2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02492550 Before NNI: tree length is 0.02492550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab7b67ba31111ebefec44e8cdd5d37806ae4f617 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51210000 Before NNI: tree length is 0.51210000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f8543715c93894e1603b11f049fc055164da686 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.305647 0.708288 0.307444 0.304804 +1 0.305647 0.000001 0.412108 0.005918 0.003279 +2 0.708288 0.412108 0.000001 0.413905 0.411266 +3 0.307444 0.005918 0.413905 0.000001 0.002640 +4 0.304804 0.003279 0.411266 0.002640 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000870_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000870_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cc3f00d7350056fb0f76dc010c8e453743dccdb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000870_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.216320 0.198979 0.214727 0.219888 +1 0.216320 0.000001 0.025461 0.024349 0.029509 +2 0.198979 0.025461 0.000001 0.023868 0.029028 +3 0.214727 0.024349 0.023868 0.000001 0.005160 +4 0.219888 0.029509 0.029028 0.005160 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5663fdf5d242e755900fbc38adb40a437e1cf0eb --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21927629 Before NNI: tree length is 0.21927625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbc868bf6e9ab8d22a1018461202df7600b8e028 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32673200 Before NNI: tree length is 0.32673200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f5976ecc4f1dbdb2778e6563ccbf98e410c64cf5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000885_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.075292 0.091573 0.076940 0.074195 +1 0.075292 0.000001 0.048045 0.003261 0.002028 +2 0.091573 0.048045 0.000001 0.049694 0.046948 +3 0.076940 0.003261 0.049694 0.000001 0.003677 +4 0.074195 0.002028 0.046948 0.003677 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c30aacfb35f02fa1ce6eb27c1e29cc81b06bf10 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09440550 Before NNI: tree length is 0.09440550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000891_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000891_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1b0cb1b16d1b21382317cab0c2e1a905cf7348a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000891_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.166516 0.293235 0.171095 0.166516 +1 0.166516 0.000001 0.279687 0.004721 0.000001 +2 0.293235 0.279687 0.000001 0.284266 0.279687 +3 0.171095 0.004721 0.284266 0.000001 0.004721 +4 0.166516 0.000001 0.279687 0.004721 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..64e5b687042da542a8e54ab2d0b568e89cf8418d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15599118 Before NNI: tree length is 0.15599125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000894_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000894_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..34d80dbf601551489fe56f8c89a1c584c8181fd9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000894_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.082248 0.187106 0.084928 0.083226 +1 0.082248 0.000001 0.209908 0.004669 0.001871 +2 0.187106 0.209908 0.000001 0.212588 0.210886 +3 0.084928 0.004669 0.212588 0.000001 0.005647 +4 0.083226 0.001871 0.210886 0.005647 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f9401f2e9839f5eb76fb1ab792bfce1d31a55e8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07046817 Before NNI: tree length is 0.07046813 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7c002e0c2018f9d32b19e5bafe382bebd818ae4e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.111594 0.234239 0.111594 0.102639 +1 0.111594 0.000001 0.226865 0.000001 0.036441 +2 0.234239 0.226865 0.000001 0.226865 0.217909 +3 0.111594 0.000001 0.226865 0.000001 0.036441 +4 0.102639 0.036441 0.217909 0.036441 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000901_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..79bf9ad42edf5b8f4d7e6f05260898cf0ee5b929 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.285618 0.382927 0.285618 0.278310 +1 0.285618 0.000001 0.461256 0.000001 0.089315 +2 0.382927 0.461256 0.000001 0.461256 0.453949 +3 0.285618 0.000001 0.461256 0.000001 0.089315 +4 0.278310 0.089315 0.453949 0.089315 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..70eaf411e51d408f0eb836d75ba45fb5032d16ed --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.100881 0.177726 0.101042 0.107174 +1 0.100881 0.000001 0.181034 0.003394 0.018893 +2 0.177726 0.181034 0.000001 0.181195 0.187327 +3 0.101042 0.003394 0.181195 0.000001 0.019054 +4 0.107174 0.018893 0.187327 0.019054 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f131b98b6cbf53aaff57abe171c66367b54715c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000905_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24419100 Before NNI: tree length is 0.24419100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7770cd263dc01007353f8d29de83e43f23e6d53f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.278236 1.213022 0.277409 0.304737 +1 0.278236 0.000001 1.039023 0.015685 0.043013 +2 1.213022 1.039023 0.000001 1.038196 1.065524 +3 0.277409 0.015685 1.038196 0.000001 0.031696 +4 0.304737 0.043013 1.065524 0.031696 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e11696259a28cdcf8c3c3b063139b6c8390e8e47 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000909_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.30208150 Before NNI: tree length is 1.30208150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000911_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000911_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bdec58e728baa16c28a2e6f7f27b5d0e5c0eafc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000911_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.27870200 Before NNI: tree length is 0.27870200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000916_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000916_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28afd0d7f82f83ad2ea621de6cb53fd1ef0b9b48 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000916_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.11907375 Before NNI: tree length is 1.11907375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000917_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c5c415be63e61d2d979a0476bbae7b449b2f0ea --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.62269550 Before NNI: tree length is 0.62269550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1a2ae5cf9f5b3c2e1bb615bcbc3dbc1f11db1873 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.066047 0.413451 0.063704 0.066047 +1 0.066047 0.000001 0.437598 0.013932 0.000001 +2 0.413451 0.437598 0.000001 0.435254 0.437598 +3 0.063704 0.013932 0.435254 0.000001 0.013932 +4 0.066047 0.000001 0.437598 0.013932 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d3ee0b109470bb65725fc9ceb81bc46d148defe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000918_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46434282 Before NNI: tree length is 0.46434275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0fe88924431bbb2844cdc30ca5ba4c2dc8f9df27 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081629 0.088535 0.079773 0.083499 +1 0.081629 0.000001 0.023672 0.005386 0.009112 +2 0.088535 0.023672 0.000001 0.021816 0.025542 +3 0.079773 0.005386 0.021816 0.000001 0.004014 +4 0.083499 0.009112 0.025542 0.004014 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..39b6a13df6855219582e236c46e6afb2777f5d61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10255300 Before NNI: tree length is 0.10255300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..838b25cbec2cfa3136f305e48776978d4c574886 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000921_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063152 0.070046 0.060269 0.060269 +1 0.063152 0.000001 0.056733 0.003571 0.003571 +2 0.070046 0.056733 0.000001 0.053850 0.053850 +3 0.060269 0.003571 0.053850 0.000001 0.000001 +4 0.060269 0.003571 0.053850 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000922_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d55c50f4152c681a6e229168e2c03c3f21beee38 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30434040 Before NNI: tree length is 0.30434037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2743ee8256dcba21b2f15d9ca3be1ee4a184648 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66147504 Before NNI: tree length is 0.66147500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2929cf8c35739a511e3cc8721bec91e111fb2928 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65942100 Before NNI: tree length is 0.65942100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000931_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000931_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5fb248b780a4448324c5ac315eed3cd198f71a80 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000931_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.201856 0.529362 0.199067 0.202403 +1 0.201856 0.000001 0.502761 0.005704 0.007463 +2 0.529362 0.502761 0.000001 0.499972 0.503308 +3 0.199067 0.005704 0.499972 0.000001 0.006251 +4 0.202403 0.007463 0.503308 0.006251 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..84dc78c32fd34a5e572bd8e4af17a232a02d009d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.296059 0.573412 0.302911 0.289973 +1 0.296059 0.000001 0.679057 0.075462 0.062524 +2 0.573412 0.679057 0.000001 0.685910 0.672972 +3 0.302911 0.075462 0.685910 0.000001 0.018691 +4 0.289973 0.062524 0.672972 0.018691 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f87ac457ac19e1872f42bc6d3a94132bc79bf1b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81829781 Before NNI: tree length is 0.81829775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8bbd474c6f524c49d5df0f6263547302df8ca4e7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.248665 0.517291 0.247730 0.247263 +1 0.248665 0.000001 0.565315 0.023579 0.023112 +2 0.517291 0.565315 0.000001 0.564380 0.563913 +3 0.247730 0.023579 0.564380 0.000001 0.010240 +4 0.247263 0.023112 0.563913 0.010240 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e6311ef2996f56a950a03dc30dca411a07cbd18 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000941_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81876600 Before NNI: tree length is 0.81876600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000942_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..501e983b5b64df7784b68aaa92920d1bb8af55ca --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.292187 0.354310 0.292187 0.292187 +1 0.292187 0.000001 0.294764 0.000001 0.000001 +2 0.354310 0.294764 0.000001 0.294764 0.294764 +3 0.292187 0.000001 0.294764 0.000001 0.000001 +4 0.292187 0.000001 0.294764 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..74f411704657d11142c202d61701c81ed42b59e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000943_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24424571 Before NNI: tree length is 0.24424575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000945_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000945_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b03f415b0a4d2795cbdc35b2465a5dea25d1814 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000945_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.272335 0.367795 0.272335 0.270206 +1 0.272335 0.000001 0.318318 0.000001 0.026287 +2 0.367795 0.318318 0.000001 0.318318 0.316188 +3 0.272335 0.000001 0.318318 0.000001 0.026287 +4 0.270206 0.026287 0.316188 0.026287 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c75fc73c2fd75773ed382ffeef7a0a99d7ec84c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.223707 0.603389 0.217600 0.213623 +1 0.223707 0.000001 0.647243 0.038184 0.050042 +2 0.603389 0.647243 0.000001 0.641135 0.637159 +3 0.217600 0.038184 0.641135 0.000001 0.043934 +4 0.213623 0.050042 0.637159 0.043934 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000949_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6984f2d3719f403112dc78eee96e90bce01a707a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.383555 0.576914 0.376824 0.391336 +1 0.383555 0.000001 0.584179 0.023979 0.018091 +2 0.576914 0.584179 0.000001 0.577448 0.591960 +3 0.376824 0.023979 0.577448 0.000001 0.031760 +4 0.391336 0.018091 0.591960 0.031760 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2a141a69adfa1d8081446700c6d1bd5c013c9056 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054868 0.142019 0.056165 0.055314 +1 0.054868 0.000001 0.137556 0.011478 0.006344 +2 0.142019 0.137556 0.000001 0.138853 0.138002 +3 0.056165 0.011478 0.138853 0.000001 0.011924 +4 0.055314 0.006344 0.138002 0.011924 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000955_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000955_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f1d70114aea10f8707b9481cca63d045c242d1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000955_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46029500 Before NNI: tree length is 0.46029500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000958_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a3ab4ae4a54bfd0cecf753f7223f4623f24b5f1 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42412650 Before NNI: tree length is 0.42412650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a9b00552c1ea99676897e25ebd72d2de018b2fd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000959_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01197750 Before NNI: tree length is 0.01197750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.99999999 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2185ca9c0c3e303ea058fbf475f57bac24f88396 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000963_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05006850 Before NNI: tree length is 0.05006850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..674678ffba768e47a3f7fd64def17402ed34a29e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.458471 0.601805 0.362316 0.475342 +1 0.458471 0.000001 0.372114 0.263727 0.045467 +2 0.601805 0.372114 0.000001 0.407061 0.388985 +3 0.362316 0.263727 0.407061 0.000001 0.280598 +4 0.475342 0.045467 0.388985 0.280598 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c202dafe3ebda2f5bbe09b4a366d54566a848480 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000965_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.90197913 Before NNI: tree length is 0.90197912 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d89a7012b8f1c8c055078ac8955b7f253a3c9b22 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40187750 Before NNI: tree length is 0.40187750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d430f606c4a44aafc8ea08c7fb6acedceb474431 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.042708 0.162067 0.044513 0.046230 +1 0.042708 0.000001 0.159045 0.003844 0.005561 +2 0.162067 0.159045 0.000001 0.160850 0.162567 +3 0.044513 0.003844 0.160850 0.000001 0.001717 +4 0.046230 0.005561 0.162567 0.001717 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..124720be6c321111269ffbc21de7368624490ab7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18645150 Before NNI: tree length is 0.18645150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..631583af1a05c14a17b7476f8f4f156a9f4f8e2d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.108930 0.344830 0.108790 0.107944 +1 0.108930 0.000001 0.358222 0.001822 0.018412 +2 0.344830 0.358222 0.000001 0.358082 0.357236 +3 0.108790 0.001822 0.358082 0.000001 0.018272 +4 0.107944 0.018412 0.357236 0.018272 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1abf398033c25a6be7f1767dd2fbb054ebf9a891 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000971_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41554500 Before NNI: tree length is 0.41554500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..beac328a31414f458ed28734d944630637174bb2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.149921 0.361630 0.144236 0.144236 +1 0.149921 0.000001 0.423880 0.007180 0.007180 +2 0.361630 0.423880 0.000001 0.418195 0.418195 +3 0.144236 0.007180 0.418195 0.000001 0.000001 +4 0.144236 0.007180 0.418195 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000974_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..99c0b3cc4fea410d796efec6fa0d2a5d2eff2c0e --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41042889 Before NNI: tree length is 0.41042888 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23bb35b59551e37e69854f8c5855b54652a096d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19524900 Before NNI: tree length is 0.19524900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df6322dd77f7beb92dbe1de0b708dadac41a9eda --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.165764 0.227786 0.165107 0.166089 +1 0.165764 0.000001 0.268504 0.011992 0.018135 +2 0.227786 0.268504 0.000001 0.267847 0.268830 +3 0.165107 0.011992 0.267847 0.000001 0.017479 +4 0.166089 0.018135 0.268830 0.017479 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1bb6108d129101a3ec181e45f3074d25990740fc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.079784 0.163971 0.085215 0.085215 +1 0.079784 0.000001 0.160853 0.006483 0.006483 +2 0.163971 0.160853 0.000001 0.166284 0.166284 +3 0.085215 0.006483 0.166284 0.000001 0.000001 +4 0.085215 0.006483 0.166284 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000980_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..36bb2c6f131a7ee8fbb67587bc827488a0603772 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29006200 Before NNI: tree length is 0.29006200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000984_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000984_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..95f1d27c7108a82209eec4eb00fe2da1802d5423 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000984_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.108929 0.254823 0.111919 0.112278 +1 0.108929 0.000001 0.262348 0.009711 0.010071 +2 0.254823 0.262348 0.000001 0.265337 0.265696 +3 0.111919 0.009711 0.265337 0.000001 0.006228 +4 0.112278 0.010071 0.265696 0.006228 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000985_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b00027037b207b71c99e34c671504f5bc0e4438 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23134675 Before NNI: tree length is 0.23134675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c1e3bb434779e4aed025561cd1efd817297a7d01 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.336397 0.488432 0.284157 0.284157 +1 0.336397 0.000001 0.534560 0.080369 0.080369 +2 0.488432 0.534560 0.000001 0.482320 0.482320 +3 0.284157 0.080369 0.482320 0.000001 0.000001 +4 0.284157 0.080369 0.482320 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ec63cd9a2138cbf0f8832465000f04fa097bb6e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000988_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56161277 Before NNI: tree length is 0.56161275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..91889e58bef729aacd4dd45bbb88967a2758fa0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000989_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.103175 0.260233 0.105765 0.105765 +1 0.103175 0.000001 0.253325 0.025714 0.025714 +2 0.260233 0.253325 0.000001 0.255915 0.255915 +3 0.105765 0.025714 0.255915 0.000001 0.000001 +4 0.105765 0.025714 0.255915 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000990_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c9a743b0bc2c862cbc9e6fb405fbb61c4893dd2a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.142116 0.246039 0.107456 0.096156 +1 0.142116 0.000001 0.271978 0.043998 0.053589 +2 0.246039 0.271978 0.000001 0.237318 0.226018 +3 0.107456 0.043998 0.237318 0.000001 0.018928 +4 0.096156 0.053589 0.226018 0.018928 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000992_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000992_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6406d168aba7ef8730e17a5c05533623e4553645 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000992_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054668 0.333760 0.021876 0.091063 +1 0.054668 0.000001 0.333642 0.048551 0.090945 +2 0.333760 0.333642 0.000001 0.327642 0.318451 +3 0.021876 0.048551 0.327642 0.000001 0.084945 +4 0.091063 0.090945 0.318451 0.084945 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c438e6cba04db85c3db7a7ddb0ad5939dcc6ed7a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000993_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07223378 Before NNI: tree length is 0.07223375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4a3db9a7d481dcfa8ef62f34702e93c938d05e40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.056880 0.036000 0.056277 0.041367 +1 0.056880 0.000001 0.048647 0.007404 0.015595 +2 0.036000 0.048647 0.000001 0.048044 0.033133 +3 0.056277 0.007404 0.048044 0.000001 0.014991 +4 0.041367 0.015595 0.033133 0.014991 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..55f63bfa23d6762177fa0b1c41eab3ecc6d688d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40733900 Before NNI: tree length is 0.40733900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd090bf43f77559694ee9b352b2e342b0143b52f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.212353 0.298848 0.212098 0.210678 +1 0.212353 0.000001 0.116289 0.006768 0.005348 +2 0.298848 0.116289 0.000001 0.116034 0.114613 +3 0.212098 0.006768 0.116034 0.000001 0.002518 +4 0.210678 0.005348 0.114613 0.002518 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c3590bf07ef153bcf1ec670b8089b2588e25d50 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001004_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.136605 0.447843 0.141089 0.141089 +1 0.136605 0.000001 0.372930 0.012736 0.012736 +2 0.447843 0.372930 0.000001 0.377414 0.377414 +3 0.141089 0.012736 0.377414 0.000001 0.000001 +4 0.141089 0.012736 0.377414 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001007_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001007_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3f42e481a719beb371e6de4754172454740881f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001007_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054361 0.240125 0.060080 0.050669 +1 0.054361 0.000001 0.254120 0.005719 0.019365 +2 0.240125 0.254120 0.000001 0.259839 0.250428 +3 0.060080 0.005719 0.259839 0.000001 0.025084 +4 0.050669 0.019365 0.250428 0.025084 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a0cd7f56b01563795a794f50e9df56ab8da0a9c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12534850 Before NNI: tree length is 0.12534850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c30f0175b054b6642e931ed25255cdd3c654373 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38351850 Before NNI: tree length is 0.38351850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001017_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001017_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..62ef9954fe095bbe06668f7ddd0d6b97d9371d19 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001017_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.236986 0.474769 0.236900 0.237409 +1 0.236986 0.000001 0.495117 0.006746 0.013565 +2 0.474769 0.495117 0.000001 0.495031 0.495540 +3 0.236900 0.006746 0.495031 0.000001 0.013479 +4 0.237409 0.013565 0.495540 0.013479 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1bc0a6a8b5438770aff12708fde006e8581c88f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001019_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10506683 Before NNI: tree length is 0.10506675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a36b395589ad2c8dcd8570fada44a1b17909a11 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22179100 Before NNI: tree length is 0.22179100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f380e5aa5b9da15777eca789d2d3cfccbdba0e61 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.145268 0.415846 0.141475 0.146348 +1 0.145268 0.000001 0.391089 0.009573 0.001080 +2 0.415846 0.391089 0.000001 0.387296 0.392169 +3 0.141475 0.009573 0.387296 0.000001 0.010653 +4 0.146348 0.001080 0.392169 0.010653 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..54d66c6ec255968e1eec34bd95df6465c0bf7422 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001022_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48007150 Before NNI: tree length is 0.48007150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6f8eaffb782c6fb32d6f9df3886e2635ab8c6d84 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.206370 0.343076 0.213834 0.203837 +1 0.206370 0.000001 0.336079 0.037044 0.010165 +2 0.343076 0.336079 0.000001 0.343543 0.333546 +3 0.213834 0.037044 0.343543 0.000001 0.034511 +4 0.203837 0.010165 0.333546 0.034511 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b5c5fc6a2b207542a8c9ac872088022de0ab7e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.079105 0.096220 0.091164 0.084065 +1 0.079105 0.000001 0.100851 0.037019 0.029920 +2 0.096220 0.100851 0.000001 0.112909 0.105810 +3 0.091164 0.037019 0.112909 0.000001 0.027496 +4 0.084065 0.029920 0.105810 0.027496 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c788782c0eedd5b7cc791ec5f17efac3a99063f5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.250183 0.365099 0.246182 0.247996 +1 0.250183 0.000001 0.406631 0.030080 0.028024 +2 0.365099 0.406631 0.000001 0.402631 0.404445 +3 0.246182 0.030080 0.402631 0.000001 0.027893 +4 0.247996 0.028024 0.404445 0.027893 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b32d745f6a89e318afe425c4fd7e4c287da4ffd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001032_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53691486 