diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..69983b87f1b351cbf1fa31788654d74ff5b6b107 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000004_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000010 0.003963 1.021863 0.000010 +1 0.000010 0.000001 0.003934 1.021834 0.000010 +2 0.003963 0.003934 0.000001 1.017795 0.003573 +3 1.021863 1.021834 1.017795 0.000001 1.021473 +4 0.000010 0.000010 0.003573 1.021473 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8251eabec47768d6ec9b7b22d85b27d40e3a420e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000010_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016522 1.171446 1.192253 0.006381 +1 0.016522 0.000001 1.472841 1.493648 0.010141 +2 1.171446 1.472841 0.000001 0.652536 1.472714 +3 1.192253 1.493648 0.652536 0.000001 1.493521 +4 0.006381 0.010141 1.472714 1.493521 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..82325834aa239216bfa15e96f367ca88db7568bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000012_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..db45069ce4f03b174ebbbea1d7634c9748f2b9e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000020_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.77881864 Before NNI: tree length is 0.78168400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 0.75837559 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..55b1488057513ae8f56600396337c9a732c7747d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000024_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033089 0.537437 0.367036 0.033582 +1 0.033089 0.000001 0.542669 0.372268 0.038813 +2 0.537437 0.542669 0.000001 0.505358 0.520985 +3 0.367036 0.372268 0.505358 0.000001 0.350584 +4 0.033582 0.038813 0.520985 0.350584 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..bd3e092b507d2be52b3953562cb6ffdd64c1654f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000025_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000662 0.026102 1.057051 0.000662 +1 0.000662 0.000001 0.026764 1.056389 0.000001 +2 0.026102 0.026764 0.000001 1.083153 0.026764 +3 1.057051 1.056389 1.083153 0.000001 0.000001 +4 0.000662 0.000001 0.026764 0.000001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000026_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d34db6ec49f95cd59ad8875d6a72c12c1ab382f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.20295409 Before NNI: tree length is 0.20295412 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000044_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000044_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc71a61b5820639df8c2d252c2124679b77456d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000044_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57328985 Before NNI: tree length is 0.57328987 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9430de271f8f679f5e70df66e3bf8b38706247b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000062_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010363 0.024347 0.404926 0.000001 +1 0.010363 0.000001 0.029887 0.410465 0.010363 +2 0.024347 0.029887 0.000001 0.418268 0.024347 +3 0.404926 0.410465 0.418268 0.000001 0.404926 +4 0.000001 0.010363 0.024347 0.404926 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..26340785d058c124815234d2f7ae80e7afc3e2b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000064_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ca739a4e233a64277406d1a11fc700990ee32d7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000065_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017933 0.606730 0.662553 0.017933 +1 0.017933 0.000001 0.604023 0.659846 0.000001 +2 0.606730 0.604023 0.000001 0.838418 0.604023 +3 0.662553 0.659846 0.838418 0.000001 0.659846 +4 0.017933 0.000001 0.604023 0.659846 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad78ae65b3b92e7ec098d0a9fe6fd795b26018c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000067_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000072_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23e57682034692202aa743f88af075b9e635c4f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.23133150 Before NNI: tree length is 0.23133150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..973cb97cbec53e3fd6ea9e4b64721c46a8faef8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000074_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,36 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.05951267 Before NNI: tree length is 1.06048562 + NNI 1: new tree length is 1.05905362 + Performed 1 NNI(s). + + Before SPR: tree length is 1.06048562 + SPR 1: new tree length is 1.05905363 + Performed 1 SPR(s). + + Explained variance : 0.68396583 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000075_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e665a2e61e8860348c61c505372e5517a38c1c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.45464975 Before NNI: tree length is 0.45464975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a710180b5d7ecd422e43bc8087d8d48c6aac120f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000077_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.39222039 Before NNI: tree length is 0.39222037 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae30b2309128c6d8f7404ec31db9eb86ffd472eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000084_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.91754550 Before NNI: tree length is 2.91754550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..748a07c6ebf50cfe808f4f085894e1c489516d57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000088_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021063 0.040185 0.233660 0.027678 +1 0.021063 0.000001 0.040916 0.234390 0.028408 +2 0.040185 0.040916 0.000001 0.240428 0.039214 +3 0.233660 0.234390 0.240428 0.000001 0.232688 +4 0.027678 0.028408 0.039214 0.232688 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3326cc7ce33754bf790c7a6fc67dd81e177f4c97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000093_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35531600 Before NNI: tree length is 0.35531600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71b928bb8021590ae3f1b1752bf1cf96da517843 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000101_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.060226 0.159605 0.344110 0.057686 +1 0.060226 0.000001 0.160096 0.344601 0.011755 +2 0.159605 0.160096 0.000001 0.347561 0.157556 +3 0.344110 0.344601 0.347561 0.000001 0.342062 +4 0.057686 0.011755 0.157556 0.342062 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b700bcaf35ca439059599dc9ce5aabd55f31be6b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000104_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.032563 0.348978 0.783932 0.008377 +1 0.032563 0.000001 0.350545 0.785498 0.029921 +2 0.348978 0.350545 0.000001 0.792489 0.346337 +3 0.783932 0.785498 0.792489 0.000001 0.781290 +4 0.008377 0.029921 0.346337 0.781290 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4566863a856de4e742f9393c3572039ab4dccf43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000112_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.36194150 Before NNI: tree length is 1.36194150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bcd6baa3e12c923321cde1b222e21525faeb41e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000115_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.13194500 Before NNI: tree length is 1.13194500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a05e61b6386f5e374028434f4f37d8b1e399729 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000125_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003123 0.085142 0.298843 0.000001 +1 0.003123 0.000001 0.084527 0.298228 0.003123 +2 0.085142 0.084527 0.000001 0.259844 0.085142 +3 0.298843 0.298228 0.259844 0.000001 0.298843 +4 0.000001 0.003123 0.085142 0.298843 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cbdf967b99b2b0ad802fc5b25edf4da7fcd6725a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001731 0.139431 0.249436 0.001731 +1 0.001731 0.000001 0.139581 0.249585 0.000001 +2 0.139431 0.139581 0.000001 0.249435 0.139581 +3 0.249436 0.249585 0.249435 0.000001 0.249585 +4 0.001731 0.000001 0.139581 0.249585 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000128_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c5df40655711b46e02082630d26ded4b1c4138c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.32009171 Before NNI: tree length is 0.32009175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2508ef442a3309d934eb4d4b4a49a74810365247 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000132_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.071469 0.138525 0.941144 0.091839 +1 0.071469 0.000001 0.209994 0.910452 0.061146 +2 0.138525 0.209994 0.000001 1.079670 0.230364 +3 0.941144 0.910452 1.079670 0.000001 0.849305 +4 0.091839 0.061146 0.230364 0.849305 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..45ae9d1a2ce7498439816f83e1623da8e8795a1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000134_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.05514575 Before NNI: tree length is 0.05514575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..600866acf9903b2ebb32d6de6637e34ec81a9fbe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000141_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.13539750 Before NNI: tree length is 0.13539750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7433c76ec53269ba3382950e4ba59ec41c3ef7ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000152_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000155_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5a45e7c5ac63872f59a1ad587112f86349d9ab1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.30231217 Before NNI: tree length is 0.30231225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a5bcba34c2d2c0b5ad32a568cb3ed93d98dcb1bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006545 0.125731 0.163976 0.010445 +1 0.006545 0.000001 0.130464 0.168708 0.015177 +2 0.125731 0.130464 0.000001 0.154852 0.121997 +3 0.163976 0.168708 0.154852 0.000001 0.160242 +4 0.010445 0.015177 0.121997 0.160242 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000176_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..76b1735242be15382e773ea938ba153341a3af39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.23127362 Before NNI: tree length is 0.23127362 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..33ea2aeb9d9aa0aa25fc12ce4776b34b52ce5d66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000180_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44758350 Before NNI: tree length is 0.44758350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000181_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000181_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..af68a995d89efc560db93a7543059de3e9dec87b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.87951118 