Before NNI: tree length is 0.53691488 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001033_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001033_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4363c59ef9355769c72d259271f31f3dd0e57f59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001033_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.283893 0.458159 0.295257 0.266340 +1 0.283893 0.000001 0.443155 0.032938 0.055709 +2 0.458159 0.443155 0.000001 0.454519 0.425602 +3 0.295257 0.032938 0.454519 0.000001 0.067073 +4 0.266340 0.055709 0.425602 0.067073 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..adba9feb3c12b536695eac0ac33ffe774da029f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001038_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10629985 Before NNI: tree length is 0.10629988 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8ef2de068933e1f52e8a73d89a7598aacbe19bf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.294792 0.484892 0.265977 0.265977 +1 0.294792 0.000001 0.527507 0.060700 0.060700 +2 0.484892 0.527507 0.000001 0.498692 0.498692 +3 0.265977 0.060700 0.498692 0.000001 0.000001 +4 0.265977 0.060700 0.498692 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001042_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4b5e485d5116699a53624f27c6db3b4b3455a4a0 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.139353 0.268392 0.138048 0.140829 +1 0.139353 0.000001 0.241955 0.007353 0.010133 +2 0.268392 0.241955 0.000001 0.240650 0.243431 +3 0.138048 0.007353 0.240650 0.000001 0.002780 +4 0.140829 0.010133 0.243431 0.002780 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd58933ed62c3d3c2656b80debad1de999675aa7 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39231285 Before NNI: tree length is 0.39231287 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..38650356ce1ebbf6ad59b96e267573dcbef18164 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001045_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006815 0.102859 0.006815 0.019959 +1 0.006815 0.000001 0.098714 0.000001 0.015815 +2 0.102859 0.098714 0.000001 0.098714 0.108959 +3 0.006815 0.000001 0.098714 0.000001 0.015815 +4 0.019959 0.015815 0.108959 0.015815 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b41df18df522f3aedc0366afffc48dc22fac39d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001047_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43784081 Before NNI: tree length is 0.43784075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f79b330289e187e26b13a4d5a542041705db2f8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001050_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08744184 Before NNI: tree length is 1.08744188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb1afc1dfcc1af7b74aeae6b0c42bf79dbd928db --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029051 0.036471 0.027552 0.027426 +1 0.029051 0.000001 0.015802 0.003865 0.001624 +2 0.036471 0.015802 0.000001 0.014303 0.014177 +3 0.027552 0.003865 0.014303 0.000001 0.002241 +4 0.027426 0.001624 0.014177 0.002241 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c4bfea7a36861bceeb1b50c4745e3b12e2fb93c0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.145942 0.290481 0.135401 0.144479 +1 0.145942 0.000001 0.251998 0.017639 0.015984 +2 0.290481 0.251998 0.000001 0.241457 0.250535 +3 0.135401 0.017639 0.241457 0.000001 0.016176 +4 0.144479 0.015984 0.250535 0.016176 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8d21acdf2b57984a9f0c4961e2d1d5f52c90251 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001054_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35502000 Before NNI: tree length is 0.35502000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2ab1717e40ea17e0a4baac1796e10d5b5a81ad5a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001055_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.125660 0.336251 0.118715 0.125660 +1 0.125660 0.000001 0.331174 0.006945 0.000001 +2 0.336251 0.331174 0.000001 0.324229 0.331174 +3 0.118715 0.006945 0.324229 0.000001 0.006945 +4 0.125660 0.000001 0.331174 0.006945 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ea3079b620182163e1ae5bf66960b6cf38f707d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001056_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.80901462 Before NNI: tree length is 1.80901462 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3dfc5967668a364b4fa83cee34c44bee3b75e2d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.122686 0.178261 0.128461 0.136427 +1 0.122686 0.000001 0.226162 0.066950 0.074916 +2 0.178261 0.226162 0.000001 0.231937 0.239902 +3 0.128461 0.066950 0.231937 0.000001 0.056458 +4 0.136427 0.074916 0.239902 0.056458 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a2ad378bce2e1318fef77be27e49e23b6acf1ba1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.051511 0.185325 0.067260 0.072954 +1 0.051511 0.000001 0.187188 0.017163 0.022857 +2 0.185325 0.187188 0.000001 0.202936 0.208630 +3 0.067260 0.017163 0.202936 0.000001 0.010249 +4 0.072954 0.022857 0.208630 0.010249 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..341b5437d3644d090b88fa33b106c06f2b2a4920 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001060_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23643919 Before NNI: tree length is 0.23643925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..82f12c7c6fd97b17448b8f3410d313f869192c58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36401125 Before NNI: tree length is 0.36401125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d167357b18a53db69e2134a0e21dc21156b49cab --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.014926 0.185196 0.088778 0.088778 +1 0.014926 0.000001 0.185246 0.088827 0.088827 +2 0.185196 0.185246 0.000001 0.184246 0.184246 +3 0.088778 0.088827 0.184246 0.000001 0.000001 +4 0.088778 0.088827 0.184246 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001067_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001067_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..488a78fcf110885f1a11045fdfc0ae3921eaba8d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001067_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30025420 Before NNI: tree length is 0.30025425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001069_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001069_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32f67dc4e717dce38978b3f282a25cf5a0260295 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001069_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30674850 Before NNI: tree length is 0.30674850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3c656c7fdd9e7dc0fea1f555b291f3578f704f0a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001075_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.191085 0.504137 0.191085 0.191085 +1 0.191085 0.000001 0.572980 0.000001 0.000001 +2 0.504137 0.572980 0.000001 0.572980 0.572980 +3 0.191085 0.000001 0.572980 0.000001 0.000001 +4 0.191085 0.000001 0.572980 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d7e35664c55f9682f8e7a154c559d6e4285871d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001076_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.186922 0.281497 0.186922 0.186922 +1 0.186922 0.000001 0.229600 0.000001 0.000001 +2 0.281497 0.229600 0.000001 0.229600 0.229600 +3 0.186922 0.000001 0.229600 0.000001 0.000001 +4 0.186922 0.000001 0.229600 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001080_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001080_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d2c8a47ce258bb6338d6955e01e4a7b20b57369 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001080_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08349000 Before NNI: tree length is 0.08349000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bb61d75286e87453c9d57ea647c42a1211433c54 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001081_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060044 0.156745 0.058075 0.060032 +1 0.060044 0.000001 0.154333 0.001970 0.005412 +2 0.156745 0.154333 0.000001 0.152363 0.154320 +3 0.058075 0.001970 0.152363 0.000001 0.003442 +4 0.060032 0.005412 0.154320 0.003442 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001083_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001083_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..60a69e8bfea85a3a05e03371b8c5731bab988005 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001083_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.83598350 Before NNI: tree length is 0.83598350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..701e16b4eb749f6b1a3b5fc7b0b654a05e67aa19 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.261745 0.528066 0.287711 0.287711 +1 0.261745 0.000001 0.472190 0.040332 0.040332 +2 0.528066 0.472190 0.000001 0.498156 0.498156 +3 0.287711 0.040332 0.498156 0.000001 0.000001 +4 0.287711 0.040332 0.498156 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..236b88100d61e18c593b49255b5c23e8e6d900a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001086_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.69423220 Before NNI: tree length is 1.69423225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001095_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001095_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..57a53abe66fc671a78712c56507e900b3489cf59 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001095_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33145029 Before NNI: tree length is 0.33145025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d140eae0826fa496697b9865efd049c71ce2e07f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41568500 Before NNI: tree length is 0.41568500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1575a74b31551868f68163f5bc2d4035e2dfa76e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001100_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77802950 Before NNI: tree length is 0.77802950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..64d989d73eedef060cefa69c1783032b8ac9189e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.184123 0.224174 0.176851 0.176851 +1 0.184123 0.000001 0.274169 0.028165 0.028165 +2 0.224174 0.274169 0.000001 0.266897 0.266897 +3 0.176851 0.028165 0.266897 0.000001 0.000001 +4 0.176851 0.028165 0.266897 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..62669fc3d049255bb6aff0c72a877db115828619 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35168000 Before NNI: tree length is 0.35168000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001104_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a104cf1247486261de37dcf786a911c0da09e8f9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057984 0.102019 0.061492 0.056968 +1 0.057984 0.000001 0.084997 0.003508 0.003352 +2 0.102019 0.084997 0.000001 0.088506 0.083982 +3 0.061492 0.003508 0.088506 0.000001 0.006860 +4 0.056968 0.003352 0.083982 0.006860 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001108_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8ce4e67188c09ce6112b5f12d23c8471e75bc969 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.459142 0.779818 0.459142 0.459142 +1 0.459142 0.000001 0.860189 0.000001 0.000001 +2 0.779818 0.860189 0.000001 0.860189 0.860189 +3 0.459142 0.000001 0.860189 0.000001 0.000001 +4 0.459142 0.000001 0.860189 0.000001 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8a34490b6853931747787b31361b3c95fb9393f5 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005340 0.002829 0.008167 0.008167 +1 0.005340 0.000001 0.008169 0.002826 0.002826 +2 0.002829 0.008169 0.000001 0.010996 0.010996 +3 0.008167 0.002826 0.010996 0.000001 0.000001 +4 0.008167 0.002826 0.010996 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f79f90e5ffc5d6ff5cdf008367dd523eb0ec0f14 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.074948 0.094576 0.070266 0.071148 +1 0.074948 0.000001 0.087652 0.013907 0.014789 +2 0.094576 0.087652 0.000001 0.082971 0.083853 +3 0.070266 0.013907 0.082971 0.000001 0.000882 +4 0.071148 0.014789 0.083853 0.000882 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5ebf9c3279b0af8e7a60a74d32c322d2bd73b287 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057000 0.075478 0.059569 0.060264 +1 0.057000 0.000001 0.087482 0.008932 0.009627 +2 0.075478 0.087482 0.000001 0.090051 0.090746 +3 0.059569 0.008932 0.090051 0.000001 0.001909 +4 0.060264 0.009627 0.090746 0.001909 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e673e261a4fdb0e93a32fd159abdff3b9965a7e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081575 0.152902 0.076972 0.076972 +1 0.081575 0.000001 0.154288 0.005275 0.005275 +2 0.152902 0.154288 0.000001 0.149685 0.149685 +3 0.076972 0.005275 0.149685 0.000001 0.000001 +4 0.076972 0.005275 0.149685 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001117_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001117_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..12fc80333e10d516b35fafade6b453f20a62a60d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001117_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.12542250 Before NNI: tree length is 0.12542250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a20399b543e671d5587ed8fd2d322c025d0c1edd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047703 0.115546 0.047703 0.047703 +1 0.047703 0.000001 0.111962 0.000001 0.000001 +2 0.115546 0.111962 0.000001 0.111962 0.111962 +3 0.047703 0.000001 0.111962 0.000001 0.000001 +4 0.047703 0.000001 0.111962 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd66c8c48110f70ed64961841e5cd53719a13367 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.038706 0.081341 0.039178 0.038706 +1 0.038706 0.000001 0.078176 0.000947 0.000001 +2 0.081341 0.078176 0.000001 0.078648 0.078176 +3 0.039178 0.000947 0.078648 0.000001 0.000947 +4 0.038706 0.000001 0.078176 0.000947 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f57654f5aa904757e92d4ee9ab2343230c4e72b7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001123_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09982150 Before NNI: tree length is 0.09982150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e63474ba49b4e3f1803c0fef23f58a0cc49b3eda --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001132_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.276492 0.312240 0.275510 0.276561 +1 0.276492 0.000001 0.304958 0.026663 0.011610 +2 0.312240 0.304958 0.000001 0.303975 0.305026 +3 0.275510 0.026663 0.303975 0.000001 0.026731 +4 0.276561 0.011610 0.305026 0.026731 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..68ade7b698841f688fc0f7af501c2443811325e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001133_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084260 0.133991 0.084853 0.084853 +1 0.084260 0.000001 0.105145 0.007720 0.007720 +2 0.133991 0.105145 0.000001 0.105737 0.105737 +3 0.084853 0.007720 0.105737 0.000001 0.000001 +4 0.084853 0.007720 0.105737 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa70d1fda5cc69655381e766f5a4c6b15f9a5007 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001135_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.45140402 Before NNI: tree length is 1.45140400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c6780f196be1af3d01ddec56511959a5929d3be6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001136_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.446082 0.659171 0.441800 0.442887 +1 0.446082 0.000001 0.663599 0.057146 0.058233 +2 0.659171 0.663599 0.000001 0.659317 0.660404 +3 0.441800 0.057146 0.659317 0.000001 0.001316 +4 0.442887 0.058233 0.660404 0.001316 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..554d1356e741d5fbffbe823b4f548bf73c0cf502 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.095538 0.222716 0.098659 0.098659 +1 0.095538 0.000001 0.228509 0.010464 0.010464 +2 0.222716 0.228509 0.000001 0.231630 0.231630 +3 0.098659 0.010464 0.231630 0.000001 0.000001 +4 0.098659 0.010464 0.231630 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..21aa5487801986d476de2618edf93ba58c79923b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28017450 Before NNI: tree length is 0.28017450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001139_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3a83ac2557968496ce2ec5620636fc9180d91d7a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.452304 0.597616 0.451507 0.448757 +1 0.452304 0.000001 0.630912 0.045276 0.017327 +2 0.597616 0.630912 0.000001 0.630116 0.627366 +3 0.451507 0.045276 0.630116 0.000001 0.041730 +4 0.448757 0.017327 0.627366 0.041730 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1c79f88757e810e2c98865503e37275185204d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30360300 Before NNI: tree length is 0.30360300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..676a2b20118ed08d613f6ce21f184784f71ebeeb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001146_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.136261 0.225518 0.136261 0.136261 +1 0.136261 0.000001 0.250268 0.000001 0.000001 +2 0.225518 0.250268 0.000001 0.250268 0.250268 +3 0.136261 0.000001 0.250268 0.000001 0.000001 +4 0.136261 0.000001 0.250268 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8aecf827b11ef380d0c0e7b09bf4584e32ae268 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001154_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56294650 Before NNI: tree length is 0.56294650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f080f11accec347694a0b78a6f67d6735845305c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05205239 Before NNI: tree length is 0.05205237 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa77fc5409d707a1e664e3c4f710de1db8b5ab15 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001160_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21611150 Before NNI: tree length is 0.21611150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3911a1ff959ff25d43766fba94ebb36a70c6f271 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14890475 Before NNI: tree length is 0.14890475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f9d85e5bba0e5280aa99c3f108ba11ef626b62f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08118700 Before NNI: tree length is 0.08118700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d85d3f199f71124fe5ada963da92a3bbef69108b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.485486 0.825643 0.483055 0.478600 +1 0.485486 0.000001 0.773647 0.040355 0.050291 +2 0.825643 0.773647 0.000001 0.771216 0.766761 +3 0.483055 0.040355 0.771216 0.000001 0.047861 +4 0.478600 0.050291 0.766761 0.047861 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85541ce3f72e8ed6fa0b5769e7b7b276dbf777e8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001166_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.08305275 Before NNI: tree length is 1.08305275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001167_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001167_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..044ac240dc01d08082980fa83213f8878179c6ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001167_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.36577138 Before NNI: tree length is 2.36577137 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001168_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001168_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..460742036b56c7dae883b9c5a49d642a67723a69 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001168_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.81444106 Before NNI: tree length is 0.81444100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001170_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001170_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b70fb8f720c3ca0f37b15b3ec606744f6876cc65 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001170_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65604900 Before NNI: tree length is 0.65604900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b7257d37d8fed4025bf031e17b7713e5c410596 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.124089 0.271749 0.128807 0.124089 +1 0.124089 0.000001 0.274685 0.010144 0.000001 +2 0.271749 0.274685 0.000001 0.279404 0.274685 +3 0.128807 0.010144 0.279404 0.000001 0.010144 +4 0.124089 0.000001 0.274685 0.010144 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d6baf54f724e649f85228c0e3b864d56207850d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34269320 Before NNI: tree length is 0.34269325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..47a3cbc8e2f6e557b834e5d3edf3d5d08f29223a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034756 0.217027 0.027786 0.034756 +1 0.034756 0.000001 0.190575 0.006970 0.000001 +2 0.217027 0.190575 0.000001 0.189242 0.190575 +3 0.027786 0.006970 0.189242 0.000001 0.006970 +4 0.034756 0.000001 0.190575 0.006970 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001173_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001173_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3de944e40f4e71f75c263be30fc059cd59eb2495 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001173_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.028230 0.122276 0.028230 0.028230 +1 0.028230 0.000001 0.118802 0.000001 0.000001 +2 0.122276 0.118802 0.000001 0.118802 0.118802 +3 0.028230 0.000001 0.118802 0.000001 0.000001 +4 0.028230 0.000001 0.118802 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001175_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001175_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..924ebbfa3eb7b40563c2b0c2dab03f13967d5c3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001175_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.105698 0.242938 0.108622 0.107313 +1 0.105698 0.000001 0.264457 0.024268 0.001615 +2 0.242938 0.264457 0.000001 0.267381 0.266071 +3 0.108622 0.024268 0.267381 0.000001 0.025883 +4 0.107313 0.001615 0.266071 0.025883 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001176_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0b252c7f0d307e2d90a0d11da95cc511c7dcb1aa --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.137976 0.464231 0.133320 0.137976 +1 0.137976 0.000001 0.455776 0.013907 0.000001 +2 0.464231 0.455776 0.000001 0.451120 0.455776 +3 0.133320 0.013907 0.451120 0.000001 0.013907 +4 0.137976 0.000001 0.455776 0.013907 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..870630e9ef251a26368c51ce618b315c8907458d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.027120 0.281749 0.027120 0.026755 +1 0.027120 0.000001 0.308869 0.000001 0.046487 +2 0.281749 0.308869 0.000001 0.308869 0.308503 +3 0.027120 0.000001 0.308869 0.000001 0.046487 +4 0.026755 0.046487 0.308503 0.046487 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001183_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001183_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6441733382e596f74440a89ca44faf614f6d78b6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001183_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.097496 0.518337 0.085931 0.041601 +1 0.097496 0.000001 0.576106 0.020529 0.055895 +2 0.518337 0.576106 0.000001 0.564540 0.520211 +3 0.085931 0.020529 0.564540 0.000001 0.044330 +4 0.041601 0.055895 0.520211 0.044330 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..59e00cf8c5d1bf11ecb49c1f0496d90a321c6f86 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001185_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29579382 Before NNI: tree length is 0.29579375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..15ae120145d98597a58383e9dc0d121f60298d2d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001189_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.094287 0.291719 0.092494 0.092494 +1 0.094287 0.000001 0.308918 0.009697 0.009697 +2 0.291719 0.308918 0.000001 0.307126 0.307126 +3 0.092494 0.009697 0.307126 0.000001 0.000001 +4 0.092494 0.009697 0.307126 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8704355c18fa66aacb4cf1c2f4a6b086b1f7fb0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17797550 Before NNI: tree length is 0.17797550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001192_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..273d3e8feda4b5c0cf4c4eee8aef0a6ff8d30792 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.050679 0.128119 0.050679 0.050679 +1 0.050679 0.000001 0.111589 0.000001 0.000001 +2 0.128119 0.111589 0.000001 0.111589 0.111589 +3 0.050679 0.000001 0.111589 0.000001 0.000001 +4 0.050679 0.000001 0.111589 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1cdef78fcf28e1e86c0e37ac00e462847acd3c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.170292 0.164371 0.170292 0.170292 +1 0.170292 0.000001 0.165059 0.000001 0.006431 +2 0.164371 0.165059 0.000001 0.165059 0.165059 +3 0.170292 0.000001 0.165059 0.000001 0.006431 +4 0.170292 0.006431 0.165059 0.006431 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..942893e37e91b3fde744c1b93c00d6d0235b8c7f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001193_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25307700 Before NNI: tree length is 0.25307700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85a8f8672263398fd94829361935372a19086333 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60404250 Before NNI: tree length is 0.60404250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..56f27ea2660cf8d416d89037ef011c869dca1d42 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65416975 Before NNI: tree length is 0.65416975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001197_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001197_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1e2f78f56d456024ba0bc61d5b6166c21b7d3257 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001197_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.119271 0.367724 0.115357 