Before NNI: tree length is 0.87951125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fcebfd227a638af47f562a8248004439f49d58c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000192_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.076227 0.073803 0.387025 0.080811 +1 0.076227 0.000001 0.093204 0.411330 0.100212 +2 0.073803 0.093204 0.000001 0.408906 0.062233 +3 0.387025 0.411330 0.408906 0.000001 0.415913 +4 0.080811 0.100212 0.062233 0.415913 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8130174142a53469ee4e367bc15695181ce281f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000196_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19792650 Before NNI: tree length is 0.19792650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5aa9bfc5c5fca27ef3a1f0b5123b2b35573ed155 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000215_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017804 0.095659 0.154637 0.013792 +1 0.017804 0.000001 0.095722 0.154700 0.011104 +2 0.095659 0.095722 0.000001 0.179296 0.091710 +3 0.154637 0.154700 0.179296 0.000001 0.150688 +4 0.013792 0.011104 0.091710 0.150688 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..32ec54e60c0797fef47939257d08f8affd52139f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000231_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.031412 0.045355 0.532443 0.030912 +1 0.031412 0.000001 0.047068 0.534156 0.001994 +2 0.045355 0.047068 0.000001 0.538866 0.046569 +3 0.532443 0.534156 0.538866 0.000001 0.533656 +4 0.030912 0.001994 0.046569 0.533656 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000232_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000232_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..256b17d264b5e3f19b879f779980202874fa1777 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.89739475 Before NNI: tree length is 0.89739475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..660df3aeb193e45f76c3aed795e967a898ddec33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000235_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36611850 Before NNI: tree length is 0.36611850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000238_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000238_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf20a679faaac4ecc9c3bb6c11bd125fe8caeeb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.30396050 Before NNI: tree length is 0.30396050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000239_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..94caf154faed03b9f198cb662e11782d150518f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.97567200 Before NNI: tree length is 0.97567200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3098520aeddec37ae2e691874e45fca8c60b2414 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000245_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.76808023 Before NNI: tree length is 0.76808025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7bc57983ce2d4110fa5df407195d2d7ab4309d3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000246_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005886 0.122937 0.218277 0.013163 +1 0.005886 0.000001 0.117051 0.212391 0.007277 +2 0.122937 0.117051 0.000001 0.196657 0.123404 +3 0.218277 0.212391 0.196657 0.000001 0.218744 +4 0.013163 0.007277 0.123404 0.218744 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4d16eef96f6f5a24464bb5ea7135ec7d5ad380b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000250_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002321 0.239091 0.489223 0.053117 +1 0.002321 0.000001 0.241212 0.491344 0.055238 +2 0.239091 0.241212 0.000001 0.433572 0.258379 +3 0.489223 0.491344 0.433572 0.000001 0.508511 +4 0.053117 0.055238 0.258379 0.508511 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..44b2fba1a848ed090334ee10a9f53ba87c6e3ec0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.238064 0.207738 0.001042 +1 0.000001 0.000001 0.238064 0.207738 0.001042 +2 0.238064 0.238064 0.000001 0.147920 0.237021 +3 0.207738 0.207738 0.147920 0.000001 0.206696 +4 0.001042 0.001042 0.237021 0.206696 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000251_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..52036982ff889d1778d5a3cc72f36e42ff6a88e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.29686127 Before NNI: tree length is 0.29686125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb37f76acbb1e7cf80db1874339d23b81234635f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000265_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000270_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000270_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..887e202b9f3c46106f789876a3e7226e582b606e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000270_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07834268 Before NNI: tree length is 0.07834275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000272_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b47d65601256321aaac1605f6fb1d9df0f24f425 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.45719000 Before NNI: tree length is 0.45719000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..42d5fe6073f4562b880da8cb27ef27015e9f29cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000275_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019887 0.098097 0.285773 0.000347 +1 0.019887 0.000001 0.117984 0.305660 0.020234 +2 0.098097 0.117984 0.000001 0.283985 0.097750 +3 0.285773 0.305660 0.283985 0.000001 0.285426 +4 0.000347 0.020234 0.097750 0.285426 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f6068f857f9abd0d1d0dd413c0560715637d14b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000276_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.089207 0.274442 0.270730 0.171055 +1 0.089207 0.000001 0.215182 0.211470 0.111795 +2 0.274442 0.215182 0.000001 0.175950 0.150124 +3 0.270730 0.211470 0.175950 0.000001 0.146412 +4 0.171055 0.111795 0.150124 0.146412 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cbb61b1bbc4b4963849e9d5a30304d743e09350 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000277_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000282_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1479f97e7733a078536fd8d1e45e16331e18c3d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.59659850 Before NNI: tree length is 0.59659850 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2c33538dd531010f841dfed7df8ee34bacaff3d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000283_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013687 0.059870 0.098423 0.012960 +1 0.013687 0.000001 0.066337 0.104890 0.019427 +2 0.059870 0.066337 0.000001 0.105597 0.057314 +3 0.098423 0.104890 0.105597 0.000001 0.095868 +4 0.012960 0.019427 0.057314 0.095868 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..67ee38885a84a5ad325f63ba7f583d63704a1936 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000288_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.04339400 Before NNI: tree length is 0.04339400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..19c9713c811345ccd0d97b33929b75db23133ea5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000290_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009768 0.026643 0.363319 0.009768 +1 0.009768 0.000001 0.020989 0.361658 0.000001 +2 0.026643 0.020989 0.000001 0.378532 0.020989 +3 0.363319 0.361658 0.378532 0.000001 0.361658 +4 0.009768 0.000001 0.020989 0.361658 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..955466159e7fb81663d190480152ebe16edc1296 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000300_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.569089 0.037046 0.276435 +1 0.000001 0.000001 0.569089 0.037046 0.276435 +2 0.569089 0.569089 0.000001 0.538925 0.806012 +3 0.037046 0.037046 0.538925 0.000001 0.273969 +4 0.276435 0.276435 0.806012 0.273969 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000305_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000305_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1d64742246a230db6df9fa91a5d3e537cdf3b3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.27826025 Before NNI: tree length is 0.27826025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6b570c8bad78428f65309b09817bb2ebce2b92c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000323_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35582575 Before NNI: tree length is 0.35582575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d201a9425eca369c24faf76a10145969c90b256 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000324_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003439 0.130627 0.369830 0.013698 +1 0.003439 0.000001 0.129011 0.368214 0.012082 +2 0.130627 0.129011 0.000001 0.337663 0.130873 +3 0.369830 0.368214 0.337663 0.000001 0.370076 +4 0.013698 0.012082 0.130873 0.370076 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f4982d3aa67ff20834b16d7c2f68108849056507 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000328_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011476 0.048806 0.345859 0.011476 +1 0.011476 0.000001 0.045731 0.342785 0.000001 +2 0.048806 0.045731 0.000001 0.355435 0.045731 +3 0.345859 0.342785 0.355435 0.000001 0.342785 +4 0.011476 0.000001 0.045731 0.342785 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..247b54d0a1c63203644bd1d72493d6e826b9c88a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000331_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040004 0.248285 0.872306 0.032679 +1 0.040004 0.000001 0.264148 0.888169 0.025487 +2 0.248285 0.264148 0.000001 0.938641 0.256823 +3 0.872306 0.888169 0.938641 0.000001 0.880844 +4 0.032679 0.025487 0.256823 0.880844 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c54204d5096fa9067164bc9e0c5db6a0456dbc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000334_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18811661 Before NNI: tree length is 0.18811662 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8628f55b2c46d4170504aad63f1336749b2b3eb8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000336_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013149 0.153942 0.447538 0.009138 +1 0.013149 0.000001 0.160155 0.453751 0.004010 +2 0.153942 0.160155 0.000001 0.453273 0.156145 +3 0.447538 0.453751 0.453273 0.000001 0.449741 +4 0.009138 0.004010 0.156145 0.449741 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000341_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ce8fd20a797efeccae5567055840560d0befaf2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 1.37453300 Before NNI: tree length is 1.37453300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..db3e55c3d6359253ff83f64bb6be1dc99cc28389 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000343_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.348071 0.844063 