0.117448 +1 0.119271 0.000001 0.355104 0.013106 0.003039 +2 0.367724 0.355104 0.000001 0.351190 0.353282 +3 0.115357 0.013106 0.351190 0.000001 0.011283 +4 0.117448 0.003039 0.353282 0.011283 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..56494e45ad3f75a1c8bd03dc462d0b26997d82b0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001200_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20481100 Before NNI: tree length is 0.20481100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001203_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001203_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..07d7c44cf5aab47c2db37ff7251d2089f446059f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001203_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.101834 0.218101 0.101834 0.101834 +1 0.101834 0.000001 0.245240 0.000001 0.000001 +2 0.218101 0.245240 0.000001 0.245240 0.245240 +3 0.101834 0.000001 0.245240 0.000001 0.000001 +4 0.101834 0.000001 0.245240 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001207_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001207_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9aa2a648a4466470acee3c7f792c1407a5083d3e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001207_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36791270 Before NNI: tree length is 0.36791275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001208_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001208_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42d0b488b9cdc718bbb720f3f0eec40c4083d1d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001208_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14283100 Before NNI: tree length is 0.14283100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001212_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fdce8d8acb91154eb517063eab163e72d275ec5 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45957050 Before NNI: tree length is 0.45957050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001213_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001213_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fc7f55d8f38fd33053d9bf752140275de9d73c27 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001213_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007151 0.040455 0.017381 0.017381 +1 0.007151 0.000001 0.044401 0.015499 0.015499 +2 0.040455 0.044401 0.000001 0.054631 0.054631 +3 0.017381 0.015499 0.054631 0.000001 0.000001 +4 0.017381 0.015499 0.054631 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001216_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001216_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..974c144a2d46793efb767914ff4fcce6f10f5aa3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001216_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07044150 Before NNI: tree length is 0.07044150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001217_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001217_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e30e0ec4e965a6c51a8030ce4b6106f38c784740 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001217_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41141450 Before NNI: tree length is 0.41141450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..925c1e3ba9ecfd630953abe3f1c57313a71e6c49 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.130557 0.381823 0.130557 0.135248 +1 0.130557 0.000001 0.358025 0.000001 0.010783 +2 0.381823 0.358025 0.000001 0.358025 0.362715 +3 0.130557 0.000001 0.358025 0.000001 0.010783 +4 0.135248 0.010783 0.362715 0.010783 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001219_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001219_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f82ad44176a1f1950df17f0414ee75becc018426 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001219_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.152110 0.287667 0.152594 0.158437 +1 0.152110 0.000001 0.249861 0.000484 0.006328 +2 0.287667 0.249861 0.000001 0.250345 0.256189 +3 0.152594 0.000484 0.250345 0.000001 0.005843 +4 0.158437 0.006328 0.256189 0.005843 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2fde1fadfefb8a03572787b1aa77f8cde2da0464 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.75027250 Before NNI: tree length is 0.75027250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..418caaa1742e7ee9520b9e7d37e513585be1f89d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18776700 Before NNI: tree length is 0.18776700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a59fed2dac7e44929e1e4f07b51bb61473c8f32 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001222_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.084243 0.124740 0.084243 0.082200 +1 0.084243 0.000001 0.134092 0.000001 0.002067 +2 0.124740 0.134092 0.000001 0.134092 0.132049 +3 0.084243 0.000001 0.134092 0.000001 0.002067 +4 0.082200 0.002067 0.132049 0.002067 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001226_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001226_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..968b419c462477f86adb8444a0339bda12f4b100 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001226_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24826100 Before NNI: tree length is 0.24826100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001227_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001227_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e77b7fa2317f734c36828fb61e1d41fad5528c2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001227_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72124927 Before NNI: tree length is 0.72124925 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001231_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001231_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4ae167574488086e7043317f17b9d79c82c0fca6 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033698 0.041019 0.033698 0.033698 +1 0.033698 0.000001 0.039838 0.000001 0.000001 +2 0.041019 0.039838 0.000001 0.039838 0.039838 +3 0.033698 0.000001 0.039838 0.000001 0.000001 +4 0.033698 0.000001 0.039838 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d1ea4407679235b9ca702418a89e13a6ec5f408c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001233_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.099334 0.261320 0.087002 0.088345 +1 0.099334 0.000001 0.268883 0.021235 0.010990 +2 0.261320 0.268883 0.000001 0.256551 0.257893 +3 0.087002 0.021235 0.256551 0.000001 0.010246 +4 0.088345 0.010990 0.257893 0.010246 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e5713385583376730a3d56baeb8639c9bdd7c3c2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001235_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20447311 Before NNI: tree length is 0.20447312 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001236_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001236_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f78f9565a360a8ae08f712447b6a2c350b00a068 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001236_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043577 0.214134 0.043855 0.043855 +1 0.043577 0.000001 0.198850 0.024748 0.024748 +2 0.214134 0.198850 0.000001 0.199128 0.199128 +3 0.043855 0.024748 0.199128 0.000001 0.000001 +4 0.043855 0.024748 0.199128 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001238_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001238_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..529557103444565176117dc46cdd0e0d89c3305b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001238_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036959 0.115608 0.036939 0.037532 +1 0.036959 0.000001 0.112363 0.004924 0.005517 +2 0.115608 0.112363 0.000001 0.112343 0.112936 +3 0.036939 0.004924 0.112343 0.000001 0.001770 +4 0.037532 0.005517 0.112936 0.001770 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32bd28239c549374e503092fec767bddb8db97b0 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08940100 Before NNI: tree length is 0.08940100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..10cb8cf3b076a06b70faad5fdecb4d1b3ea6a92d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001244_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.73865630 Before NNI: tree length is 0.73865625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001246_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f62622c6f1ac7cb9e4d140898017175a58d9a37 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04900000 Before NNI: tree length is 0.04900000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ef9aff630a9d069973c5e5babf11ad92f1ac7a98 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.209801 0.372750 0.225432 0.220885 +1 0.209801 0.000001 0.404657 0.026664 0.035871 +2 0.372750 0.404657 0.000001 0.420288 0.415740 +3 0.225432 0.026664 0.420288 0.000001 0.051502 +4 0.220885 0.035871 0.415740 0.051502 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001249_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001249_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..17f931612f4b83bb5b74bc86f9333b2d59cadbc5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001249_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31963119 Before NNI: tree length is 0.31963125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001250_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d594601b39e8459deaa45680e1fb0881ae6c3412 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25299350 Before NNI: tree length is 0.25299350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ac7ce5a5469d3297f26b87a205e5f48f86541b98 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001256_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.095388 0.123750 0.096074 0.095120 +1 0.095388 0.000001 0.125794 0.008807 0.007853 +2 0.123750 0.125794 0.000001 0.126479 0.125525 +3 0.096074 0.008807 0.126479 0.000001 0.005200 +4 0.095120 0.007853 0.125525 0.005200 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001260_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c7dde70642460e5a4a61893c6ae47ca4893a0dd2 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060954 0.280614 0.066168 0.066168 +1 0.060954 0.000001 0.287751 0.027341 0.027341 +2 0.280614 0.287751 0.000001 0.292965 0.292965 +3 0.066168 0.027341 0.292965 0.000001 0.000001 +4 0.066168 0.027341 0.292965 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92f01f1bcd0ec2bab8d12cc29f348ddd3b5f1bd9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001261_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14044225 Before NNI: tree length is 0.14044225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9632fffb5c8d48fd4f9bf12c0a4b35cdc8ddb6b4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.054390 0.242538 0.050601 0.050601 +1 0.054390 0.000001 0.239427 0.006098 0.006098 +2 0.242538 0.239427 0.000001 0.235639 0.235639 +3 0.050601 0.006098 0.235639 0.000001 0.000001 +4 0.050601 0.006098 0.235639 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..da156084b6ed3fdc3997105d177b53b40c18f27d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.07688576 Before NNI: tree length is 1.07688575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001268_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001268_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f488ed358f2311b835e866ef2ec9a61170a24e9a --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.113309 0.090516 0.113309 0.113309 +1 0.113309 0.000001 0.078793 0.000001 0.000001 +2 0.090516 0.078793 0.000001 0.078793 0.078793 +3 0.113309 0.000001 0.078793 0.000001 0.000001 +4 0.113309 0.000001 0.078793 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9b6bbe51b888dbe546d34aa0f218ad88eb04f1f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001269_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09383300 Before NNI: tree length is 0.09383300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001270_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001270_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c4ddf5a5b2fe2db7bbc1381469a08aead2319675 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001270_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.148136 0.233790 0.151713 0.151713 +1 0.148136 0.000001 0.238494 0.003577 0.003577 +2 0.233790 0.238494 0.000001 0.242071 0.242071 +3 0.151713 0.003577 0.242071 0.000001 0.000001 +4 0.151713 0.003577 0.242071 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f76e87b903897a8000cc3364b82a884458eefd09 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.222951 0.295924 0.221356 0.228470 +1 0.222951 0.000001 0.336070 0.013506 0.020619 +2 0.295924 0.336070 0.000001 0.334475 0.341588 +3 0.221356 0.013506 0.334475 0.000001 0.007114 +4 0.228470 0.020619 0.341588 0.007114 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001282_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6df511d68bab5fdc97ddbb798b5cc7d0738049f3 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.156096 0.275921 0.147451 0.151022 +1 0.156096 0.000001 0.307945 0.031656 0.035228 +2 0.275921 0.307945 0.000001 0.299300 0.302872 +3 0.147451 0.031656 0.299300 0.000001 0.012138 +4 0.151022 0.035228 0.302872 0.012138 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7b050b4a78ff52bb8a48ebe08702b9769fc81cf --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.200154 0.409997 0.198046 0.192556 +1 0.200154 0.000001 0.394172 0.004469 0.021926 +2 0.409997 0.394172 0.000001 0.392063 0.386573 +3 0.198046 0.004469 0.392063 0.000001 0.019818 +4 0.192556 0.021926 0.386573 0.019818 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f8ef324dd5c3b32a681695ea74a3e5641fca6089 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.200201 0.265668 0.205308 0.198440 +1 0.200201 0.000001 0.176820 0.013673 0.008519 +2 0.265668 0.176820 0.000001 0.181927 0.175059 +3 0.205308 0.013673 0.181927 0.000001 0.013626 +4 0.198440 0.008519 0.175059 0.013626 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d1bf70d6975b8545bb86029584fe268005d3295 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33411350 Before NNI: tree length is 0.33411350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..92556ea96166ad85c0e98a42e7da23ea60099e87 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025506 0.038268 0.029533 0.018031 +1 0.025506 0.000001 0.036687 0.004889 0.009884 +2 0.038268 0.036687 0.000001 0.040713 0.029212 +3 0.029533 0.004889 0.040713 0.000001 0.013910 +4 0.018031 0.009884 0.029212 0.013910 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3a84f88c9fb370b66ec8284780b029105634f8c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001290_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057987 0.033063 0.011816 0.033922 +1 0.057987 0.000001 0.030133 0.060217 0.028766 +2 0.033063 0.030133 0.000001 0.035292 0.006067 +3 0.011816 0.060217 0.035292 0.000001 0.036152 +4 0.033922 0.028766 0.006067 0.036152 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b6952c255c9b6d5d950e8458ce67ef2d423c38f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001291_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.055527 0.038442 0.054896 0.052878 +1 0.055527 0.000001 0.054862 0.059074 0.002649 +2 0.038442 0.054862 0.000001 0.054231 0.052213 +3 0.054896 0.059074 0.054231 0.000001 0.056425 +4 0.052878 0.002649 0.052213 0.056425 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001292_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001292_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2339e31355329420f3c16cc798451e29a24e616b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001292_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03465904 Before NNI: tree length is 0.03465900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001293_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001293_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c56977c9573fe606fa52102c553b730998eb01df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001293_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13083825 Before NNI: tree length is 0.13083825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e03b23b5dd363b217d06162c12c1dfa649d272d --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.53053800 Before NNI: tree length is 0.53053800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f7bbed206e4e083bfb5db985b22210cc01d95f1b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.405260 0.540664 0.405260 0.384328 +1 0.405260 0.000001 0.519572 0.000001 0.050262 +2 0.540664 0.519572 0.000001 0.519572 0.498640 +3 0.405260 0.000001 0.519572 0.000001 0.050262 +4 0.384328 0.050262 0.498640 0.050262 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1c4c7b4be326e895815de2bc110e6fe54de03de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001304_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.74741350 Before NNI: tree length is 0.74741350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0d2838a31257d6269b1e8a462626e843b7e9aaaf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.112619 0.159468 0.112619 0.107841 +1 0.112619 0.000001 0.157249 0.000001 0.014815 +2 0.159468 0.157249 0.000001 0.157249 0.152472 +3 0.112619 0.000001 0.157249 0.000001 0.014815 +4 0.107841 0.014815 0.152472 0.014815 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3edf55e7542d04a17056fa8e7c364d5be4fcbe3f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001305_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21968723 Before NNI: tree length is 0.21968725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f428b6aa8aecadec05de7732e6cab1cc4a5c0dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33009450 Before NNI: tree length is 0.33009450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001317_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001317_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..939b473ea865d53737f4002a17f7b6eec7ac0924 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001317_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029570 0.113239 0.029745 0.030822 +1 0.029570 0.000001 0.111094 0.006393 0.007470 +2 0.113239 0.111094 0.000001 0.111269 0.112346 +3 0.029745 0.006393 0.111269 0.000001 0.006157 +4 0.030822 0.007470 0.112346 0.006157 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001321_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001321_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ffbfa103e50a3710ff2af00edec3166708772fb1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001321_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.01760588 Before NNI: tree length is 0.01760587 + 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/OG0001327_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dd36278eb34e94de850efc03b9157e27a40fca91 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.149554 0.150842 0.149626 0.146320 +1 0.149554 0.000001 0.008106 0.003357 0.005791 +2 0.150842 0.008106 0.000001 0.008179 0.007079 +3 0.149626 0.003357 0.008179 0.000001 0.005864 +4 0.146320 0.005791 0.007079 0.005864 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9131db38418c1d96eafb1683e9ded352135abf3c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15724437 Before NNI: tree length is 0.15724437 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55d65ada016179d0abbc25ee9b408f4c555af3d4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.308293 0.319442 0.308293 0.308293 +1 0.308293 0.000001 0.040355 0.000001 0.000001 +2 0.319442 0.040355 0.000001 0.040355 0.040355 +3 0.308293 0.000001 0.040355 0.000001 0.000001 +4 0.308293 0.000001 0.040355 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..948600393357412b3d33aebe200f5417206cc3d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.236556 0.433871 0.246857 0.241651 +1 0.236556 0.000001 0.402335 0.040023 0.005095 +2 0.433871 0.402335 0.000001 0.412636 0.407429 +3 0.246857 0.040023 0.412636 0.000001 0.045118 +4 0.241651 0.005095 0.407429 0.045118 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c03b7ab9419a7c5e4af19f6e288fe96b7aa5c458 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56663786 Before NNI: tree length is 0.56663787 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..26bf6894411170ddcc99f72230690521e08d29e2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.154471 0.287203 0.158153 0.159361 +1 0.154471 0.000001 0.300467 0.015790 0.016998 +2 0.287203 0.300467 0.000001 0.304149 0.305357 +3 0.158153 0.015790 0.304149 0.000001 0.017082 +4 0.159361 0.016998 0.305357 0.017082 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f19f9aa141ad6ea84587be57def06fd9c3dddd8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001337_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38995150 Before NNI: tree length is 0.38995150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1b8b9dfc98b9b7c2d0fc5722fca2fb77e98acad --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10089310 Before NNI: tree length is 0.10089313 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..46264ccba21e13aff681b0dd451e16cc32d29f6d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.093076 0.242650 0.085854 0.096082 +1 0.093076 0.000001 0.250082 0.008945 0.013023 +2 0.242650 0.250082 0.000001 0.242861 0.253088 +3 0.085854 0.008945 0.242861 0.000001 0.011950 +4 0.096082 0.013023 0.253088 0.011950 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b703c6b22c0a7d3b9faa49eb1f1bde39dd3a6a4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001343_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30177995 Before NNI: tree length is 0.30178000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001344_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001344_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5a4b7a4920bf2bdb816d11f38fb1ef0429f8c93f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001344_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.105082 0.146659 0.109354 0.106416 +1 0.105082 0.000001 0.073385 0.008585 0.010766 +2 0.146659 0.073385 0.000001 0.077657 0.074720 +3 0.109354 0.008585 0.077657 0.000001 0.015037 +4 0.106416 0.010766 0.074720 0.015037 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cee1efa17b775667594a9cf9d136730099b4b2b6 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14977175 Before NNI: tree length is 0.14977175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c2bb4cefcbd35c09016dbd44253772f9b5a07b5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.455726 0.780620 0.471246 0.460839 +1 0.455726 0.000001 0.336840 0.027465 0.035005 +2 0.780620 0.336840 0.000001 0.340168 0.359899 +3 0.471246 0.027465 0.340168 0.000001 0.050524 +4 0.460839 0.035005 0.359899 0.050524 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..512a5de7aa5567b4894e9c29fd5106389420393f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65170373 Before NNI: tree length is 0.65170375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..557d423f3dabb313007737d163a3ff47c5c30404 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.081571 0.145449 0.077952 0.077952 +1 0.081571 0.000001 0.137194 0.005222 0.005222 +2 0.145449 0.137194 0.000001 0.133575 0.133575 +3 0.077952 0.005222 0.133575 0.000001 0.000001 +4 0.077952 0.005222 0.133575 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..705f0a847ef86d38743acbee83c3428705772874 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18290900 Before NNI: tree length is 0.18290900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0360fb6aa684afeb0b1e32b7839e6a7a1b0b998 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001361_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.43430075 Before NNI: tree length is 0.43430075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001364_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001364_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..668e34d217516994139bb379bb8d313b7b0951f5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001364_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36401830 Before NNI: tree length is 0.36401825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001368_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001368_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d3fb0f306cab3d8c0b29b4672056cf1280a119d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001368_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22901475 Before NNI: tree length is 0.22901475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001369_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001369_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ae64d7801685320a16b6769a44db22cd028a8bee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001369_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023371 0.023274 0.036712 0.023275 +1 0.023371 0.000001 0.033782 0.013341 0.000096 +2 0.023274 0.033782 0.000001 0.047123 0.033686 +3 0.036712 0.013341 0.047123 0.000001 0.013437 +4 0.023275 0.000096 0.033686 0.013437 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42e33504c09021169d1f354c7dbc276512a1df5f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17407940 Before NNI: tree length is 0.17407937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..242be414d9632a50d1388dbb4895b5730a258209 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.347737 0.497069 0.358444 0.351747 +1 0.347737 0.000001 0.429313 0.029554 0.022856 +2 0.497069 0.429313 0.000001 0.440020 0.433323 +3 0.358444 0.029554 0.440020 0.000001 0.019515 +4 0.351747 0.022856 0.433323 0.019515 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d9bacd8e972c7935cc2756ca7ecc21ecd3f3d3da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.171235 0.333287 0.171201 0.171235 +1 0.171235 0.000001 0.351826 0.010291 0.000001 +2 0.333287 0.351826 0.000001 0.351792 0.351826 +3 0.171201 0.010291 0.351792 0.000001 0.010291 +4 0.171235 0.000001 0.351826 0.010291 