0.028977 +1 0.000001 0.000001 0.348071 0.844063 0.028977 +2 0.348071 0.348071 0.000001 0.495992 0.356725 +3 0.844063 0.844063 0.495992 0.000001 0.852717 +4 0.028977 0.028977 0.356725 0.852717 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000344_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000344_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..34443cf6cdd73504661bc8e67b7f4fd1b721a283 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.16229400 Before NNI: tree length is 0.16229400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad54a439bc156b58e20d333853e4fc29da2f7521 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000365_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006700 0.084615 0.166713 0.007004 +1 0.006700 0.000001 0.088609 0.170707 0.010998 +2 0.084615 0.088609 0.000001 0.186859 0.087468 +3 0.166713 0.170707 0.186859 0.000001 0.169566 +4 0.007004 0.010998 0.087468 0.169566 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a91911610d13f1162004f52e1690fdde99740a1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000367_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.035356 0.246890 0.375883 0.036231 +1 0.035356 0.000001 0.247696 0.376689 0.017399 +2 0.246890 0.247696 0.000001 0.447453 0.248571 +3 0.375883 0.376689 0.447453 0.000001 0.377565 +4 0.036231 0.017399 0.248571 0.377565 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5922302efe4916220aca59a25773bdb6d75298b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000376_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.030492 0.182061 0.396565 0.024426 +1 0.030492 0.000001 0.185136 0.399640 0.011130 +2 0.182061 0.185136 0.000001 0.387678 0.179069 +3 0.396565 0.399640 0.387678 0.000001 0.393573 +4 0.024426 0.011130 0.179069 0.393573 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000377_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000377_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b764897a5729535515854e3614665797789ea1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.73969050 Before NNI: tree length is 0.73969050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9f93e045698471b97f948c60e29c928d16953a93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000378_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033870 0.123746 0.336059 0.023705 +1 0.033870 0.000001 0.118255 0.330569 0.010734 +2 0.123746 0.118255 0.000001 0.301767 0.108089 +3 0.336059 0.330569 0.301767 0.000001 0.320403 +4 0.023705 0.010734 0.108089 0.320403 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0247e549a7d969d566239ed7327b6a8864875a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000379_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.35072621 Before NNI: tree length is 0.35072625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000385_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000385_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8c3b77cecb1119633208cb757a285be4ab51c182 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000385_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005736 0.058967 0.151756 0.012346 +1 0.005736 0.000001 0.060954 0.153743 0.014332 +2 0.058967 0.060954 0.000001 0.137851 0.057707 +3 0.151756 0.153743 0.137851 0.000001 0.150496 +4 0.012346 0.014332 0.057707 0.150496 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000387_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000387_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..42132cefd2e52e89ed262597ab90bc249008f28f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.31070422 Before NNI: tree length is 0.31070425 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e43a3f8e5a2e0020bc6b7809889fd7d9cac0237a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000390_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.080009 0.361932 0.376080 0.100248 +1 0.080009 0.000001 0.360111 0.374260 0.037349 +2 0.361932 0.360111 0.000001 0.363488 0.380349 +3 0.376080 0.374260 0.363488 0.000001 0.394498 +4 0.100248 0.037349 0.380349 0.394498 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..de9c8a9858a8ea1d8d7aed8cf6e8b2a718d02482 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000403_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012294 0.343001 0.549908 0.012294 +1 0.012294 0.000001 0.355295 0.562202 0.000001 +2 0.343001 0.355295 0.000001 0.531420 0.355295 +3 0.549908 0.562202 0.531420 0.000001 0.562202 +4 0.012294 0.000001 0.355295 0.562202 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c78391adc14dfe9e4455d2fea1c27d45aeef356 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000404_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.51368500 Before NNI: tree length is 1.51368500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc6d21934e73b7b65ae95ea14b0f96af51327ee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000411_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.19900696 Before NNI: tree length is 0.19900700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5eccfafea6a96690eec91195f982a6febb7d4f18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047953 0.348866 0.428318 0.047953 +1 0.047953 0.000001 0.342746 0.422198 0.000001 +2 0.348866 0.342746 0.000001 0.393334 0.342746 +3 0.428318 0.422198 0.393334 0.000001 0.422198 +4 0.047953 0.000001 0.342746 0.422198 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000414_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..27f2957c3adf75e3f37bff0cc6151b8031817308 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.60617600 Before NNI: tree length is 0.60617600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbfe03b4950fb65f436ac776535b76f0c604b8d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000416_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11522740 Before NNI: tree length is 0.11522737 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7c715a5ad9f6292e60ca916951ccbe5d9dc01855 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000421_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.025063 0.009264 0.117807 0.000001 +1 0.025063 0.000001 0.024997 0.133540 0.025063 +2 0.009264 0.024997 0.000001 0.114675 0.009264 +3 0.117807 0.133540 0.114675 0.000001 0.117807 +4 0.000001 0.025063 0.009264 0.117807 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e4bc34bb65b81df636b1e59b1ca61c840031b83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000439_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.16325625 Before NNI: tree length is 0.16325625 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..647b03ed3dc64c7490c9ce85a588761c6da52bdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000448_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001043 0.077779 0.312090 0.015331 +1 0.001043 0.000001 0.078822 0.313133 0.014288 +2 0.077779 0.078822 0.000001 0.307633 0.093110 +3 0.312090 0.313133 0.307633 0.000001 0.327421 +4 0.015331 0.014288 0.093110 0.327421 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000469_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000469_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..97715ed8441f4eade29ab2405fba7d98866ad148 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.24976500 Before NNI: tree length is 0.24976500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000470_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000470_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc24db180c7b86656fff6eb5d1eaa70869dd0046 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.60032950 Before NNI: tree length is 0.60032950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5e802a4ae181aab1c866f4b673de3c542a7fdbf0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000485_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.048095 0.149564 0.006584 +1 0.000001 0.000001 0.048095 0.149564 0.006584 +2 0.048095 0.048095 0.000001 0.148972 0.041511 +3 0.149564 0.149564 0.148972 0.000001 0.142980 +4 0.006584 0.006584 0.041511 0.142980 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..dbbb12df240e33f67a06c7c6a4eca6edd23bdbae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000497_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012938 0.137684 0.499328 0.001384 +1 0.012938 0.000001 0.138463 0.500107 0.011554 +2 0.137684 0.138463 0.000001 0.542376 0.136300 +3 0.499328 0.500107 0.542376 0.000001 0.497944 +4 0.001384 0.011554 0.136300 0.497944 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36c9aedd62526a1015d12c186036401e400fe7bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000508_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010984 0.095356 0.270933 0.028464 +1 0.010984 0.000001 0.092733 0.268310 0.025842 +2 0.095356 0.092733 0.000001 0.261925 0.104322 +3 0.270933 0.268310 0.261925 0.000001 0.279898 +4 0.028464 0.025842 0.104322 0.279898 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..41e1d9f2e0ffa5c26df79e1044b9e9a3417d7749 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000511_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009247 0.066301 0.171252 0.005398 +1 0.009247 0.000001 0.066835 0.171785 0.011049 +2 0.066301 0.066835 0.000001 0.162382 0.068102 +3 0.171252 0.171785 0.162382 0.000001 0.173053 +4 0.005398 0.011049 0.068102 0.173053 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cb8011325817216d28ba6ec1bce3444c8c85f01b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000525_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.278650 0.049033 0.329355 0.043495 +1 0.278650 0.000001 0.294174 0.225646 0.288636 +2 0.049033 0.294174 0.000001 0.344878 0.037121 +3 0.329355 0.225646 0.344878 0.000001 0.339340 +4 0.043495 0.288636 0.037121 0.339340 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be405ea7f0a9ce61034b7bfd3082eb7a3f4eac9a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000528_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000530_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000530_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d9a877315c2e61474b996fef3f4d310aefe104ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000530_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013175 0.041330 0.109001 0.017508 +1 0.013175 0.000001 0.043387 0.111059 0.019566 +2 0.041330 0.043387 0.000001 0.124708 0.038273 +3 0.109001 0.111059 0.124708 0.000001 0.105944 +4 0.017508 0.019566 0.038273 0.105944 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9217e39db2688ec5d955c2117cec2c0d3dcdfb56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000536_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.079731 0.514113 1.080421 0.099453 +1 0.079731 0.000001 0.527285 1.093594 0.061618 +2 0.514113 0.527285 0.000001 1.203480 0.547007 +3 1.080421 1.093594 1.203480 0.000001 1.113316 +4 0.099453 0.061618 0.547007 1.113316 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d2afae8311fa37654615d5a7e63481193d8670fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000537_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.51787675 