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001375_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001375_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bdb686ce4c2c4e9d4f981196e3499050bb42e60a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001375_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.42214000 Before NNI: tree length is 0.42214000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8900576d3b97d523c953d6609822772f9d0e6d79 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.266975 0.481195 0.274470 0.275772 +1 0.266975 0.000001 0.412497 0.022248 0.023549 +2 0.481195 0.412497 0.000001 0.419991 0.421293 +3 0.274470 0.022248 0.419991 0.000001 0.017632 +4 0.275772 0.023549 0.421293 0.017632 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8081686e16c84e7aad34fb2a9045aeba5e88e906 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001379_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60467147 Before NNI: tree length is 0.60467150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001380_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001380_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7b4cd11283e15ef64858126c2853f7d172a6e41 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001380_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.058795 0.083476 0.059009 0.058991 +1 0.058795 0.000001 0.056520 0.014098 0.014081 +2 0.083476 0.056520 0.000001 0.056734 0.056717 +3 0.059009 0.014098 0.056734 0.000001 0.008677 +4 0.058991 0.014081 0.056717 0.008677 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..546e2f8758cb448b37cd0107f956d8757b0978b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001381_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.104711 0.192684 0.106909 0.104711 +1 0.104711 0.000001 0.229356 0.004983 0.000001 +2 0.192684 0.229356 0.000001 0.231554 0.229356 +3 0.106909 0.004983 0.231554 0.000001 0.004983 +4 0.104711 0.000001 0.229356 0.004983 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3f8848d98dd25c8efbd88ee6fda0463208a76a69 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.145012 0.378686 0.161151 0.155801 +1 0.145012 0.000001 0.385388 0.032236 0.026886 +2 0.378686 0.385388 0.000001 0.401527 0.396177 +3 0.161151 0.032236 0.401527 0.000001 0.016108 +4 0.155801 0.026886 0.396177 0.016108 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001385_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001385_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9baebad00b4f22bc8d8768f4c8c0079f42188de3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001385_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.053044 0.114624 0.046034 0.046139 +1 0.053044 0.000001 0.127662 0.011694 0.011798 +2 0.114624 0.127662 0.000001 0.120651 0.120756 +3 0.046034 0.011694 0.120651 0.000001 0.002051 +4 0.046139 0.011798 0.120756 0.002051 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4812c5a0884d3b3f0c30896f1179e862b94dba44 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061687 0.266377 0.148599 0.148859 +1 0.061687 0.000001 0.243631 0.125854 0.126113 +2 0.266377 0.243631 0.000001 0.246260 0.246520 +3 0.148599 0.125854 0.246260 0.000001 0.009829 +4 0.148859 0.126113 0.246520 0.009829 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e81afbb059a6b25330e5e8c8a4bc0d2db2235e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35112059 Before NNI: tree length is 0.35112062 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3f504900bb97a761cea37f94798d55db5205588b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001395_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31539954 Before NNI: tree length is 0.31539950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001396_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001396_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..92ee1b1c198dbe1493eca1648a69ec4963b6d9b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001396_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22318600 Before NNI: tree length is 0.22318600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e539071e6b864fdf25d54571b55a070f141e8358 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001398_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.063740 0.281260 0.063238 0.070585 +1 0.063740 0.000001 0.288641 0.000502 0.006845 +2 0.281260 0.288641 0.000001 0.288139 0.295486 +3 0.063238 0.000502 0.288139 0.000001 0.007347 +4 0.070585 0.006845 0.295486 0.007347 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001400_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3880be88d34e5ed7e5c5de7b397754f2e1e0ad08 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29034185 Before NNI: tree length is 0.29034188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..66ff787552c468d70b28dd3cad57804d14fa9549 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001401_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.105821 0.333064 0.102987 0.107309 +1 0.105821 0.000001 0.315907 0.028740 0.018402 +2 0.333064 0.315907 0.000001 0.313073 0.317394 +3 0.102987 0.028740 0.313073 0.000001 0.030227 +4 0.107309 0.018402 0.317394 0.030227 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001405_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001405_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8e0ab945325534e2c96673e63f449203ce008d35 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001405_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.061295 0.483680 0.058961 0.063237 +1 0.061295 0.000001 0.518192 0.014500 0.005727 +2 0.483680 0.518192 0.000001 0.515857 0.520134 +3 0.058961 0.014500 0.515857 0.000001 0.016442 +4 0.063237 0.005727 0.520134 0.016442 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..94734c5e48f94b736b74823831916ca726dc1e88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001406_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.142979 0.388054 0.138119 0.130430 +1 0.142979 0.000001 0.368993 0.007994 0.015318 +2 0.388054 0.368993 0.000001 0.364134 0.356445 +3 0.138119 0.007994 0.364134 0.000001 0.010459 +4 0.130430 0.015318 0.356445 0.010459 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b1824da51134a8cd8cf9df81edc0c8ca623286be --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.088445 0.143409 0.090837 0.090837 +1 0.088445 0.000001 0.130405 0.012529 0.012529 +2 0.143409 0.130405 0.000001 0.132798 0.132798 +3 0.090837 0.012529 0.132798 0.000001 0.000001 +4 0.090837 0.012529 0.132798 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1aa3b9e02f77edf42c28c5daac8c41fde97d362f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001421_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.068337 0.079305 0.065101 0.065101 +1 0.068337 0.000001 0.045042 0.008208 0.008208 +2 0.079305 0.045042 0.000001 0.041807 0.041807 +3 0.065101 0.008208 0.041807 0.000001 0.000001 +4 0.065101 0.008208 0.041807 0.000001 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001427_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..83626558b2ab31e288149c77768c8a0b9e96602b --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033526 0.156145 0.034978 0.030880 +1 0.033526 0.000001 0.149209 0.011535 0.007437 +2 0.156145 0.149209 0.000001 0.150661 0.146563 +3 0.034978 0.011535 0.150661 0.000001 0.005237 +4 0.030880 0.007437 0.146563 0.005237 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001435_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa158af6be7a6b34fbb604ad2f684c488f36adaf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47741050 Before NNI: tree length is 0.47741050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001436_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001436_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd1c3fe8b79d101fee1d8ac5d84952a781a6710b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001436_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.70036752 Before NNI: tree length is 0.70036750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d209380336cdd4412958a112ea6abea4f82fa7a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001441_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31446950 Before NNI: tree length is 0.31446950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d5c76e8aea8cca85d9638ab9f864bcd00e0b664b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20951700 Before NNI: tree length is 0.20951700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001445_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001445_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..51b7ba18c23e63d5792c66efeb239d4115d662a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001445_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47098800 Before NNI: tree length is 0.47098800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..27e0702d7546352283c6a54010c7ef1bf6816bfd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.118992 0.210836 0.118992 0.134042 +1 0.118992 0.000001 0.285759 0.000001 0.027975 +2 0.210836 0.285759 0.000001 0.285759 0.300809 +3 0.118992 0.000001 0.285759 0.000001 0.027975 +4 0.134042 0.027975 0.300809 0.027975 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8416b8516bb029149c92398ad39da76124e5a042 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.314234 0.505173 0.307405 0.300964 +1 0.314234 0.000001 0.449524 0.052295 0.045853 +2 0.505173 0.449524 0.000001 0.442696 0.436255 +3 0.307405 0.052295 0.442696 0.000001 0.018965 +4 0.300964 0.045853 0.436255 0.018965 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001449_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001449_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c07402073d19f436657c1c2715597a84bab5716e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001449_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.160984 0.147338 0.155720 0.161810 +1 0.160984 0.000001 0.158141 0.024498 0.030588 +2 0.147338 0.158141 0.000001 0.152877 0.158966 +3 0.155720 0.024498 0.152877 0.000001 0.017915 +4 0.161810 0.030588 0.158966 0.017915 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001451_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fc354cca7fec5fb35a837e713e4b7e072e8672f9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.297333 0.459186 0.331861 0.330179 +1 0.297333 0.000001 0.490315 0.090646 0.088963 +2 0.459186 0.490315 0.000001 0.524844 0.523162 +3 0.331861 0.090646 0.524844 0.000001 0.025497 +4 0.330179 0.088963 0.523162 0.025497 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001452_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001452_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ea2205324a5f056443ae6044dc5155cf16d116a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001452_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31189650 Before NNI: tree length is 0.31189650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001455_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001455_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a256e2eca91f80e64627dc598bce2136ce64f8ec --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.394026 1.164256 0.429551 0.416322 +1 0.394026 0.000001 1.132317 0.051877 0.038649 +2 1.164256 1.132317 0.000001 1.167842 1.154614 +3 0.429551 0.051877 1.167842 0.000001 0.031359 +4 0.416322 0.038649 1.154614 0.031359 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac88c7c6a4aed047960df63ceb8e0d5702864a3a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001456_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14699050 Before NNI: tree length is 0.14699050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f33d52be3d72a23fc9f52b0a762524d6860b4878 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06735100 Before NNI: tree length is 0.06735100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e3076c0966e8bde6bf456085b8d8e8c0ed4e0d73 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040275 0.072523 0.040275 0.043266 +1 0.040275 0.000001 0.089448 0.000001 0.003604 +2 0.072523 0.089448 0.000001 0.089448 0.092439 +3 0.040275 0.000001 0.089448 0.000001 0.003604 +4 0.043266 0.003604 0.092439 0.003604 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001462_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001462_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..43d15c48a1f1f9f66792d7483f05fd4579d325bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001462_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.049126 0.000001 0.000001 +1 0.000001 0.000001 0.049126 0.000001 0.000001 +2 0.049126 0.049126 0.000001 0.049126 0.049126 +3 0.000001 0.000001 0.049126 0.000001 0.000001 +4 0.000001 0.000001 0.049126 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a118e8e0546913d93a5c0c76b5fbfc128db75c5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001465_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45758150 Before NNI: tree length is 0.45758150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb01fd50721cb845d68fb8579f3999be21659f7a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.63528650 Before NNI: tree length is 0.63528650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9df09cd325b145d295d52556a6b17fbe5fa467db --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.183114 0.351184 0.210975 0.202255 +1 0.183114 0.000001 0.311830 0.094991 0.086271 +2 0.351184 0.311830 0.000001 0.339691 0.330971 +3 0.210975 0.094991 0.339691 0.000001 0.046988 +4 0.202255 0.086271 0.330971 0.046988 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..98103046a52e26f33d18567955d2d8216558f624 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.26577275 Before NNI: tree length is 0.26577275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f1d53a54d551c2d24e8947c53656d4f63e7fc62b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016930 0.146967 0.015889 0.021823 +1 0.016930 0.000001 0.150986 0.004757 0.006904 +2 0.146967 0.150986 0.000001 0.149946 0.155880 +3 0.015889 0.004757 0.149946 0.000001 0.009651 +4 0.021823 0.006904 0.155880 0.009651 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001474_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001474_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6ba113658fafb33f88559b6f6edc816dda1d80e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001474_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31155232 Before NNI: tree length is 0.31155225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001479_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001479_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d7a4e566ec98a4442771f7422cd0a8f733fcba0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001479_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.090658 0.330491 0.086197 0.088296 +1 0.090658 0.000001 0.323140 0.007240 0.002363 +2 0.330491 0.323140 0.000001 0.318679 0.320778 +3 0.086197 0.007240 0.318679 0.000001 0.004877 +4 0.088296 0.002363 0.320778 0.004877 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8747579c9ad735b3d15bcfa181acc28d2166535 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001486_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.65257638 Before NNI: tree length is 0.65257637 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001492_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..28521b5c69281b432413eb5b2791b24a98cd62f2 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33171266 Before NNI: tree length is 0.33171262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c03ab7776f2769dfe98fe337813eb0e46fdb63b0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001495_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.234438 0.420854 0.269376 0.259728 +1 0.234438 0.000001 0.400765 0.074539 0.064890 +2 0.420854 0.400765 0.000001 0.435704 0.426055 +3 0.269376 0.074539 0.435704 0.000001 0.010753 +4 0.259728 0.064890 0.426055 0.010753 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001496_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001496_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4766ddb0a739d491de7db0107c83cede0d7c6eff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001496_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.30627825 Before NNI: tree length is 0.30627825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001498_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..406ec1b5dddac0cb29413ca73020f1d2376f1b41 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22182000 Before NNI: tree length is 0.22182000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b46feb200d09dd029eb0639aee11eb527ad8a17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001501_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07126509 Before NNI: tree length is 0.07126512 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8b5c63bc94e2e2bb494c57fa95b0cf430042f5da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041675 0.063780 0.039092 0.041675 +1 0.041675 0.000001 0.069458 0.002583 0.000001 +2 0.063780 0.069458 0.000001 0.066875 0.069458 +3 0.039092 0.002583 0.066875 0.000001 0.002583 +4 0.041675 0.000001 0.069458 0.002583 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4aa2a48295d9bc780183451365e95eb58bf5192a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.315899 0.773270 0.319687 0.292700 +1 0.315899 0.000001 0.815738 0.007273 0.040749 +2 0.773270 0.815738 0.000001 0.819525 0.792539 +3 0.319687 0.007273 0.819525 0.000001 0.044536 +4 0.292700 0.040749 0.792539 0.044536 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c74f0a0407c0cd4fa422da55fa2f88d7f9ff120d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.96675860 Before NNI: tree length is 0.96675863 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2fa739752040f40c3d779663553d1f79896d355f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001511_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48577800 Before NNI: tree length is 0.48577800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001512_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a1bbc139aecc8de4e2ff38e250b3051364cbeaa --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28106710 Before NNI: tree length is 0.28106713 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001514_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001514_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d2d5922aac9d4bc7b1369858b1e8a9673ad21e08 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001514_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.345937 0.453621 0.341674 0.339473 +1 0.345937 0.000001 0.374579 0.019524 0.010390 +2 0.453621 0.374579 0.000001 0.370316 0.368115 +3 0.341674 0.019524 0.370316 0.000001 0.013060 +4 0.339473 0.010390 0.368115 0.013060 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..284aabc95b40c29896612c4b0da99fc1233e5a2c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.196289 0.323691 0.194214 0.196289 +1 0.196289 0.000001 0.320924 0.012500 0.000001 +2 0.323691 0.320924 0.000001 0.318850 0.320924 +3 0.194214 0.012500 0.318850 0.000001 0.012500 +4 0.196289 0.000001 0.320924 0.012500 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001516_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001516_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..75298dbe90f59e49c2ab3b6d4ea3bf14e54306af --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001516_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.48032350 Before NNI: tree length is 0.48032350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be17508ea694dc5972ce09b5e906ac2750d4534d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.088177 0.114084 0.088177 0.088177 +1 0.088177 0.000001 0.118874 0.000001 0.000001 +2 0.114084 0.118874 0.000001 0.118874 0.118874 +3 0.088177 0.000001 0.118874 0.000001 0.000001 +4 0.088177 0.000001 0.118874 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85d50f3d1b41efe2f8e0945e65d82da3c5b46f53 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16056850 Before NNI: tree length is 0.16056850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0ab8cfb7b9ae3b2d15bd039ebff20a16f3aa047f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.227188 0.682079 0.227188 0.227188 +1 0.227188 0.000001 0.703158 0.000001 0.000001 +2 0.682079 0.703158 0.000001 0.703158 0.703158 +3 0.227188 0.000001 0.703158 0.000001 0.000001 +4 0.227188 0.000001 0.703158 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b0a09e596cafc5da6694a721359374d93059cd2b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001522_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15511550 Before NNI: tree length is 0.15511550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001524_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001524_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..53279953de833202f0f9c6ff6708aa27eac9b32e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001524_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18416069 Before NNI: tree length is 0.18416075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001525_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..22c53fc2e989a6e6fe49c795b491cb2b1a8e8850 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06317045 Before NNI: tree length is 0.06317050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..82a682111485ed74438e5e90e112933c71c36b41 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001529_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17045329 Before NNI: tree length is 0.17045325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001532_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001532_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..db89ebc56e880cc3dab16585d3e6b76ba16ddeee --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001532_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.261366 0.030211 0.267568 0.273637 +1 0.261366 0.000001 0.269195 0.021153 0.027223 +2 0.030211 0.269195 0.000001 0.275398 0.281467 +3 0.267568 0.021153 0.275398 0.000001 0.006069 +4 0.273637 0.027223 0.281467 0.006069 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55aafb75d0e87e8c6c0720c9421767660de68b49 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001534_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.217398 0.202984 0.219626 0.215485 +1 0.217398 0.000001 0.045784 0.045904 0.041763 +2 0.202984 0.045784 0.000001 0.048012 0.043871 +3 0.219626 0.045904 0.048012 0.000001 0.027876 +4 0.215485 0.041763 0.043871 0.027876 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..10f81f00208688bbf9d9ea48c8c2479003958bdb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001540_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.89158400 Before NNI: tree length is 0.89158400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001542_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b8a5d36887d0c4353abd4a8fe1730a9e4d57e1b7 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.340185 0.397960 0.303130 0.331573 +1 0.340185 0.000001 0.365509 0.075666 0.032831 +2 0.397960 0.365509 0.000001 0.328454 0.356897 +3 0.303130 0.075666 0.328454 0.000001 0.067054 +4 0.331573 0.032831 0.356897 0.067054 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001544_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001544_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e5592b626d211b664560f3802ae06063424942a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001544_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057042 0.204463 0.059393 0.061672 +1 0.057042 0.000001 0.190583 0.009069 0.011348 +2 0.204463 0.190583 0.000001 0.192934 0.195213 +3 0.059393 0.009069 0.192934 0.000001 0.008811 +4 0.061672 0.011348 0.195213 0.008811 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbf86c7145c1e06f0b2a3ebbb1de5bd48c73a924 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001545_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.85937150 Before NNI: tree length is 0.85937150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0696cc68416f44b1f4b89a9e984d19cecc044ea5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.152014 0.217404 0.152014 0.152014 +1 0.152014 0.000001 0.238857 0.000001 0.000001 +2 0.217404 0.238857 0.000001 0.238857 0.238857 +3 0.152014 0.000001 0.238857 0.000001 0.000001 +4 0.152014 0.000001 0.238857 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001549_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001549_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/OG0001549_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/OG0001550_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001550_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..621f76332f4b6a5d993091f8608c833e37013b50 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.391684 0.403792 0.385698 0.391684 +1 0.391684 0.000001 0.426566 0.011336 0.000001 +2 0.403792 0.426566 0.000001 0.420580 0.426566 +3 0.385698 0.011336 0.420580 0.000001 0.011336 +4 0.391684 0.000001 0.426566 0.011336 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..429248db3d8c3f8006e135f3e231fc4e42326d17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.221279 0.390720 0.221279 0.221279 +1 0.221279 0.000001 0.362110 0.000001 0.000001 +2 0.390720 0.362110 0.000001 0.362110 0.362110 +3 0.221279 0.000001 0.362110 0.000001 0.000001 +4 0.221279 0.000001 0.362110 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..69713f5254db64ee8c675a06c91d4c8e53e41816 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001560_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38353350 Before NNI: tree length is 0.38353350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001563_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a7bc1f87b29180b7b2767818199dc310034c2c4 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08410504 Before NNI: tree length is 0.08410500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1616d9e68fd8df2d5fe5594302db03c276a7524a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.164831 0.282490 0.113754 0.106538 +1 0.164831 0.000001 0.276445 0.063613 0.058293 +2 0.282490 0.276445 0.000001 0.225368 0.218152 +3 0.113754 0.063613 0.225368 0.000001 0.007216 +4 0.106538 0.058293 0.218152 0.007216 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001570_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001570_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2f37b87e8dbd91dc2df26343d34a67bc7c794a39 