Before NNI: tree length is 0.51787675 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2e6525179b3e678727c9d7054ac37ebe7a5b18f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000539_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007490 0.201788 0.300008 0.004775 +1 0.007490 0.000001 0.204320 0.302541 0.004139 +2 0.201788 0.204320 0.000001 0.275720 0.201604 +3 0.300008 0.302541 0.275720 0.000001 0.299825 +4 0.004775 0.004139 0.201604 0.299825 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..4a989b80bd3c7fd304d9c4a8bd8318620033e88b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000543_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036190 0.369887 0.588405 0.046530 +1 0.036190 0.000001 0.372300 0.590818 0.021728 +2 0.369887 0.372300 0.000001 0.505017 0.382640 +3 0.588405 0.590818 0.505017 0.000001 0.601158 +4 0.046530 0.021728 0.382640 0.601158 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..795dfa662ef3a60253530ed6b909f3d853fa2958 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000547_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022476 0.228923 0.571066 0.004465 +1 0.022476 0.000001 0.214182 0.556325 0.020985 +2 0.228923 0.214182 0.000001 0.510310 0.227432 +3 0.571066 0.556325 0.510310 0.000001 0.569574 +4 0.004465 0.020985 0.227432 0.569574 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000558_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000558_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0a63d6efd05ae648c46570b2875616683b26361 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.34951412 Before NNI: tree length is 0.34951413 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..568aa4636180926f444f90c4947fdb827ab3446d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000565_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.207157 0.247835 0.165534 0.013271 +1 0.207157 0.000001 0.159894 0.251631 0.205289 +2 0.247835 0.159894 0.000001 0.292309 0.245967 +3 0.165534 0.251631 0.292309 0.000001 0.163666 +4 0.013271 0.205289 0.245967 0.163666 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000578_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000578_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..38d07011082538594623a5bcc42459e24aeb7bc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.19344883 Before NNI: tree length is 0.19344875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3f1ea2281285f2d23ec73a3381358b40181ee959 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000581_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002734 0.083295 0.282614 0.037868 +1 0.002734 0.000001 0.086029 0.285348 0.040602 +2 0.083295 0.086029 0.000001 0.303607 0.072257 +3 0.282614 0.285348 0.303607 0.000001 0.271576 +4 0.037868 0.040602 0.072257 0.271576 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..3fac077b01d6ecb08bbb68eb09bd8d9edfeb4594 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000582_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002516 0.069837 0.264155 0.009673 +1 0.002516 0.000001 0.070696 0.265014 0.010531 +2 0.069837 0.070696 0.000001 0.241145 0.071683 +3 0.264155 0.265014 0.241145 0.000001 0.266001 +4 0.009673 0.010531 0.071683 0.266001 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b2debfc4b42317e4fc9cbe618a43b0b1c399ba2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000598_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.020266 0.166504 0.237182 0.006934 +1 0.020266 0.000001 0.165148 0.235826 0.015215 +2 0.166504 0.165148 0.000001 0.211157 0.161453 +3 0.237182 0.235826 0.211157 0.000001 0.232131 +4 0.006934 0.015215 0.161453 0.232131 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7e39a25a7bca7bc72491b8c72393c1d9847dc743 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000612_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.021044 0.320829 0.393319 0.036249 +1 0.021044 0.000001 0.302840 0.375330 0.018260 +2 0.320829 0.302840 0.000001 0.391231 0.305226 +3 0.393319 0.375330 0.391231 0.000001 0.377716 +4 0.036249 0.018260 0.305226 0.377716 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000621_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000621_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..471f7517a141ff8585e3bceea20cfdad7f79d11f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.58324176 Before NNI: tree length is 0.58324175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..af69a3292353cb5a6ddd98fb84cd7630d44e1767 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000623_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.057019 0.334903 0.719642 0.076813 +1 0.057019 0.000001 0.309445 0.694184 0.035640 +2 0.334903 0.309445 0.000001 0.641627 0.329240 +3 0.719642 0.694184 0.641627 0.000001 0.713979 +4 0.076813 0.035640 0.329240 0.713979 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c3ae20128b00221f0f0e0880e3c7a05c130a027 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000633_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.20901900 Before NNI: tree length is 0.20901900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..87831b85631b55ed6e89ffe16afdd4cb2ee246dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.004173 0.071623 0.228250 0.010078 +1 0.004173 0.000001 0.071576 0.228203 0.007411 +2 0.071623 0.071576 0.000001 0.210321 0.077481 +3 0.228250 0.228203 0.210321 0.000001 0.234108 +4 0.010078 0.007411 0.077481 0.234108 