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001570_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.158134 0.487601 0.160747 0.153572 +1 0.158134 0.000001 0.468545 0.006375 0.050655 +2 0.487601 0.468545 0.000001 0.471158 0.463983 +3 0.160747 0.006375 0.471158 0.000001 0.053268 +4 0.153572 0.050655 0.463983 0.053268 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ebfa2668903bdd37ab647c4aa1d13aca580c2a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60404969 Before NNI: tree length is 0.60404975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..96dd53de7630960f794284f08c7c3af6da339ea7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029585 0.083874 0.035367 0.029585 +1 0.029585 0.000001 0.075215 0.014270 0.000001 +2 0.083874 0.075215 0.000001 0.080997 0.075215 +3 0.035367 0.014270 0.080997 0.000001 0.014270 +4 0.029585 0.000001 0.075215 0.014270 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb3185e481e66729b10c2d65a94d4c85fedd0e58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001577_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10436350 Before NNI: tree length is 0.10436350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aac5ad7c23db88a0ea378465baa41e3a59bf1d82 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29501525 Before NNI: tree length is 0.29501525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001581_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001581_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..03980025066d22a6f9254b4871252a2d00e29eb9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001581_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.083295 0.303607 0.086029 0.072257 +1 0.083295 0.000001 0.282614 0.002734 0.037868 +2 0.303607 0.282614 0.000001 0.285348 0.271576 +3 0.086029 0.002734 0.285348 0.000001 0.040602 +4 0.072257 0.037868 0.271576 0.040602 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001586_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1da978745587c39e62c6ffbc45d5c3dc6bcec911 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.23522000 Before NNI: tree length is 1.23522000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001587_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..467f050c098c93f00d611b04d381dcc1e6a98894 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.069308 0.148920 0.069780 0.075127 +1 0.069308 0.000001 0.153810 0.007260 0.012607 +2 0.148920 0.153810 0.000001 0.154282 0.159629 +3 0.069780 0.007260 0.154282 0.000001 0.009191 +4 0.075127 0.012607 0.159629 0.009191 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1bdf01fe69093e368800287e1db835fa917b4aca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.222913 0.249068 0.224737 0.227586 +1 0.222913 0.000001 0.233587 0.046784 0.043252 +2 0.249068 0.233587 0.000001 0.235410 0.238260 +3 0.224737 0.046784 0.235410 0.000001 0.051457 +4 0.227586 0.043252 0.238260 0.051457 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1092af3a42e3ba20f00fadbc639783476130ae1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001592_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.21264538 Before NNI: tree length is 1.21264538 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de9a87f548ead571f3ae683931f2ddb68a416946 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.052754 0.088454 0.048306 0.049779 +1 0.052754 0.000001 0.104678 0.016630 0.006353 +2 0.088454 0.104678 0.000001 0.100230 0.101703 +3 0.048306 0.016630 0.100230 0.000001 0.013656 +4 0.049779 0.006353 0.101703 0.013656 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e964f0cb8b9feee855c0dd27a00cfd13a8f6cc3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45213675 Before NNI: tree length is 0.45213675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001600_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001600_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..48f2474aec656c711009f1a701ae693233d218d2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001600_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.182563 0.298794 0.180010 0.177598 +1 0.182563 0.000001 0.210658 0.005072 0.009458 +2 0.298794 0.210658 0.000001 0.208106 0.205694 +3 0.180010 0.005072 0.208106 0.000001 0.006906 +4 0.177598 0.009458 0.205694 0.006906 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd7f9a4b9aa87200fcd4df30de87b89ba9c7658c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20221950 Before NNI: tree length is 0.20221950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001603_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d6050cff3fa19ee14da2a14c4d2cd4ef19329950 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.294049 0.374901 0.274408 0.274612 +1 0.294049 0.000001 0.350615 0.035851 0.036055 +2 0.374901 0.350615 0.000001 0.330975 0.331178 +3 0.274408 0.035851 0.330975 0.000001 0.009120 +4 0.274612 0.036055 0.331178 0.009120 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b6e149c2ffc84f1ba3a7cfcc5327caade0519f3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.149031 0.221137 0.152061 0.149031 +1 0.149031 0.000001 0.134183 0.007843 0.000001 +2 0.221137 0.134183 0.000001 0.137214 0.134183 +3 0.152061 0.007843 0.137214 0.000001 0.007843 +4 0.149031 0.000001 0.134183 0.007843 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f9cd1218d63f350e1e10d3f0c445698949bcb69 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25761276 Before NNI: tree length is 0.25761275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001609_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001609_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..15b15c356d19264da51e03f799b315fd8632efa2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001609_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31635050 Before NNI: tree length is 0.31635050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0789156ce43597e37066bdbb97c123b73068f95e --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.160793 0.307853 0.164231 0.172329 +1 0.160793 0.000001 0.276824 0.008803 0.016901 +2 0.307853 0.276824 0.000001 0.280262 0.288360 +3 0.164231 0.008803 0.280262 0.000001 0.008098 +4 0.172329 0.016901 0.288360 0.008098 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1083ad9fa412ecc84289b2294c80e42954953d6b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.228923 0.510310 0.214182 0.227432 +1 0.228923 0.000001 0.571066 0.022476 0.004465 +2 0.510310 0.571066 0.000001 0.556325 0.569574 +3 0.214182 0.022476 0.556325 0.000001 0.020985 +4 0.227432 0.004465 0.569574 0.020985 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7358c0ac365fd50fcf382a2b51a77833757e4d24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.66050385 Before NNI: tree length is 0.66050387 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001612_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001612_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f79d8e3699dfb0ef5b70df41c438b627a82911f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001612_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.023876 0.073839 0.025921 0.023876 +1 0.023876 0.000001 0.083423 0.002460 0.000001 +2 0.073839 0.083423 0.000001 0.085468 0.083423 +3 0.025921 0.002460 0.085468 0.000001 0.002460 +4 0.023876 0.000001 0.083423 0.002460 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001615_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001615_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d838adee1704526cab511fe9cdf8d24c9def17ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001615_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76699000 Before NNI: tree length is 0.76699000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1ccd7ad72309a803eeed3211badc373577c2a1a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001616_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29132000 Before NNI: tree length is 0.29132000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..38916e118bc95680e22ba03f1bd2b7d9054f0a5c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.159511 0.380849 0.176514 0.158581 +1 0.159511 0.000001 0.437294 0.017003 0.025024 +2 0.380849 0.437294 0.000001 0.454296 0.436363 +3 0.176514 0.017003 0.454296 0.000001 0.042027 +4 0.158581 0.025024 0.436363 0.042027 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001627_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3225c43bf204cfbffad6c12b3e6340bfa2c95280 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56798190 Before NNI: tree length is 0.56798188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c03a129b3f8dba2bdcc02bf283ac680a3d46a3d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001628_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041330 0.124708 0.043388 0.038273 +1 0.041330 0.000001 0.109001 0.013175 0.017508 +2 0.124708 0.109001 0.000001 0.111059 0.105944 +3 0.043388 0.013175 0.111059 0.000001 0.019566 +4 0.038273 0.017508 0.105944 0.019566 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001629_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001629_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1bd1ca1f0666a85b2d80aaa595860686449b9ca5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001629_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32752650 Before NNI: tree length is 0.32752650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be405ea7f0a9ce61034b7bfd3082eb7a3f4eac9a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001630_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10102850 Before NNI: tree length is 0.10102850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..888d75391cbcbba32fee44de704c5959a9e304cf --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24544100 Before NNI: tree length is 0.24544100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001633_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1332d3f84e4d82e2f230164de35ef96caf575355 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.46531975 Before NNI: tree length is 0.46531975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001636_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001636_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f7dd1aafe8db0fba18bbe07d5d6b2f8e266a3f0c --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.083242 0.104057 0.082819 0.080405 +1 0.083242 0.000001 0.110182 0.017955 0.012456 +2 0.104057 0.110182 0.000001 0.109759 0.107344 +3 0.082819 0.017955 0.109759 0.000001 0.015118 +4 0.080405 0.012456 0.107344 0.015118 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..939cfbe0f116aad1653071ab8eadd0fb4e54317d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.203770 0.163862 0.198627 0.193196 +1 0.203770 0.000001 0.228281 0.039545 0.034113 +2 0.163862 0.228281 0.000001 0.223138 0.217707 +3 0.198627 0.039545 0.223138 0.000001 0.020498 +4 0.193196 0.034113 0.217707 0.020498 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001638_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001638_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..555da83a26e5379f1377614a0095012fd925d1f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001638_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.420543 0.431283 0.442494 0.432258 +1 0.420543 0.000001 0.458383 0.048356 0.038120 +2 0.431283 0.458383 0.000001 0.480334 0.470098 +3 0.442494 0.048356 0.480334 0.000001 0.030389 +4 0.432258 0.038120 0.470098 0.030389 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2de88965c4b0396f0fd5aa355d0f61e8efa3ed4b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.144063 0.171894 0.144921 0.153244 +1 0.144063 0.000001 0.170710 0.013141 0.012739 +2 0.171894 0.170710 0.000001 0.171568 0.179890 +3 0.144921 0.013141 0.171568 0.000001 0.022322 +4 0.153244 0.012739 0.179890 0.022322 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001640_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001640_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc7bbafef7d4ec736d4972c43c7804f58062000b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001640_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.29383075 Before NNI: tree length is 0.29383075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001641_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001641_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3d51ee1481a5784bb7a30dca3ddeb43d52c4a089 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001641_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.456654 0.665541 0.437947 0.459031 +1 0.456654 0.000001 0.652459 0.052698 0.059215 +2 0.665541 0.652459 0.000001 0.633753 0.654837 +3 0.437947 0.052698 0.633753 0.000001 0.055076 +4 0.459031 0.059215 0.654837 0.055076 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001646_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001646_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4be91ea6462baa0e8aa98495f95bb0e66e447ecc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001646_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.37200379 Before NNI: tree length is 0.37200375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..df47c388430625120dc72ea3015c16a0eaec10cc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.239574 0.277054 0.245671 0.240112 +1 0.239574 0.000001 0.162045 0.018329 0.012769 +2 0.277054 0.162045 0.000001 0.168143 0.162583 +3 0.245671 0.018329 0.168143 0.000001 0.005560 +4 0.240112 0.012769 0.162583 0.005560 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2aec91fc036cde1b3e456c40fc46ec7f4ea12a9f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034942 0.068714 0.033532 0.032676 +1 0.034942 0.000001 0.078581 0.003813 0.002436 +2 0.068714 0.078581 0.000001 0.077171 0.076316 +3 0.033532 0.003813 0.077171 0.000001 0.001548 +4 0.032676 0.002436 0.076316 0.001548 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fecad938a8135f884e160db1face34793585335 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001654_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09240540 Before NNI: tree length is 0.09240537 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001657_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001657_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f329bc6aaf7b36e2efaa7359ab1a4f705812c385 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001657_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.58986650 Before NNI: tree length is 0.58986650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001663_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cf375d6c5db77c8f19d53419e18d803d8ded8cbb --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.065169 0.097545 0.068202 0.070144 +1 0.065169 0.000001 0.056770 0.005687 0.007629 +2 0.097545 0.056770 0.000001 0.059803 0.061745 +3 0.068202 0.005687 0.059803 0.000001 0.006070 +4 0.070144 0.007629 0.061745 0.006070 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a9aac792bd027125d6f8d192c289f8c7133740a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001670_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32906600 Before NNI: tree length is 0.32906600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a839639e88f5938dbf04507df5298f2916f3455 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001671_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31778656 Before NNI: tree length is 0.31778650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f6b8875dc5f6fef51430e31c456db59f7322dff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001672_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.188480 0.443645 0.197374 0.192425 +1 0.188480 0.000001 0.334791 0.014423 0.019244 +2 0.443645 0.334791 0.000001 0.343685 0.338737 +3 0.197374 0.014423 0.343685 0.000001 0.028138 +4 0.192425 0.019244 0.338737 0.028138 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5db46632043c08e2b7ebb067778b9f26d83646da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001673_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.194289 0.857700 0.195310 0.203065 +1 0.194289 0.000001 0.845885 0.001021 0.008776 +2 0.857700 0.845885 0.000001 0.846906 0.854661 +3 0.195310 0.001021 0.846906 0.000001 0.007755 +4 0.203065 0.008776 0.854661 0.007755 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001676_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..14dbe3fb235efccf8d2fb97c53101a913ed9f258 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.153677 0.270196 0.153078 0.150686 +1 0.153677 0.000001 0.275752 0.010645 0.003038 +2 0.270196 0.275752 0.000001 0.275153 0.272760 +3 0.153078 0.010645 0.275153 0.000001 0.007653 +4 0.150686 0.003038 0.272760 0.007653 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5fbc94f340af2d5682e2eac0e770bf6b01b075fe --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.059658 0.167694 0.055779 0.051174 +1 0.059658 0.000001 0.173783 0.018438 0.013834 +2 0.167694 0.173783 0.000001 0.169904 0.165300 +3 0.055779 0.018438 0.169904 0.000001 0.008504 +4 0.051174 0.013834 0.165300 0.008504 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001685_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001685_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d2fd7d4eac6c8ed41c0fbcbe4b3a7adaf407fd2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001685_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.193307 0.460794 0.188897 0.179338 +1 0.193307 0.000001 0.445669 0.004409 0.014920 +2 0.460794 0.445669 0.000001 0.441259 0.431700 +3 0.188897 0.004409 0.441259 0.000001 0.010511 +4 0.179338 0.014920 0.431700 0.010511 0.000001 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001686_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a84e78d8fac9e63d537c67fcd0103c2ced75f27c --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23811455 Before NNI: tree length is 0.23811450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..389d4e712612c8e831ec37e25e2f8d88f39b32e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.170952 0.460574 0.173698 0.160719 +1 0.170952 0.000001 0.437132 0.008700 0.011673 +2 0.460574 0.437132 0.000001 0.439878 0.426900 +3 0.173698 0.008700 0.439878 0.000001 0.014419 +4 0.160719 0.011673 0.426900 0.014419 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f38bea39e65b01edd3c6f29985aadd53bb32aa71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.54077220 Before NNI: tree length is 0.54077225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc24db180c7b86656fff6eb5d1eaa70869dd0046 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.60032950 Before NNI: tree length is 0.60032950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88372aa1aeea2de10f914871fceb2be61dab9746 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.046347 0.079438 0.046347 0.046347 +1 0.046347 0.000001 0.095312 0.000001 0.000001 +2 0.079438 0.095312 0.000001 0.095312 0.095312 +3 0.046347 0.000001 0.095312 0.000001 0.000001 +4 0.046347 0.000001 0.095312 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1458cc7f133a044e44d6ca369cb0c1a34937ceb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11054950 Before NNI: tree length is 0.11054950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..00e34584f194030044082a8bef6e5a2ceeda331f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.044836 0.076779 0.042395 0.042395 +1 0.044836 0.000001 0.090492 0.003711 0.003711 +2 0.076779 0.090492 0.000001 0.088050 0.088050 +3 0.042395 0.003711 0.088050 0.000001 0.000001 +4 0.042395 0.003711 0.088050 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6800526c94e895fe9bc4b45be00be109751c693 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.10668870 Before NNI: tree length is 0.10668875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d739c482274e35425226b15bdc1ba9226ad10638 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001699_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.51706875 Before NNI: tree length is 1.51706875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69b2e4b6361073c5f63360b4caad93dd04a1bf4b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.362158 0.371340 0.361004 0.360536 +1 0.362158 0.000001 0.454261 0.010548 0.003884 +2 0.371340 0.454261 0.000001 0.453107 0.452639 +3 0.361004 0.010548 0.453107 0.000001 0.008927 +4 0.360536 0.003884 0.452639 0.008927 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..baaa130e77bbe60dde90db0c82554deb352a6755 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001700_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59970775 Before NNI: tree length is 0.59970775 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..584b0d9b2c314173c8ee56cfdfd82f0099c1b075 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.216375 0.266099 0.217975 0.225436 +1 0.216375 0.000001 0.242364 0.007271 0.014731 +2 0.266099 0.242364 0.000001 0.243964 0.251425 +3 0.217975 0.007271 0.243964 0.000001 0.011500 +4 0.225436 0.014731 0.251425 0.011500 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_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001704_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c19a742414e4d5ebf82d721163c828df8f8fa66b --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.55362800 Before NNI: tree length is 0.55362800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001707_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001707_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94921e92e5ac83e0e78c97bb0a19fc059294f3a0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001707_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.21304325 Before NNI: tree length is 1.21304325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed8c98842e14b7d63b887793417093adce76d57b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11597625 Before NNI: tree length is 0.11597625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63faff994b79258f96d6f25f6b21558d82243330 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001711_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32555850 Before NNI: tree length is 0.32555850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4aeff82c780a369de962fe2a3f7de0dec79aa504 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.041879 0.124782 0.047237 0.047237 +1 0.041879 0.000001 0.130571 0.005410 0.005410 +2 0.124782 0.130571 0.000001 0.135929 0.135929 +3 0.047237 0.005410 0.135929 0.000001 0.000001 +4 0.047237 0.005410 0.135929 0.000001 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001716_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001716_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bf66f6b5d1a54f954ab27d8c376be8171d7478c9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001716_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.106299 0.156988 0.107078 0.106311 +1 0.106299 0.000001 0.161751 0.062588 0.061821 +2 0.156988 0.161751 0.000001 0.162529 0.161762 +3 0.107078 0.062588 0.162529 0.000001 0.036935 +4 0.106311 0.061821 0.161762 0.036935 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2b181269c0671518bf138c2b707ca72cb4e32408 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017152 0.417212 0.016460 0.020223 +1 0.017152 0.000001 0.420293 0.007620 0.008097 +2 0.417212 0.420293 0.000001 0.419602 0.423364 +3 0.016460 0.007620 0.419602 0.000001 0.010690 +4 0.020223 0.008097 0.423364 0.010690 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4504a217f3792c3f1e78c7d817b013cac81122f4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.41287408 Before NNI: tree length is 0.41287400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cfc7367e09115736f8d810a6b3ed15127793528d --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.053586 0.115191 0.044411 0.047535 +1 0.053586 0.000001 0.122337 0.036716 0.039840 +2 0.115191 0.122337 0.000001 0.113161 0.116285 +3 0.044411 0.036716 0.113161 0.000001 0.004734 +4 0.047535 0.039840 0.116285 0.004734 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001723_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001723_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3da6368649fcf91c76d8a1a51ccce64838d715ab --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001723_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.046446 0.210750 0.046446 0.040085 +1 0.046446 0.000001 0.211564 0.000001 0.006957 +2 0.210750 0.211564 0.000001 0.211564 0.205203 +3 0.046446 0.000001 0.211564 0.000001 0.006957 +4 0.040085 0.006957 0.205203 0.006957 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001724_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001724_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42f1861836f677821915741b4af58d4e7dada52f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001724_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.308846 0.808325 0.308846 0.304803 +1 0.308846 0.000001 0.735846 0.000001 0.007463 +2 0.808325 0.735846 0.000001 0.735846 0.731804 +3 0.308846 0.000001 0.735846 0.000001 0.007463 +4 0.304803 0.007463 0.731804 0.007463 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..063edfe68ca784f5a64a9802027aac65fcf2d478 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.290076 0.560130 0.292064 0.284077 +1 0.290076 0.000001 0.507062 0.021163 0.020758 +2 0.560130 0.507062 0.000001 0.509050 0.501063 +3 0.292064 0.021163 0.509050 0.000001 0.022745 +4 0.284077 0.020758 0.501063 0.022745 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001726_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001726_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd9f539787d36ff31c6b63dd47594d31bae853cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001726_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19857511 Before NNI: tree length is 0.19857513 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f24bd35d33155814fd0a976ae3fa1432210fd7eb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39672700 Before NNI: tree length is 0.39672700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..85c3aa51a6a243f4396cf68944004398e7c02397 --- /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_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.06440875 Before NNI: tree length is 0.06440875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001735_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001735_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c898f0fbdc13e0222066d8a5c66e466776df445 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001735_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07269109 Before NNI: tree length is 0.07269112 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001737_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001737_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..be868ce0bee8eb21beae2a3b8c3f3dc077da15c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001737_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.056522 0.017093 0.044409 0.056522 +1 0.056522 0.000001 0.039429 0.012113 0.000001 +2 0.017093 0.039429 0.000001 0.027316 0.039429 +3 0.044409 0.012113 0.027316 0.000001 0.012113 +4 0.056522 0.000001 0.039429 0.012113 0.000001 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001738_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f4aee53a132f7336729be09f88e4faa795010c64 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009264 0.114675 0.024997 0.009264 +1 0.009264 0.000001 0.117807 0.025063 0.000001 +2 0.114675 0.117807 0.000001 0.133540 0.117807 +3 0.024997 0.025063 0.133540 0.000001 0.025063 +4 0.009264 0.000001 0.117807 0.025063 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001759_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001759_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..015980e5b11f2c09753fcce9ee81cdd180ebe66a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001759_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.45333550 Before NNI: tree length is 0.45333550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b46782bb6a204a7018da1c722363142fcea7c5c6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.209630 0.761165 0.235417 0.224402 +1 0.209630 0.000001 0.782250 0.026396 0.015381 +2 0.761165 0.782250 0.000001 0.808036 0.797022 +3 0.235417 0.026396 0.808036 0.000001 0.026439 +4 0.224402 0.015381 0.797022 0.026439 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e01021ded15faebac88907c98078336002d6faa9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001760_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.91032584 Before NNI: tree length is 0.91032588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001762_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001762_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1850252ed57fee683b530c4af2101bbff990412c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001762_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21970262 Before NNI: tree length is 0.21970262 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001764_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7506ab0420bb580f01e28ef01440d1dfd3b73da9 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.359738 0.761228 0.410768 0.401332 +1 0.359738 0.000001 0.741399 0.077866 0.068431 +2 0.761228 0.741399 0.000001 0.792430 0.782994 +3 0.410768 0.077866 0.792430 0.000001 0.027322 +4 0.401332 0.068431 0.782994 0.027322 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001765_tree_id.txt.dist.phylip_fastme_stat.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001765_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3e0c67bf07c156c5a7e3f0a7b86072774087d40 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001765_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44963500 Before NNI: tree length is 0.44963500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + 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 b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Distances_SpeciesTree/OG0001767_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fd9de991bff476895b9bbde2dd644e7d672b38a1 --- /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 @@ -0,0 +1,6 @@ +5 +0 0.000001 0.560517 1.451330 0.549845 0.565548 +1 0.560517 0.000001 1.457288 0.073220 0.088924 +2 1.451330 1.457288 0.000001 1.446616 1.462319 +3 0.549845 0.073220 1.446616 0.000001 0.015703 +4 0.565548 0.088924 1.462319 0.015703 0.000001 diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbdc78a80af4c6d8ca31433459b47db7c8edba88 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt @@ -0,0 +1,2 @@ +(((4_579:0.00000000,3_356:0.00000000):0.00116114,((0_377:0.04208040,0_373:0.00090960):0.01706028,0_394:0.00046546):0.00100654):0.00165752,1_602:0.00758284,2_2137:0.04633916); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2474c86f556d60faa352d73014427f291917c19d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt @@ -0,0 +1,2 @@ +((3_697:0.00112550,0_1837:0.00352750):0.00052400,(((2_2203:1.31174070,4_917:-0.68772370):0.03769970,0_804:1.30472800):1.19028617,1_974:-0.00694217):0.00899222,4_918:0.09708395); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..554d32ddbe201be5fecce4b3685ea0bd87360e12 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt @@ -0,0 +1,2 @@ +(((1_861:0.02612650,3_592:0.04317450):0.69497075,((3_582:0.00290412,1_851:0.01139387):0.75345837,0_2002:1.06260013):0.35233950):0.47720050,4_812:0.86043362,2_1900:0.58953737); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6314e1949aac09529d8fc1521bafedc1af8ee0d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt @@ -0,0 +1,2 @@ +((((3_461:0.01044031,(1_722:0.00959819,4_686:0.03364081):0.01586819):0.40820531,0_2132:0.54098144):0.27913606,2_2026:0.73087094):0.40074156,2_668:0.77847450,2_669:0.94980450); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..239e9bb64e2816f11641cc336529d8230ef670e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt @@ -0,0 +1,2 @@ +((((1_987:0.00000000,3_711:0.00000000):0.00000000,4_931:0.00000000):0.01517700,2_1707:0.07289100):0.98459350,0_175:0.97280300,0_1816:0.86234100); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..810d032ba2ed4318d7ffeccf0b129a7541a4beaf --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt @@ -0,0 +1,2 @@ +((4_933:-0.00016156,2_1705:0.01198156):0.00016206,((0_176:0.41517519,0_1817:0.48871881):0.70446406,1_989:-0.00016156):0.00016206,3_713:-0.00016156); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc8c8c141f0b8beddabe2ce2ead99084573b53df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt @@ -0,0 +1,2 @@ +((3_2137:-0.05750094,((1_190:-0.07330556,0_187:0.51692156):0.07590019,2_139:-0.07142019):0.07318719):0.07503194,3_1974:1.14174644,4_190:-0.05792844); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6442f56da06d2788920209f179b20aeb2d3edba --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt @@ -0,0 +1,2 @@ +((4_576:-0.00209832,(2_1037:1.12543663,2_435:0.96855938):0.58571971):0.00569338,(2_2147:0.00926000,0_386:0.00380700):0.00273800,1_605:0.00076194); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ac8066be5c66174c949efaba57842491abe4251 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt @@ -0,0 +1,2 @@ +(0_446:1.44313107,((1_544:1.44500744,1_33:1.24672156):0.08640290,(4_2148:0.19384638,1_2213:0.25098762):0.53974128):0.09227583,2_410:1.57250193); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92a9b29db1d4119698e1313ee6a3e3d40256937d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt @@ -0,0 +1,2 @@ +((0_577:0.33351368,(1_2101:-0.15058583,(3_1825:0.17770625,2_501:0.65466475):0.42771580):0.19032916):0.07398380,4_2047:0.06527142,3_1826:0.13320558); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a75cb9f126a882a24d2a6714c8a645ef0249b9d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1707:0.01137062,(4_1925:0.01487913,1_1990:0.00099388):0.00529638):0.18740838,2_711:0.39173512):0.99920087,0_1065:0.00000000,1_1731:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea3e2d77b8945ea5e43e2a156be64cb3b256d5b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt @@ -0,0 +1,2 @@ +((3_1347:0.00000000,4_1562:0.00000000):0.01584050,((2_1097:0.21228200,2_30:1.03458200):0.14859650,0_1166:0.10246700):0.05418750,1_1633:0.00729550); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..12d023cd18e729e2a6ccdf11852f1759f757b160 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt @@ -0,0 +1,2 @@ +((0_2388:0.04598211,(0_1193:2.48045050,2_2271:0.02622050):0.03369273):0.00283560,(4_485:0.02194197,1_486:0.00744403):0.01816968,3_215:0.04167322); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..900ae8973af8768d790c62a6fd9103d08b4995b2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt @@ -0,0 +1,2 @@ +(1_473:0.01016619,((0_2398:0.02347656,(0_1196:1.79847494,2_2281:0.12364106):0.09330994):0.00238419,4_472:0.01335306):0.00415844,3_203:0.01089681); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..293fe8645aa08019e0779267ca8dd8265c1d9522 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt @@ -0,0 +1,2 @@ +((((3_64:0.00437356,1_339:0.00218344):0.00178681,4_346:0.01081769):0.00641581,2_2404:0.04615369):0.00440931,0_2545:0.00604444,0_1227:1.02832456); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..17378ebc4d773af242e232af512efb1707761705 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt @@ -0,0 +1,2 @@ +((1_1530:0.00000000,0_1313:0.00000000):0.00000000,((2_441:0.16727925,1_2188:0.04275675):1.47059617,3_1251:0.00279783):0.00174217,4_1457:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3968c87c4b66500dbf3248f98d4f5304cb91cd2d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1230:0.32512644,0_2218:0.97416356):0.52417881,4_1436:-0.03705081):0.04075831,(0_1338:0.13852519,1_1509:-0.02055919):0.05108081,3_1229:0.02038819); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..289e15563befc9dd01e1c91b1d904d5704e0ae3e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt @@ -0,0 +1,2 @@ +((3_1050:0.02795256,(1_1321:0.02063044,4_1275:0.01390156):0.00523794):0.24634694,(1_1893:2.62664694,0_1494:0.14971206):0.14746544,2_1389:0.35584806); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..31f5975596b8efaba876833257fc57237a029a2a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt @@ -0,0 +1,2 @@ +(((3_799:0.00231856,(4_1021:0.00099494,1_1071:0.00130106):0.00113144):0.02080894,0_1745:0.02402206):0.04474094,3_357:1.00686169,2_1637:0.06379331); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9c59f5146fb4747fe375d2716d1d7243e7a93bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt @@ -0,0 +1,2 @@ +((3_788:0.00000050,1_1060:0.00000050):0.00000000,((2_1647:0.10956125,0_1757:0.30384175):0.07321095,0_1756:0.03652889):0.04585461,4_1009:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..39af97c1f9915d247f40ee3716141dcf411d71cc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1902:0.28769537,(0_2009:0.00586313,4_809:0.00736487):0.26265812):0.14070963,0_2007:1.36523513):0.38519487,1_853:0.00000000,3_584:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ceaa1ef3e32785c3b33ac829b8d1f3bace30ee17 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt @@ -0,0 +1,2 @@ +(((4_636:0.01427629,(3_412:0.00176296,1_666:0.00083404):0.01650460):0.27801927,0_2212:0.24171930):0.61325802,2_2387:0.88280888,0_2213:0.11430212); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..719a1d36096a9435597e30e4e42c39539a9df531 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt @@ -0,0 +1,2 @@ +((4_308:0.00253150,3_25:0.00859850):0.00818525,(0_18:0.08658725,2_14:0.30109075):0.08176525,1_301:0.01370875); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..29f72257460deab0d3144f232f0c4ec7c413142f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt @@ -0,0 +1,2 @@ +((1_283:0.00000050,3_0:0.00000050):0.00000000,(0_53:0.02610350,2_32:0.11056950):0.01359600,4_290:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c05bef3dd964b0cf45762db5b7c5b53e4452c63d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt @@ -0,0 +1,2 @@ +(4_289:0.00000000,((0_54:0.02219600,2_33:0.07557100):0.04824550,1_282:0.00234750):0.00234750,3_2256:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..67ea9d6fc4b3897470a7bef88e18ef0f430f2598 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt @@ -0,0 +1,2 @@ +((0_86:0.01841800,2_57:0.27745500):0.02689194,(4_257:0.00000000,3_2223:0.00000000):0.00191217,1_259:0.00065183); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bf83199fb98019c13c2a725440551a4a44b2ac0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt @@ -0,0 +1,2 @@ +(3_2217:0.00474012,((2_66:0.77519400,0_96:0.25711900):0.29261033,4_251:0.01859400):0.02013750,1_253:0.00613788); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f3ad8b358ff63738df54abe0ab36e46cf395873 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt @@ -0,0 +1,2 @@ +((3_2196:0.01640584,4_233:0.00908116):0.01152747,(0_119:0.15731000,2_86:0.78133100):0.07890459,1_232:0.01207045); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a079bf9e488fb7390fe7dfcf7588f521d731da0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt @@ -0,0 +1,2 @@ +((4_205:-0.00062500,(2_112:0.07002600,1_205:-0.00062500):0.00062500):0.00046900,3_2149:0.00945925,0_163:0.05190975); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..71747b56da2c69a918fc0674058bd210804c40a6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt @@ -0,0 +1,2 @@ +((0_180:0.23138463,3_2140:0.01396038):0.00943712,(1_194:0.00337213,4_196:0.00538387):0.00942662,2_134:0.02141538); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..eebffc4bd06d95adb5f9c7f1156de3a26d7dd806 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt @@ -0,0 +1,2 @@ +((4_189:0.03469793,(3_2136:0.01483023,1_189:0.02613777):0.01780200):0.16340457,0_192:0.20484950,2_140:0.20798250); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a1f3fd87db3c59577cc36d92be4f204cf7ab7a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt @@ -0,0 +1,2 @@ +(((2_144:-0.00005950,0_197:0.02246350):0.00228000,1_185:0.00666850):0.00073350,3_2132:0.00000000,4_185:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..956e003e2448cfab77640267e5df6454da6c8fd6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt @@ -0,0 +1,2 @@ +(2_153:0.44883605,((1_175:0.00737417,4_172:0.00165483):0.00301062,3_2122:0.00386036):0.00228314,0_208:0.00670995); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..556aa2894d4d1da66c32460955a8077e6b1ab50c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt @@ -0,0 +1,2 @@ +(3_2101:0.00174638,(1_136:0.00180838,(2_164:0.18314038,0_230:0.02579762):0.04238213):0.00443363,4_144:0.00404563); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c4359156c4c2aae42badc3f16942e7a42373b54 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt @@ -0,0 +1,2 @@ +(4_140:0.00000000,((2_168:0.07523050,0_234:0.02761850):0.02411150,3_2097:0.00744000):0.02353900,1_132:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a81d9535b70e886526bfbbed204672bfef257e95 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt @@ -0,0 +1,2 @@ +((2_182:0.78540098,(0_248:0.25696023,1_119:0.11879277):0.01839592):0.16793396,4_127:0.02678750,3_2084:0.00927750); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..48d73ecef59ce0af8d60d25b0a97da6d48c411c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt @@ -0,0 +1,2 @@ +(((1_117:0.04328750,0_250:0.05196050):0.00256775,2_184:0.08267625):0.03938675,3_2082:0.01270450,4_125:0.00748750); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..813ed633ea4d15a81fef41f2989fb972458ae8a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt @@ -0,0 +1,2 @@ +((3_2073:0.00000050,1_109:0.00000050):0.00000000,(0_262:0.04378100,2_204:0.13830300):0.08513950,4_104:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000326_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000326_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..41db302a676b1f9998e41919342098014867f611 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000326_tree_id.txt @@ -0,0 +1,2 @@ +((3_2054:0.01666875,(0_282:0.21075250,2_228:0.46807950):0.26076775):0.00983425,1_90:0.00236600,4_85:0.00720300); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9321e4a3c4551c646277f3350c3c404a91c06ffd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt @@ -0,0 +1,2 @@ +(1_89:0.00071485,(3_2053:0.00896211,(0_283:0.04615250,2_229:0.20762250):0.03231487):0.00818489,4_84:0.00000915); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c69a9a68e806501e467657d8a11ae99ae3c958a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt @@ -0,0 +1,2 @@ +(2_230:0.00534725,(0_284:0.01714425,(1_88:0.00000000,4_83:0.00000000):0.01554075):0.00388525,3_2052:0.01006175); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f61e863ab6c7c7098c4ae950bb4db8bc61efe442 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt @@ -0,0 +1,2 @@ +(((0_292:0.12045050,2_237:0.48668950):0.05300500,1_80:0.01326250):0.02029750,4_75:0.00000000,3_2044:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e73684f6d58d9d25b49df098b511c35948640eb0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt @@ -0,0 +1,2 @@ +((1_29:0.00232437,3_1997:0.00134563):0.00166137,(0_350:0.08319787,2_446:0.18224413):0.10268938,4_28:0.00323862); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d358559530e4802311e0b84b743f465e187a547c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt @@ -0,0 +1,2 @@ +(((0_360:0.08046000,2_343:0.33782900):0.06052741,1_17:0.01845622):0.01170078,3_1986:0.01404109,4_17:0.01608691); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92f48ae7f08098e814a40f12eec44e82a3d9d39b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt @@ -0,0 +1,2 @@ +((1_12:0.00000000,(2_348:0.02001650,0_366:0.02708350):0.03393950):0.00000000,3_1981:0.00000000,4_12:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000384_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000384_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a169f0aa078871ffecf681bfd78898cdfa15ff05 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000384_tree_id.txt @@ -0,0 +1,2 @@ +((0_372:0.10160825,(2_639:0.02036525,2_1792:0.12513275):0.08781375):0.68822575,2_316:0.74239375,2_1185:0.27315025); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..42d9b900a5f5e520e90a998f7146bda245a47164 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt @@ -0,0 +1,2 @@ +((2_2141:0.03457950,0_392:0.14353050):0.16016648,(1_611:0.00151917,4_570:0.00199583):0.29905261,2_2140:-0.14403176); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c39933832fd0acc0614fb6173efae6189876d333 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt @@ -0,0 +1,2 @@ +((2_352:0.28838000,0_399:0.06487100):0.09196050,(4_6:0.00000000,3_1962:0.00000000):0.00237100,1_6:-0.00237100); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..435169820605dcc989c2754caec95b5fb2619bc6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2240:-0.00030437,3_1944:0.00122838):0.00247713,4_2182:0.00470787):0.04295213,2_371:0.30823163,0_418:0.20024638); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe4c68ce1ece31f2df7ee3fada5b8f11eb21de68 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt @@ -0,0 +1,2 @@ +((0_427:1.19929233,2_1495:0.27232867):0.24226333,(4_1169:0.00000000,3_940:0.00000000):0.01332201,1_1212:0.11759199); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0438fdaf974cd44c83bea1505e734410aae3a6df --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt @@ -0,0 +1,2 @@ +((3_1928:0.01334562,(1_2226:0.00491238,4_2166:0.00741662):0.00565987):0.01931088,0_432:0.03095187,2_386:0.22643512); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c1281434b694dce08a284576e6fc53bed6c1024a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1911:0.01682841,4_2140:0.00541959):0.00159410,0_444:0.04007857):0.00083679,1_2207:0.00738317,2_476:0.32425383); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b744cc4d1cc9b16ca263d017b0b214d9556b3b5a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt @@ -0,0 +1,2 @@ +(3_1904:0.00746738,((0_459:0.03103613,2_415:0.29174387):0.00459738,1_2193:0.00028662):0.00176537,4_2125:0.00075462); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..23914304d3522f828e6cef759d00437affee6e4b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt @@ -0,0 +1,2 @@ +(((4_210:0.00000050,3_2154:0.00000050):0.07320166,0_510:1.08314484):0.10301195,2_438:0.08773533,0_496:0.07857667); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..53f2731b0e850213df751056f9ec67977276d8ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt @@ -0,0 +1,2 @@ +(2_1697:0.78252138,((4_943:0.00551862,3_724:0.01112837):0.24686787,1_1002:0.28395612):0.10703488,0_525:0.45230463); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..53361e1ad87cb6dbd49b6320905312766adc4eb9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt @@ -0,0 +1,2 @@ +(0_541:0.27434812,(0_724:0.09995254,(1_2010:0.00402533,4_1939:0.00402867):0.08387685):0.01669196,2_470:0.27915188); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..650125750a9d86ae2abbc0cade6a8aa9b36c16ce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2121:0.01675313,4_2067:0.01628488):0.01377512,3_1846:0.01841838):0.18590963,2_478:0.17415587,0_550:0.25066212); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..718b1b524cf15a18793162a9ec321417da640762 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1842:0.00200157,1_2117:0.00167143):0.00302372,4_2063:0.00681018):0.12266869,0_556:0.27871583,2_484:0.16527917); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2896fd0125587ccf5abca0b0c451abec7e72884 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt @@ -0,0 +1,2 @@ +(4_2045:0.00000000,(3_1824:0.01592637,(0_578:0.44009250,2_502:0.80033650):0.21912496):0.00619163,1_2100:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d39f21a9b955f191c896ab42c0997fb56b7fb210 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt @@ -0,0 +1,2 @@ +((0_2601:0.33542479,(0_596:0.04497025,2_521:0.06159975):0.11279125):0.13467921,4_2030:0.00000000,3_1810:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6815c53275243331bcf46dcfa62d37832c5515ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1776:0.01181675,4_1996:0.01248925):0.01199275,1_2057:0.00369625):0.06673825,0_644:0.07558325,2_562:0.33051275); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..56fa378e25260da132a42939ee6efa0c3958fa2c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt @@ -0,0 +1,2 @@ +(3_1775:0.01148637,(4_1995:0.05855387,(2_563:0.60707088,0_645:0.17638113):0.11796313):0.00157063,1_2056:-0.00251737); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1ce768e6c2343310a591690a682a5e447162a55 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt @@ -0,0 +1,2 @@ +((0_648:0.08073725,2_565:0.29642675):0.07334350,(1_2053:0.01775825,4_1992:0.01171975):0.00837400,3_1772:0.03596050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ade4f81a7278bbd6e164f21016acdaf0f03222fa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt @@ -0,0 +1,2 @@ +((1_2052:0.00808838,3_1770:0.00909462):0.00969240,(0_649:0.16537783,2_566:0.22799617):0.04257683,4_1991:0.02258814); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3150f5ae33a1aaa7427c27b17ea17d693932d00f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt @@ -0,0 +1,2 @@ +((1_2046:0.00000000,3_1764:0.00000000):0.00292200,(2_571:0.80596050,0_654:0.56345750):0.05190550,4_1987:0.00013800); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..190034c91088e3550845db64f3e0e9048db39068 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt @@ -0,0 +1,2 @@ +(((2_573:0.31264033,0_656:0.13843767):0.07606299,4_1985:0.00150198):0.00160502,3_1762:0.00000000,1_2044:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5da4dd09d3a1972c1834a14d71d8a56672069282 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt @@ -0,0 +1,2 @@ +(3_1761:0.00000050,(4_1984:-0.00053956,(2_576:0.11076483,0_657:0.05817517):0.07560431):0.00232206,1_2043:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d5dbc864303bdb67faf6adaec84d009f64f03c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1711:-0.00037639,1_1994:0.00703239):0.00093563,4_1929:0.16534576):0.16113607,0_693:0.09766933,2_708:0.09612267); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ecac060d0f95143d9620fde199f9e2c51a88fa0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt @@ -0,0 +1,2 @@ +((4_1931:0.04108613,(3_1713:0.01276462,1_1996:0.01175338):0.02530437):0.07587238,0_745:0.15979787,2_709:0.20540313); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c1e2671a199ebb2afb1965e1af3e47cfa8184ec5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt @@ -0,0 +1,2 @@ +((1_1965:0.01129961,(4_1903:0.00000050,3_1685:0.00000050):0.00685889):0.04451570,2_736:0.02482550,0_775:0.21716650); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..193f08d76de21d29d52b630449211515b655702d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1664:0.00360001,4_1882:0.00389999):0.00613335,1_1943:0.00411497):0.10093390,2_757:0.47094967,0_819:0.09229833); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000568_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000568_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2468c1921167b88297ccc0498a5e3b0d24984793 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000568_tree_id.txt @@ -0,0 +1,2 @@ +(((0_841:0.01999567,2_780:0.03517233):0.19309446,1_1934:0.00180337):0.01014963,4_1861:-0.00054604,3_1639:0.00908904); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000569_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000569_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2456cbc633edaca54644168679208d3fcebca06 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000569_tree_id.txt @@ -0,0 +1,2 @@ +(4_1860:0.00061050,(3_1638:-0.00017587,(2_783:0.01792050,0_844:0.08288250):0.03276288):0.00204537,1_1933:0.00810950); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..248402cccbabb90c37ceacf11c187032dd316da3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt @@ -0,0 +1,2 @@ +(1_1927:0.00623775,(4_1854:0.00283475,(2_788:0.11783775,0_850:0.01371925):0.01117175):0.00274175,3_1632:0.00491525); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed2c36f93d4af4fc20c58382a85bfb0297b8c407 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt @@ -0,0 +1,2 @@ +(((0_857:0.57097125,3_1626:-0.00023225):0.00023225,4_1848:-0.00023225):0.00023225,2_793:0.01153225,1_1921:-0.00023225); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..84d93300d7346e94a879b5a2b7624d4b2b41488d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt @@ -0,0 +1,2 @@ +((3_1624:0.00579373,(4_1846:0.00000000,1_1919:0.00000000):0.00394627):0.01577274,2_795:0.01061617,0_859:0.23341883); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a59ac2c04909c947d6aaccceef9bd6cde4b63f89 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1622:0.00000000,2_797:0.00000000):0.00126000,1_1917:0.00555800):0.00214450,0_861:0.45401000,4_1844:0.00638800); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..13bcd3444d5428162bb062ec2e4fea2d494555f1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt @@ -0,0 +1,2 @@ +((1_1912:0.00616200,(0_867:0.04305500,2_809:0.31651800):0.05912350):0.00482000,4_1839:0.00000000,3_1617:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab140e18ab8202322ce059f6cec33a9c683d81d1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt @@ -0,0 +1,2 @@ +(1_1910:0.00736232,(3_1615:0.01109396,(2_811:0.34136100,0_869:0.01451400):0.01136032):0.00217104,4_1837:0.00525768); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92feb632129cfdf9b50a46f4e7d31f496f814911 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt @@ -0,0 +1,2 @@ +(1_1906:0.01504959,((3_1611:0.06781967,0_873:0.01150933):0.00830739,2_814:0.88447718):0.00508232,4_1833:0.00422441); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ab361805293f62fd6a688af39c68cbd7fae05dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt @@ -0,0 +1,2 @@ +((1_1903:-0.07526856,0_874:0.42664156):0.08206264,(2_422:0.94109800,2_815:0.78648200):0.28196622,4_1830:0.01119892); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f407ce9abf1894626ea6e67f1def217edbae96d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt @@ -0,0 +1,2 @@ +(4_1813:0.01379588,(2_826:0.00578762,(2_278:1.64784713,1_1891:1.14837787):1.02769438):0.00498087,0_886:0.01381712); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc1989f33aee25785869a1ec1474e89e52ef312b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt @@ -0,0 +1,2 @@ +((0_914:0.00905800,(2_846:0.05770900,1_1867:0.00135000):0.00584450):0.00901300,4_1787:0.00000000,3_1574:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000617_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000617_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..21e50c5acfbcc2bccee2ece2368e83d740d5a8ff --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000617_tree_id.txt @@ -0,0 +1,2 @@ +((1_1851:0.02372625,(3_1558:0.00284400,4_1772:0.00402900):0.00776325):0.14690725,2_865:0.11676025,0_923:0.19099575); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fdd597cf396016b82a41100f4ef0993c5df5ac55 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt @@ -0,0 +1,2 @@ +((1_1849:0.00000000,4_1770:0.00000000):0.00000000,(0_929:0.00000000,2_870:0.00000000):0.01336300,3_1556:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd40f9528917d284b5883a18e541064251aeadc8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt @@ -0,0 +1,2 @@ +(1_1831:0.00692310,(3_1538:0.01604503,(2_886:0.22569983,0_947:0.07700917):0.03640784):0.02227097,4_1752:0.00338290); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e5a36db3f94bb37b8c15845198296ca9f3424f7b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt @@ -0,0 +1,2 @@ +((3_1536:0.00739413,4_1750:0.00575187):0.03181587,(0_949:0.07660312,2_888:0.38509888):0.03918338,1_1829:0.08435713); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c7fc223804c9aa3309f9a11ff50b59fbb1d02e6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt @@ -0,0 +1,2 @@ +((0_958:0.11167300,2_899:0.41036000):0.11989900,(3_1528:0.00000000,1_1821:0.00000000):0.01104800,4_1742:0.00805400); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae8e5f41f877fad331b3a38737dd2e88a68e256c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt @@ -0,0 +1,2 @@ +((2_901:0.04917742,(0_962:0.00299442,1_1817:0.00617758):0.00187047):0.01298278,3_1524:0.00337083,4_1738:0.00283717); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000651_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000651_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..86e09c3c085490f102a211fae06b00fa2c16935d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000651_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1809:0.00025355,4_1730:0.01128245):0.00651524,3_1516:0.00311774):0.07793277,0_971:0.06923317,2_910:0.13774783); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa3174f6b4196c559f4a3642a8453ab1e512e8ce --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt @@ -0,0 +1,2 @@ +(2_966:0.44571100,((1_1763:0.00000000,4_1685:0.00000000):0.04552850,3_1471:0.01392750):0.03932450,0_1026:0.07351500); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ff3e7c1cb1344d209cec93ba9b8edd86dec6a55 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt @@ -0,0 +1,2 @@ +(4_1683:0.00528488,((0_1028:0.14088387,2_968:0.13041212):0.09927888,3_1469:0.01848063):0.00288137,1_1761:0.00835912); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c1da0fdbcb39b5d349c0a21bab02b1a1e67b04cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt @@ -0,0 +1,2 @@ +((4_1678:0.00088407,(1_1756:0.00111440,3_1464:0.00683560):0.00314710):0.02036763,2_974:0.07717983,0_1038:0.02153517); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb06294e7e86bfff95ac976226a15fbe8eac9c45 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt @@ -0,0 +1,2 @@ +((1_1753:0.00000000,(4_1675:0.00000000,2_977:0.04660600):0.00000000):0.00000000,3_1461:0.00000000,0_1041:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..14e3148055e502f5dbb2f407352a8ce9ba570d58 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1743:0.00619749,4_1665:0.00396451):0.00724045,0_1050:0.00853027):0.02784696,2_987:0.22318083,3_1451:0.01680217); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..680f71a4769be6ea6c9e78d51933aab4f45ab1dc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt @@ -0,0 +1,2 @@ +((1_1741:0.01057642,(4_1663:0.00600101,2_989:0.00558999):0.00137291):0.00511703,0_1052:0.00491633,3_1449:0.01042267); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..18ee4dbbeceed2a9e60a096d6774e898fec8fa6f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1072:0.05762150,2_996:0.14749950):0.04351850,1_1727:-0.00022650):0.00022650,4_1656:0.00844050,3_1444:-0.00022650); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6295f32b2f219c68630b8f38530e38071bca70c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt @@ -0,0 +1,2 @@ +(4_1647:0.00163959,(1_1718:0.00434776,(2_1005:0.15973633,0_1080:0.05462467):0.05287092):0.00448174,3_1435:0.00110641); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..31c43b6e31058d525fa0bda684bfdd01473faffb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1697:0.00000000,3_1414:0.00000000):0.01712678,4_1626:0.00376922):0.04845724,0_1101:0.05837450,2_1027:0.08527550); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a3a693ad3c0ea33412146d07f1ac0a8fcad6fbb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1034:0.20395050,0_1105:0.05840850):0.08373750,1_1693:0.00000000):0.00000000,4_1622:0.00000000,3_1410:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d8b8b69ba2a19da426cf3a4357dc7b4d3e33ef5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt @@ -0,0 +1,2 @@ +(1_1685:0.00058550,((2_1043:0.04730475,0_1113:0.03116725):0.02488375,3_1402:0.00049125):0.00279975,4_1614:0.00234050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebb5f7c84d03e15a4f423cb1a1df734791d5ee5e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1607:0.00000000,3_1395:0.00000000):0.00000000,1_1678:0.00000000):0.01011700,0_1121:0.01019400,2_1051:0.03267700); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d71b4195d64e73b6f5b8d6970a2f9d5d4f8a0833 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt @@ -0,0 +1,2 @@ +((2_1070:0.02436900,(1_1660:0.00000000,4_1589:0.00000000):0.00000000):-0.00000000,0_1139:0.00000000,3_1377:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..57eea0a39d36170775b8fc63df28b4c9369bb83a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt @@ -0,0 +1,2 @@ +((3_1369:-0.00002263,(2_1078:0.03158362,1_1652:-0.00002262):0.00002262):0.00002263,0_1147:0.00392863,4_1581:-0.00002263); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000793_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000793_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..520b22b312e7e9488616eef31490fad03896c57f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000793_tree_id.txt @@ -0,0 +1,2 @@ +(3_1361:-0.00087368,((2_1086:0.11284200,0_1155:0.02894400):0.05268486,1_1644:0.00465857):0.00724643,4_1573:0.00814768); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..036296c47a2ec4eaccbc60ec9ebd6cba3c848ed8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt @@ -0,0 +1,2 @@ +((1_1640:0.00000000,(2_1090:0.03546050,0_1159:-0.00044950):0.02085850):0.00000000,3_1357:0.00000000,4_1569:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb5331a3d973148defa06d29e8634c2b565accd3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1220:0.06212817,2_1132:0.25989683):0.05658771,3_1309:0.00520363):0.00218337,1_1594:0.00267141,4_1524:0.00911259); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a7c98fc8ff346cdc09e655b7249569d1e061b932 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt @@ -0,0 +1,2 @@ +((4_1522:0.02560889,(1_1592:0.00359277,3_1307:0.03252023):0.00620961):0.04387812,0_1222:0.05772983,2_1134:0.14109317); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0393f55ee69cefc5561e70f6a526e802c01a81e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt @@ -0,0 +1,2 @@ +((4_1518:0.02553462,(3_1303:0.05899662,1_1588:0.01426037):0.02086037):0.20041388,0_1226:0.24092963,2_1138:0.99197837); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc855552dbff3412e50864bee671736b50c072a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt @@ -0,0 +1,2 @@ +(4_1508:0.02416837,((2_1147:0.33469063,0_1237:0.32337237):0.33989463,1_1579:0.00959438):0.00928662,3_1294:0.00375462); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5920915b020b438338272681fa83910d7155b662 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt @@ -0,0 +1,2 @@ +((3_1270:0.00023829,(1_1548:0.00000000,4_1475:0.00000000):0.00354371):0.01046443,0_1267:0.08203633,2_1176:0.01026167); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..55f91cd094c2f54dd5790d752498867d2d3ef367 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt @@ -0,0 +1,2 @@ +(3_1267:0.00230375,(1_1545:0.00090600,(0_1269:0.00230225,2_1179:0.00136775):0.01204700):0.00093550,4_1472:0.00506325); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb05df89b8692eaee0db7789e6cf13bd34e4c444 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt @@ -0,0 +1,2 @@ +(1_1544:0.00000000,((2_1180:-0.01446450,0_1270:0.96905550):0.03370800,4_1471:0.00395500):0.02893000,3_1266:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec63533dfbf5588729b64c156b99bfa389d90e32 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt @@ -0,0 +1,2 @@ +(1_1520:0.00127000,((2_1219:0.22230300,0_1325:0.15776100):0.13115175,4_1447:0.00677225):0.00151125,3_1240:0.00173300); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..88fa3d22e142007fc5ab72a5975c9ea0e753d899 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt @@ -0,0 +1,2 @@ +(4_1443:0.00571659,((0_1329:0.12623817,2_1223:0.76407183):0.08545224,3_1236:0.02922822):0.01879428,1_1516:0.00292941); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d7217b4f3000430b103207d8c25a066fd49e0d6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt @@ -0,0 +1,2 @@ +(2_1225:0.24393000,((1_1514:0.00000000,3_1234:0.00000000):0.02180250,4_1441:0.02834450):0.01012350,0_1333:0.02253100); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..be36ad70921ce0b5b4e4f28ac34691b07ca24cdc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1203:0.00227400,1_1483:0.00837100):0.00518275,4_1410:0.00549375):0.03768325,0_1363:0.05016475,2_1255:0.14501625); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cd0264dfaa30b10f620fdfc511172bbdd0cdc38 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1182:0.00000000,1_1463:0.00000000):0.00111429,4_1390:0.00179071):0.01916457,2_1283:0.13918300,0_1383:0.03943300); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c738e71cf5cea3ad2908459a7f3bb6ec83953436 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt @@ -0,0 +1,2 @@ +((4_1388:0.05215669,(1_1461:0.00000000,3_1180:0.00000000):0.06051331):0.11115956,0_1385:0.27502333,2_1285:0.50468567); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec1ba2ce3c19eea234341dabb2acf12b568344d9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt @@ -0,0 +1,2 @@ +((4_1386:0.00400546,1_1459:0.00345754):0.00078852,(2_1286:0.41513350,0_1387:0.11422850):0.08338099,3_1178:0.00145749); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a715432cc15cd54468c39ead37a7f9a61f551e9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1168:0.00000000,1_1427:0.00000000):0.00000000,4_1376:0.00000000):0.37471200,0_1397:0.24429700,2_1297:0.19975600); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8d1aad950776d688482c2bef6ace5412e201768 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt @@ -0,0 +1,2 @@ +((3_1157:0.00862378,(4_1365:0.01293601,1_1416:0.00515499):0.01020062):0.18005473,0_1406:0.18814500,2_1308:0.38876900); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f27cf46384f9431effd5a0c8b485d5af653f23ad --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt @@ -0,0 +1,2 @@ +(1_1412:0.00000000,(3_1153:0.01380325,(2_1313:0.54536025,0_1410:0.31051775):0.27198775):0.00779575,4_1361:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..23b7b9f14c8d658f301eaec1dd3f3642d6022bae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt @@ -0,0 +1,2 @@ +((0_1418:0.03249991,(2_1321:0.09140050,3_1145:0.02121250):0.01309250):0.04887409,4_1353:0.00000000,1_1404:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..586db6d8230818672357874d2ab8eae1a4f0a84b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1351:0.00000000,1_1402:0.00000000):0.00000000,3_1143:0.00000000):0.01248450,0_1420:0.00822050,2_1323:0.02936250); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..188eed03831495f3428b58c9f596f61250b98b96 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt @@ -0,0 +1,2 @@ +((4_1346:0.06809775,(3_1138:0.00000000,1_1397:0.00000000):0.01889925):0.09666775,0_1424:0.11793875,2_1328:0.39673725); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c75a7771b09f0c9f632482d1aa5cdfd3ef762aa4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt @@ -0,0 +1,2 @@ +((3_1128:0.00737513,(4_1336:0.00115538,1_1387:0.00118463):0.00402787):0.06943188,2_1341:0.23900837,0_1433:0.08824563); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0f3b23b2a381cc993224b9e61a08e8dcf3a70c8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt @@ -0,0 +1,2 @@ +((4_1334:0.00923049,(1_1385:0.00632438,3_1126:0.00566762):0.00258057):0.09433591,2_1343:0.16526317,0_1435:0.06252283); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f3950667926beb5c671c06da4090f4b3043849a7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt @@ -0,0 +1,2 @@ +(4_1326:0.00329352,(1_1377:0.00336109,(0_1444:0.05070233,2_1351:0.20412067):0.05486603):0.00341591,3_1118:0.00293448); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3561e0bfbd1ed0af0ee5aaece5c08fe943609078 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1460:0.01016100,2_1371:0.11239300):0.02216700,4_1307:0.00000000):0.00000000,3_1097:0.00000000,1_1358:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c2b09fca3331732d85a535899be9b14dc2e62186 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt @@ -0,0 +1,2 @@ +((1_1354:0.02502674,(4_1303:0.00000000,3_1093:0.00000000):0.08874426):0.12392425,0_1463:0.45950933,2_1375:1.15466467); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..55accc035b2b8af4e0c4366dfd23903d653a21f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt @@ -0,0 +1,2 @@ +((3_1062:0.00389134,(0_1481:0.05803417,2_1376:0.20889483):0.06141828):0.01428466,1_1333:0.00000000,4_1287:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..69410e95bc6069e67912d80da7d27e6cf29f45a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt @@ -0,0 +1,2 @@ +((1_1327:0.00253813,(0_1487:0.00330813,2_1382:0.10895988):0.00297788):0.00312537,3_1056:0.00123637,4_1281:0.00320263); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3b9c62e18fd7d939110a2e703074d93cb4e2f23 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt @@ -0,0 +1,2 @@ +(3_1048:0.00000000,((0_1496:0.09612525,2_1391:0.19691475):0.05412725,4_1273:-0.00004675):0.00970175,1_1319:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d154b55554e9dec632d11dc41a17fcf469a1b6ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt @@ -0,0 +1,2 @@ +((4_1271:0.00699375,(1_1317:0.00341600,3_1046:0.00333000):0.00315475):0.12209625,2_1393:0.36644975,0_1498:0.10831925); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5cc51452807ee2d3e98c2e2d51d6ae07bbacae34 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1269:0.00000000,1_1315:0.00000000):0.00136975,3_1044:-0.00136975):0.00694575,0_1500:-0.00074875,2_1395:0.09675075); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e751c6a3f975a135032ff347f8e344bb751cdc9b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt @@ -0,0 +1,2 @@ +((3_1035:0.00085688,(4_1260:0.00720737,1_1306:0.00055762):0.00162813):0.05662562,2_1404:0.20695262,0_1508:0.04316738); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b29e14e2e57547c602251037a55bf2e4e55f007 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1257:0.01019850,3_1032:0.01729750):0.00724100,1_1303:0.01248000):0.02938800,0_1511:0.03723750,2_1407:0.05898250); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4dc24832fab033f2968872177bdf01f46e85ba92 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt @@ -0,0 +1,2 @@ +((2_1410:0.30871017,0_1514:0.14944883):0.09781353,(3_1029:0.02215099,1_1300:0.01078701):0.02584396,4_1254:0.01907802); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..791fc8db27d253f198c9c99f0c469576e96685e1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt @@ -0,0 +1,2 @@ +(3_1017:0.01243687,((0_1526:0.05350762,2_1422:0.26592237):0.03974387,1_1287:0.01416663):0.00410937,4_1242:0.00242613); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5b14611e9431dae9f3895c9575ccce2b89f3bf14 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt @@ -0,0 +1,2 @@ +((1_1284:0.00000000,3_1014:0.00000000):0.00000000,(4_1239:0.11198850,2_1425:0.24804950):0.12119950,0_1529:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d8bde4fa6aeb1fad15699af5b59531b111079d5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt @@ -0,0 +1,2 @@ +((0_1532:-0.00006663,(1_1281:0.00216262,3_1011:0.00741738):0.00005862):0.00006662,4_1236:-0.00006662,2_1428:0.16884462); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..770f9b5cdf4d0e8b6b24484054ca32b24d9350d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt @@ -0,0 +1,2 @@ +(4_1228:0.03221161,(1_1273:0.03058764,(0_1540:0.03739283,2_1436:0.14086817):0.05470571):0.01211636,3_1003:0.02424639); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..256332ae56812e1f3af6dcc7f62ca087dee12814 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt @@ -0,0 +1,2 @@ +(4_1218:0.00000050,(1_1261:0.01383775,(2_1449:0.18410425,0_1553:0.04441775):0.05362975):0.00426375,3_993:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..549b01ab93f06de2cb1dab38aa1b85ea1c310e84 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt @@ -0,0 +1,2 @@ +((3_987:0.00000000,1_1255:0.00000000):0.00000000,(2_1455:0.20422550,0_1559:0.05541850):0.04453850,4_1212:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0311455f0295ce1d68a263efea1582b3b336d7d8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt @@ -0,0 +1,2 @@ +((1_1254:0.00000050,(0_1560:0.07471350,2_1456:0.38092650):0.10819200):-0.00000000,3_986:0.00000050,4_1211:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4850187c12cff07f89c29b486a97f89b08d109a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt @@ -0,0 +1,2 @@ +(3_979:0.00000000,(4_1204:0.00056660,(0_1567:0.01073217,2_1463:0.05731783):0.01403470):0.00083840,1_1247:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a91d3cedd1f2eb05a283a74b5d92d03d34b21dc1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt @@ -0,0 +1,2 @@ +((3_961:0.00244312,(1_1233:0.00731212,4_1190:0.00043388):0.00032588):0.12293238,0_1575:0.08145813,2_1470:0.20106288); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a494fe763675f7ee4af1104483d52d33a091f81 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt @@ -0,0 +1,2 @@ +(4_1183:0.00000000,(1_1226:0.00429683,(0_1583:0.09782233,2_1478:0.25122467):0.04000594):0.00345517,3_954:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d06631cab1447b9e7319e1bc142c47f50aebb8bc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt @@ -0,0 +1,2 @@ +((1_1203:0.00318175,(3_931:0.00060725,4_1161:0.00130175):0.00514325):0.03132075,0_1607:0.02249800,2_1504:0.05298000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e62ba21d2087d546119c4c3d3e68f3e33ec0f887 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt @@ -0,0 +1,2 @@ +((4_1158:0.00000000,1_1200:0.00000000):0.00000000,(2_1507:0.05546250,0_1610:0.01573550):0.05422350,3_928:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..16bfa6b232d20e6337005850f666fe71ba1700a9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt @@ -0,0 +1,2 @@ +((4_1136:0.00689012,1_1178:0.01043688):0.01259963,(0_1633:0.20950388,2_1530:0.38811212):0.21976363,3_906:0.02223987); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7df165321cd366939d229d9c59b6d474f0ee33ef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt @@ -0,0 +1,2 @@ +((4_1135:0.00046577,3_905:0.00244823):0.00383651,(2_1531:0.06430667,0_1634:0.01334933):0.01492758,1_1177:0.00588041); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe6accb3aca54db0a4e503c426fe0626d385a125 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1133:0.00594816,1_1175:-0.00053116):0.00053116,3_903:0.00000000):0.05413862,2_1532:0.41922450,0_1636:0.05334150); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..76b0c8074bfedc86bbb32d87c5b577a3be8d6b43 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt @@ -0,0 +1,2 @@ +((4_1125:0.00000000,1_1168:0.00000000):0.00198375,(0_1643:0.05596725,2_1539:0.25209975):0.06993675,3_896:0.00610225); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e354a9b8a37f31c7825950a860decee3945917f0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1547:0.19630737,0_1650:0.05435963):0.04883487,3_888:0.01111462):0.00239488,4_1117:0.00990262,1_1160:0.01028837); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e71b25a11e9c20d559e962784e4f1919d654187b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1116:0.00074875,3_887:-0.00074875):0.00074875,1_1159:-0.00074875):0.01151575,0_1651:0.01418575,2_1548:0.02485325); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d26cd2776458c7a0ca77ef839a1ed7c52c1d5b87 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1151:0.00000000,3_880:0.00000000):0.00000000,4_1105:0.00000000):0.00455200,2_1555:0.06463800,0_1659:0.01199600); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b766200ac2683720d1db9acc8033abe1b5c77a5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt @@ -0,0 +1,2 @@ +((0_1661:0.03105713,(2_1558:0.13046912,4_1103:0.00306687):0.00477738):0.00484687,3_878:0.00039862,1_1149:0.01096537); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..77a49f582d0d36a21322a676635c14fa13b024c4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt @@ -0,0 +1,2 @@ +(3_877:0.01896210,((0_1662:0.26874067,2_1559:0.55690233):0.18815623,4_1102:0.02170269):0.00719581,1_1148:0.02139290); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..072dbac7b4062c5587ba4507f7ea071e5b7b9f1a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt @@ -0,0 +1,2 @@ +((1_1147:0.08975062,(4_1101:0.11970737,3_876:0.08384963):0.02918987):0.52267687,0_1663:0.77781263,2_1560:0.74278437); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..587d7f1102382b76970f7037a6bb56fb0a2cce4a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1128:-0.00000888,4_1078:0.00465388):0.00014662,3_856:0.00542887):0.01756662,0_1684:0.02276712,2_1581:0.24523087); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3af809ffe11e99b85b565d2b6c06805057e9309c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt @@ -0,0 +1,2 @@ +((1_1113:0.00148747,4_1063:-0.00003147):0.00003197,(2_1596:0.18156250,0_1699:0.05906850):0.06659337,3_841:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..27ec0e4616958b16d1e4f468d2da129829d290a1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt @@ -0,0 +1,2 @@ +((1_1105:0.00215050,(2_1603:0.10141350,0_1710:0.22610050):0.07581400):0.00366350,4_1055:0.00000000,3_833:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..94a2ca4cd07af7670724f9ca91c986d438ab4628 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1033:0.00000000,3_811:0.00000000):0.00000000,1_1083:0.00000000):0.02479350,0_1732:0.01935350,2_1625:0.07660650); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..061d0661ce57a668a1b9bebcb92f7f467d0bc089 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt @@ -0,0 +1,2 @@ +((4_1031:0.00778975,(1_1081:0.00000050,3_809:0.00000050):0.00164375):0.08924875,0_1734:0.22359225,2_1627:0.39897375); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..787997da8983b6b0519705de9b0ab7d678f40cf5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt @@ -0,0 +1,2 @@ +((0_1748:0.02010200,2_1640:0.09550600):0.01438484,(4_1018:0.00118125,3_796:0.00058875):0.00186349,1_1068:0.00247184); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bba0ac27bab1d75ec4a3ac0e6cf548a06ce94d7e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt @@ -0,0 +1,2 @@ +((4_1006:0.00000000,(0_1760:0.00962200,2_1650:0.03453600):0.00484100):0.00000000,1_1057:0.00000000,3_785:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e65d9ac15bc611a0f06e2ec17a0a2ade2b631ff7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt @@ -0,0 +1,2 @@ +((2_1657:0.19587767,0_1768:0.14274233):0.09894141,(4_999:-0.00012794,1_1050:0.00109894):0.00012794,3_778:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8460cafd4cf0e8fa0e7fc275702daa6418035a6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt @@ -0,0 +1,2 @@ +((4_997:0.00174288,3_776:0.00025712):0.00041038,(0_1770:0.46174988,2_1659:0.19380712):0.10472987,1_1048:0.00173513); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..84dfd54e558356e193abf4758abb5380c91e94a6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt @@ -0,0 +1,2 @@ +((0_1776:0.25107483,2_1664:0.10677817):0.07675995,(3_771:0.00000000,4_992:0.00000000):0.00321165,1_1043:0.01307335); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..12e6bd81ca1b4258c1077a90ccac824c009fdb4f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt @@ -0,0 +1,2 @@ +((4_988:0.00000000,3_767:0.00000000):0.00667975,(0_1781:0.12898675,2_1668:0.42343025):0.11414175,1_1039:-0.00183675); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5b5a5b7086b6bdbe79f7740af7968af6ce13d50a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt @@ -0,0 +1,2 @@ +((3_766:0.00000000,4_987:0.00000000):0.00937476,(0_1782:0.45132767,2_1669:0.37533733):0.23898408,1_1038:0.00186124); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f2672abe9c99cb7a7dbd042a7a80e0d620ebfef --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt @@ -0,0 +1,2 @@ +(((3_749:0.00000000,4_968:0.00000000):0.00357701,1_1021:-0.00022101):0.07641983,0_1789:0.07171583,2_1677:0.16207417); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..765a5b87e487def113b5eb3025248041ec7a62cb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt @@ -0,0 +1,2 @@ +(4_965:0.02062375,(3_746:0.01222375,(2_1680:0.24905275,0_1791:0.29362225):0.12976425):0.00889625,1_1018:0.01183525); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7e69cc8c6317745f5a5b21091ae54a84cae73e2f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt @@ -0,0 +1,2 @@ +((3_744:0.00918737,1_1016:0.00024663):0.00880713,(0_1793:0.06519938,2_1682:0.16773963):0.02461463,4_963:0.00790837); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1e56843b2a574df8bdb3691027c37a17df22744 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt @@ -0,0 +1,2 @@ +(((4_960:0.01100350,3_741:0.00004650):0.00437050,1_1013:0.00533000):0.05821800,2_1685:0.22661800,0_1796:0.09311600); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..27b7890c02e563b1b73a9427c4d92b64c24c5f2b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt @@ -0,0 +1,2 @@ +((4_944:0.00796162,1_1003:0.00092738):0.00230637,(0_1809:0.02834413,2_1695:0.23876987):0.05367537,3_725:0.00437513); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff7828368a0db28ebaa3082ae9bfb1081a0a7a24 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt @@ -0,0 +1,2 @@ +(((1_995:0.00891963,3_717:-0.00005563):0.00420138,4_937:0.00580113):0.00030438,2_1701:0.00048162,0_1812:0.01279338); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7164cb1cf983df3b514a09d1d9a7c4755ebed853 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt @@ -0,0 +1,2 @@ +((4_901:0.00000000,1_958:0.00000000):0.00000000,(0_1855:0.05554150,2_1800:0.16495550):0.02553450,3_681:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8e73610b329ead18d2a56ad78b8bea592cc737a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt @@ -0,0 +1,2 @@ +(0_1860:0.00532075,((1_952:0.00468800,2_1806:0.00675400):0.00296425,3_675:0.00499825):0.00168275,4_895:0.00801625); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..266f33c1f10d8d04686e27652e3b4fe47a2108ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt @@ -0,0 +1,2 @@ +(((3_662:-0.00021162,1_939:0.00256462):0.00021162,4_882:-0.00021163):0.01821313,2_1820:0.06505562,0_1874:0.01284437); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1a9b7773f209f151d2d1ff650e3ff1dc0b6bd71 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt @@ -0,0 +1,2 @@ +(3_652:0.00793703,((0_1881:0.07060350,2_1828:0.21659950):0.07781348,1_930:0.00605393):0.00179907,4_876:0.00914497); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..562390c3444c867f956f1621218cec1eb5f98b32 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt @@ -0,0 +1,2 @@ +((4_848:0.00535432,(3_627:0.00438715,1_899:0.00159785):0.00121917):0.01933528,2_1860:0.10891083,0_1965:0.01860617); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..803ac7ced2684b4e72fd4e12917d5eba8cf430ae --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt @@ -0,0 +1,2 @@ +(((1_897:0.00000000,3_625:0.00000000):0.00000000,4_846:0.00000000):0.01467050,2_1864:0.35122950,0_1967:0.14397250); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..073ef53fb0aa642cf4e989be09224915b0d1dde6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt @@ -0,0 +1,2 @@ +(((3_623:0.00081912,1_895:0.01771788):0.00447860,4_843:0.00260327):0.07141393,2_1867:0.26892300,0_1969:0.06834500); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c3b7f90ec6cd52fdf5709630b19ebf5009935de --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt @@ -0,0 +1,2 @@ +(1_886:0.00021338,(3_614:0.00243963,(0_1979:0.02204987,2_1877:0.11921513):0.02623638):0.00163837,4_834:0.00228663); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..01267b3a5a0e269e1bd12a19d95a6abfaabd6906 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt @@ -0,0 +1,2 @@ +((1_877:0.00737662,(4_825:0.00946688,3_605:0.00816512):0.00670588):0.09176187,0_1989:0.16783687,2_1886:0.31335813); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd0d81cf09b61fd902c32f94150b984b1273047b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt @@ -0,0 +1,2 @@ +((4_821:0.00000000,1_873:0.00000000):0.00000000,(0_1993:0.00295200,2_1890:0.08909600):0.01012000,3_601:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..36adeee670ee9da8ca6b6ea5c8fbe7db55ec8b0f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt @@ -0,0 +1,2 @@ +((1_872:0.01928350,(4_820:0.00000050,3_600:0.00000050):0.00100100):0.00319150,2_1891:0.07000800,0_1994:0.05556900); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a38ec504d99d8d53a9f3109e3631e36d5e4227e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt @@ -0,0 +1,2 @@ +((2_1895:0.07512688,1_867:0.10475413):0.13023313,(4_816:0.05843213,0_1998:0.04025088):0.00675762,3_596:0.06421937); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..350d699303482a6d7a88647139b6d39e5296fede --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt @@ -0,0 +1,2 @@ +(((1_863:0.00540750,3_594:0.00249050):0.12593600,0_2000:0.19048050):0.22126400,4_814:0.69237925,2_1897:0.43842275); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a0a07438d09a1f4931d5350ffdcc6788fa118d0 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt @@ -0,0 +1,2 @@ +(3_574:0.00502064,(4_802:0.00185178,(0_2016:0.03295133,2_1909:0.15883567):0.05415626):0.00236122,1_843:0.00255836); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dcfb5248e9bf7207f8943aba2cb6bf09e72bd7aa --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt @@ -0,0 +1,2 @@ +((4_801:0.00093500,(1_842:-0.00014300,3_573:0.00837300):0.00236300):0.04947750,0_2017:0.04693300,2_1910:0.18226000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d9c64bee1d84baf62d23dce62649a861749dfc3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt @@ -0,0 +1,2 @@ +(1_836:0.00642663,((0_2023:0.08101962,2_1916:0.30703437):0.04802562,4_795:0.00138488):0.00750663,3_567:0.00156737); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..260ebcbdc3795595ddf848ae1b0e7b9dfdf0a0da --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt @@ -0,0 +1,2 @@ +((1_834:0.00845287,(3_565:0.00616638,4_793:0.00424463):0.00079713):0.03729913,2_1918:0.20251612,0_2025:0.04589987); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b1ff6c6ed7aec1b141f82db3e51285f1aeb9018 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt @@ -0,0 +1,2 @@ +(1_831:0.00000000,((2_1921:0.14935883,0_2028:0.01225817):0.02592749,3_562:0.00785097):0.00586903,4_790:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bee1f6f3f79a7ac059b0213be7c28cbd40f34dd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt @@ -0,0 +1,2 @@ +((4_781:0.00000000,3_553:0.00000000):0.00810100,(2_1930:0.05157050,0_2036:0.02268250):0.01772050,1_822:0.00316700); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9990811fdb7ba11c0688db47d131b1356129a74 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt @@ -0,0 +1,2 @@ +(4_762:0.00157868,((2_1951:0.21477800,0_2061:0.11864500):0.09016358,1_793:0.01265573):0.00676227,3_534:0.00001132); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2baf78363512cd151567de196912c8c43a9b9ac --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt @@ -0,0 +1,2 @@ +((1_788:0.00423212,(4_757:0.00161188,3_529:-0.00047488):0.00318138):0.04148188,0_2066:0.07720713,2_1956:0.20445487); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..93c2794819b08dd93f609a1d79ce7af6569da166 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt @@ -0,0 +1,2 @@ +(4_756:-0.00028850,((2_1957:0.11339325,0_2067:0.03191775):0.03777750,1_787:-0.00028850):0.00028850,3_528:0.00028850); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dbfc06c24f301fbdb1d72dde4bb42176a3c6f30c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt @@ -0,0 +1,2 @@ +((1_779:0.00531975,3_519:0.00145125):0.00118425,(0_2075:0.04329675,2_1967:0.08404025):0.01841225,4_746:0.00305225); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..839555ea8f54c5d5172dc4a494a984d492185c1a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1992:0.06958300,0_2099:0.01450800):0.02380850,4_722:0.00000050):0.00000000,3_495:0.00000050,1_755:0.00000050); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ef2aa0b6ceca9673a880415716a27166a357c3c3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt @@ -0,0 +1,2 @@ +((2_1997:0.23314683,0_2103:0.02158117):0.01844766,(4_718:0.01580477,1_751:0.00451623):0.00528582,3_491:0.01276974); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001479_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001479_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a812e9eca5af7f96a5a17869ea1a0f217f91c47c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001479_tree_id.txt @@ -0,0 +1,2 @@ +((3_486:0.00138912,(0_2108:0.04900437,2_2002:0.28148662):0.03580337):0.00348788,4_713:-0.00041162,1_746:0.00236262); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001483_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001483_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7128977ced51c9d1ecb17cf8dddf0dfbf7de95e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001483_tree_id.txt @@ -0,0 +1,2 @@ +(((1_740:0.00252237,4_704:0.00186863):0.00206262,3_479:0.00676738):0.06616562,2_2008:0.10159913,0_2113:0.08313188); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad422145703ff91213799789639437348f2de469 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt @@ -0,0 +1,2 @@ +(1_738:0.00000000,(4_702:0.00617925,(2_2010:0.17454325,0_2115:0.07133675):0.07146425):0.00261275,3_477:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a26bcd664a55c2e6007b3103c3d8700d31e9a6b7 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt @@ -0,0 +1,2 @@ +((3_467:-0.00022437,(1_728:0.00636138,4_692:-0.00022437):0.00022437):0.03211988,0_2126:0.02212012,2_2020:0.13202487); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bcaa680d529879226fea6b72731222110787316 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt @@ -0,0 +1,2 @@ +((3_450:0.02809801,(1_710:0.01087386,4_674:0.01917714):0.01530101):0.08181531,0_2144:0.08223633,2_2042:0.35580267); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a73ac21411148385ba023101eb5396eef3733db9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2061:0.15880050,0_2190:0.03744550):0.03442803,3_432:0.00893158):0.01137842,1_692:0.00000000,4_656:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..63850623a505b0b41f2a1fa381be06b94d943c99 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt @@ -0,0 +1,2 @@ +((4_633:0.00051698,(3_409:0.00000000,1_663:0.00000000):0.00302502):0.03223416,0_2216:0.02833350,2_2084:0.11250950); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ec5a5a8293f8622387b63dbbbdec9520fc66f0b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt @@ -0,0 +1,2 @@ +((3_406:0.00267500,(1_660:0.00000000,4_630:0.00000000):0.00866100):0.19856800,0_2221:0.18445500,2_2087:0.21933700); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3630e44b47362c1245d67f10375a9203547182a2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt @@ -0,0 +1,2 @@ +(1_658:0.00000000,(4_628:0.00235275,(0_2229:0.06204125,2_2089:0.18216475):0.08819425):0.00391425,3_404:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..67eebf6217f4a808e5de35380e10bdc2c7ce24a3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt @@ -0,0 +1,2 @@ +(((1_634:0.00188074,3_380:0.00449426):0.02572757,4_604:0.02304627):0.04193030,2_2108:0.39900600,0_2253:0.08859500); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1a9edaf875293887e138643d2c4b0f4767a4ac5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt @@ -0,0 +1,2 @@ +((0_2262:0.32488700,2_2118:0.52356400):0.23078530,(3_371:0.02040163,4_595:0.00998937):0.04279658,1_625:0.04652060); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..884d3265afdb5722b4d517222baa20d175c47edc --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt @@ -0,0 +1,2 @@ +((4_592:0.00575925,(1_622:0.00082850,3_368:0.00168750):0.00308475):0.04251025,0_2265:0.02341325,2_2123:0.21773175); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c4728de986feb5c74d72d2b565cf26d38d43331 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt @@ -0,0 +1,2 @@ +(((0_2282:-0.00093712,1_160:0.01591012):0.00403637,3_343:-0.00266288):0.00550088,4_1951:0.00334887,2_659:1.52720013); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c6cd7bd16c2933cde466effe3f08b86fccc4019 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt @@ -0,0 +1,2 @@ +((2_2197:0.06028333,0_2307:0.06843667):0.02952849,(3_291:0.00716506,4_551:0.00834594):0.00211129,1_550:0.01470812); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f213b1db094386abd7b4eab2a6373e1b6a98bca --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt @@ -0,0 +1,2 @@ +((0_2324:0.05319119,(3_277:0.01119562,4_546:0.01459338):0.07940737):0.25901814,1_543:0.16845683,2_2207:0.12704317); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa7aec51056a5a09ff1cab11491bd6ecb658d349 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt @@ -0,0 +1,2 @@ +((0_2327:0.10044175,2_2210:0.21785225):0.16555075,(4_543:0.00429625,1_540:0.00502575):0.02065775,3_274:0.00364675); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ca8340348f95e4f4631d0d2f98c9eb4c4c22276f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt @@ -0,0 +1,2 @@ +(((1_536:0.01189050,3_270:0.00440750):0.00903539,4_539:0.02241370):0.03338927,2_2214:0.07990883,0_2331:0.04117417); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d06f44bb3775b9c37c7b77c35abe71b2ab901e5 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt @@ -0,0 +1,2 @@ +((3_267:0.00159974,(1_533:0.00000000,4_536:0.00000000):0.00049526):0.00878908,2_2218:0.09796750,0_2336:0.01548850); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..65e0272f1a0f1ff74805af4f774136e04b622ea1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt @@ -0,0 +1,2 @@ +((4_504:0.00722562,(0_2371:0.02851837,2_2253:0.09618963):0.00252887):0.00472388,1_504:0.00555862,3_234:0.00761638); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..03db3aa17dad50d1bf853cd7e742cba65e08aed1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt @@ -0,0 +1,2 @@ +((1_499:0.00872750,4_499:0.01381650):0.00901923,(0_2374:0.03522626,2_2256:0.01262874):0.00266863,3_230:0.01894177); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dbef94b17cdb6d77017850695626ce3381c3ad04 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt @@ -0,0 +1,2 @@ +((4_492:0.05021450,(3_222:0.02733625,0_2382:0.05006875):0.00279000):0.00455950,2_2263:0.05141475,1_493:0.05905725); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..60209e1286053c42b2763e477c4a734c93ba2b70 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt @@ -0,0 +1,2 @@ +(0_2386:0.02132962,(1_489:0.01675463,(3_218:0.08747088,2_2268:0.13817513):0.17442488):0.01094887,4_488:0.01579138); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea814afc3f05dce09f6b308e59f9b387f54986d3 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt @@ -0,0 +1,2 @@ +(4_471:0.00534412,((0_2399:0.02482362,2_2282:0.14666838):0.02086388,1_472:0.00860662):0.00097837,3_202:0.00700988); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..24b440573d82581aeac27faa87312347448e209a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt @@ -0,0 +1,2 @@ +((3_184:0.00869714,(1_457:0.00000050,4_457:0.00000050):0.00410636):0.13936121,0_2414:0.14607750,2_2297:0.49151450); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..546595a9c8a998afd0f465f74020fe3396339142 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt @@ -0,0 +1,2 @@ +(1_449:-0.00017200,((0_2422:0.13074750,2_2305:0.08570450):0.13679850,3_176:-0.00017200):0.00017200,4_449:0.00247300); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..82c4ddef02cc0a1b871c475bf608fdc66fcf3596 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt @@ -0,0 +1,2 @@ +(((4_431:0.01634138,3_158:0.03968862):0.08942687,1_428:0.06958162):0.29686238,0_2451:0.14349713,2_2323:0.45916488); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..47e76a196a2f8e04fc7e11eaa8fb7088d3dd47d2 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt @@ -0,0 +1,2 @@ +(((0_2455:0.02678433,2_2326:0.14090967):0.02171491,1_425:0.01115874):0.00072526,3_155:0.00655404,4_428:0.00194996); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..879f2fad63adc4bbf426aa981866b0dfb2606c7a --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt @@ -0,0 +1,2 @@ +((3_154:-0.00076723,1_424:0.00440923):0.01003527,(0_2456:0.10421600,2_2327:0.35657800):0.07464601,4_427:0.00047596); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab1bcb89ca90872540b12c911ecf76c468cb196d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt @@ -0,0 +1,2 @@ +((2_2330:0.11681313,0_2459:0.29290787):0.10694938,(3_151:0.00422388,4_424:0.00266513):0.00075588,1_421:0.00426213); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d33e5709d6cc3432480f1206974b8301724b8fb8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt @@ -0,0 +1,2 @@ +((3_117:0.00346400,(1_385:0.00251325,4_391:0.00558375):0.00164250):0.00596100,2_2362:0.41017675,0_2494:0.00703525); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fbb9fd4f29f22fe2cb2c96c52b1c73c80c40817d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt @@ -0,0 +1,2 @@ +(((0_2504:0.17157200,2_2375:0.38855800):0.10512541,4_382:0.00737923):0.00379077,3_109:0.01157538,1_376:0.00958762); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4f8274d1f3af2a285f1bf4f4721ba2045f22452 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt @@ -0,0 +1,2 @@ +(((0_2506:0.02721400,2_2378:0.02911400):0.02914300,4_379:0.00000000):0.00000000,1_373:0.00000000,3_106:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f58574c457f8e1178873e13ebaf2069df88e75b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2390:0.00829425,0_2518:0.08774775):0.01120675,3_93:0.00642875):0.00227025,1_360:0.00665300,4_366:0.00077600); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa5ab62905c8d766185502f2ea6af2d64f4be68b --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt @@ -0,0 +1,2 @@ +(((4_351:-0.00217150,2_2399:0.29229250):0.01323675,1_344:-0.00411075):0.01733325,0_2540:0.59526725,3_69:-0.00835325); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e06460606cbded988d90c8e472d33590d27311d --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt @@ -0,0 +1,2 @@ +((4_349:0.03379125,(3_67:0.02184300,1_342:0.06350000):0.01525575):0.13951075,2_2401:0.29597400,0_2542:0.19249300); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf503ad7c51d9b69e3b22ff9070cd222ccb9456e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2402:0.12556850,0_2543:0.19297650):0.03340211,3_66:-0.00011416):0.00011416,1_341:0.00813000,4_348:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd85d147c2d2b82f062947082e1a034d7051dac4 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt @@ -0,0 +1,2 @@ +(((3_54:-0.00021940,4_336:0.00378140):0.03710838,1_329:0.03062202):0.06133730,2_2415:0.52548883,0_2563:0.11153017); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..085b1fd7b02e3e839c6caf161c3c5959a6c21b9e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt @@ -0,0 +1,2 @@ +(4_332:0.00771230,(1_325:0.00030465,(0_2567:0.09427267,2_2418:0.66689233):0.11505288):0.00736435,3_50:0.01872670); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..de5461d33682d9948ffb4b6f17867aadd04964bb --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt @@ -0,0 +1,2 @@ +((1_323:-0.00042427,4_330:0.01036227):0.00580749,(2_2420:0.08586383,0_2569:0.05716117):0.05424507,3_48:0.00626277); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..83d8f7963481e30f8a1965335ee6724f4803af2e --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt @@ -0,0 +1,2 @@ +((4_1919:0.02243520,3_1701:0.01116580):0.00259225,(2_717:0.02134733,2_723:0.73938167):0.00830168,1_1984:0.01059398); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..951e69384e35698ee909dee794fdddea13d9a41c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt @@ -0,0 +1,2 @@ +((1_263:0.00000000,0_75:0.45316000):0.00000000,3_2229:0.00000000,4_261:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7fd06763073074667dd3408fec1bf68eefdb10ec --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt @@ -0,0 +1,2 @@ +(1_192:0.28449416,(2_135:0.18249675,2_115:1.96286725):0.11365825,0_179:0.26732884); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..43c9c84670108fc4999e347158f8292719d157f8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt @@ -0,0 +1,2 @@ +(0_220:0.22482420,(3_2110:0.00369075,1_145:0.00516125):0.04697925,4_153:0.03927080); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ad399c688ed32b81eeb01386c19b3fa1b023ce9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt @@ -0,0 +1,2 @@ +(0_251:0.47734775,(4_123:0.00700425,1_115:0.00390975):0.06340775,2_186:0.23407625); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5147c7faa5c338372029652797aff79353436b8 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt @@ -0,0 +1,2 @@ +((1_48:0.00949800,3_2012:0.00106600):0.00244300,4_43:0.00355279,0_336:0.11154321); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..03df7087694dae06bfdef8b57cd80a6af63761f9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt @@ -0,0 +1,2 @@ +(1_47:0.01401494,(3_2011:0.00573125,4_42:0.00641575):0.00512375,0_337:0.15978406); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..efc17b1f1a32b15f7b94976b100fb1956a64e6b9 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt @@ -0,0 +1,2 @@ +((2_2142:0.00714975,4_571:0.00310725):0.00018975,0_391:-0.00027021,1_610:0.00903221); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e20db5f251dbdaf0fe0ad3f55c83848be47dbb6 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt @@ -0,0 +1,2 @@ +(1_2198:0.00000000,(2_683:0.40411850,0_445:0.15344050):0.50890750,4_2130:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..04eac6b0a6fe7ef7b111bd69b5a95bb13ce1bf0c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt @@ -0,0 +1,2 @@ +(0_517:0.07451400,(3_1872:0.00000000,1_2148:0.00000000):0.04569900,0_2586:1.77901400); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0278772db60e86d47e2be3b67fea7dd01a1f9c1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt @@ -0,0 +1,2 @@ +((0_522:0.19952200,4_2087:-0.00000000):0.00000000,3_1866:0.00000000,1_2142:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9401b8d8596cf32148ab4802b844141b9f2b5590 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt @@ -0,0 +1,2 @@ +(4_2077:0.00734190,(3_1856:0.05366900,0_535:0.56645800):0.00616200,1_2132:0.01124310); 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+ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..41c6f9676e0d1b2d67c28a0a8ee9462277b542b1 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt @@ -0,0 +1,2 @@ +(0_2607:1.48600598,(0_1547:0.00451975,1_1267:0.00154825):0.94140675,2_1443:-0.46794898); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..79292799c6f4a3e161fa3d459e6cafe298a74158 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt @@ -0,0 +1,2 @@ +(1_713:0.03023643,(4_677:0.05170100,3_453:0.03559800):0.01163850,0_2141:0.55630557); 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+ diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..01b82926dfc4526f4d7a9f8d5b3d49e55c3f5d53 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt @@ -0,0 +1,2 @@ +((0_2365:0.80451750,3_241:0.04108550):0.02753000,4_511:0.02466650,2_2246:0.09073950); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a90d948020874facdbd985f1f8a44ceca1d5dde --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt @@ -0,0 +1,2 @@ +((1_44:0.00809625,2_282:0.15509075):0.00602025,4_39:0.00102038,3_2008:0.00001962); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..da6fb4f0735e4b17232bf6ef32f7204ce6b810cd --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt @@ -0,0 +1,2 @@ +(3_2249:0.00934425,(2_39:0.37975425,4_282:0.01117275):0.00676325,1_276:0.02557275); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1640311d698c1b3c0399a4ba7758f5858b22367c --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt @@ -0,0 +1,2 @@ +((1_454:0.00000000,3_181:0.00000000):0.00000000,2_2300:0.27142500,4_454:0.00000000); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f606a11c0e8f3bd72157d648117d2d1ce23b703 --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt @@ -0,0 +1,2 @@ +((1_1065:0.00413725,3_793:0.00711975):0.17821125,4_1015:0.06572190,2_1642:0.29637510); + diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e3dbc4b1e8ec1a3d29a805cfb5633680b89f17f --- /dev/null +++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt @@ -0,0 +1,2 @@ +(2_681:0.01102936,(2_1369:2.33820750,2_644:0.08158150):0.16378600,2_704:0.02496864); 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