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000635_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f1bbe5cbe8cf47a9465c617e7576cda4376363f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.26381800 Before NNI: tree length is 0.26381800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000639_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..53279953de833202f0f9c6ff6708aa27eac9b32e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.18416069 Before NNI: tree length is 0.18416075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cd4cc5f2a4c183cc16e6ed60bad8804c746887f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000644_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.337116 0.490833 0.020058 +1 0.000001 0.000001 0.337116 0.490833 0.020058 +2 0.337116 0.337116 0.000001 0.362605 0.350285 +3 0.490833 0.490833 0.362605 0.000001 0.504003 +4 0.020058 0.020058 0.350285 0.504003 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..33da25b1353bf9cd7f01756c2586be446fc5b5a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000646_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.088177 0.118874 0.000001 +1 0.000001 0.000001 0.088177 0.118874 0.000001 +2 0.088177 0.088177 0.000001 0.114084 0.088177 +3 0.118874 0.118874 0.114084 0.000001 0.118874 +4 0.000001 0.000001 0.088177 0.118874 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000659_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000659_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..58dc82473ba3b901bd83170d5474596110d8c8cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000659_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.02509500 Before NNI: tree length is 0.02509500 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000660_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000660_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..349eef46a94fd39efd9173398144e0bc345927d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000660_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015778 0.065470 0.029687 0.012222 +1 0.015778 0.000001 0.064605 0.028822 0.003557 +2 0.065470 0.064605 0.000001 0.072682 0.061048 +3 0.029687 0.028822 0.072682 0.000001 0.025265 +4 0.012222 0.003557 0.061048 0.025265 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..414a7679ff23ff8708141079b893ca36506f3e94 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000669_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.21955180 Before NNI: tree length is 0.21955175 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..737ed3f7afdc61b1d202ffe7c644d56e338decd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000676_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013161 0.358673 0.454811 0.022200 +1 0.013161 0.000001 0.359746 0.455885 0.009040 +2 0.358673 0.359746 0.000001 0.459355 0.368786 +3 0.454811 0.455885 0.459355 0.000001 0.464924 +4 0.022200 0.009040 0.368786 0.464924 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2cf31716cd094c72ebc65abcc762510c865b190 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000684_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.14496050 Before NNI: tree length is 0.14496050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8f001ea4ee35357911fadaa4fe240d5b06e39c18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000687_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.009970 0.160117 0.000001 +1 0.000001 0.000001 0.009970 0.160117 0.000001 +2 0.009970 0.009970 0.000001 0.165874 0.009970 +3 0.160117 0.160117 0.165874 0.000001 0.160117 +4 0.000001 0.000001 0.009970 0.160117 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..18acd0c5a0acdf784ba28b399946606eb6462878 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000693_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019734 0.209135 0.451139 0.029167 +1 0.019734 0.000001 0.197165 0.439168 0.017197 +2 0.209135 0.197165 0.000001 0.435023 0.195526 +3 0.451139 0.439168 0.435023 0.000001 0.437529 +4 0.029167 0.017197 0.195526 0.437529 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000700_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000700_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4667bc6d52c935c9e58178c27ef24c37ce54c9c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.04912750 Before NNI: tree length is 0.04912750 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78660655152e893ed397e8c81bdd7e00708d05b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000708_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.075030 0.080049 0.005490 +1 0.000001 0.000001 0.075030 0.080049 0.005490 +2 0.075030 0.075030 0.000001 0.100370 0.079689 +3 0.080049 0.080049 0.100370 0.000001 0.084708 +4 0.005490 0.005490 0.079689 0.084708 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..b03ea05ad39f71abe7469c0cb49cf0af9774bd40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000719_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012656 0.287668 0.564158 0.008468 +1 0.012656 0.000001 0.294163 0.570653 0.004211 +2 0.287668 0.294163 0.000001 0.556464 0.289976 +3 0.564158 0.570653 0.556464 0.000001 0.566466 +4 0.008468 0.004211 0.289976 0.566466 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..db615dc55ce3baa44ffeaf01dc627e8136284483 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000721_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.011244 0.124540 0.232867 0.010273 +1 0.011244 0.000001 0.132178 0.240505 0.004469 +2 0.124540 0.132178 0.000001 0.216529 0.131207 +3 0.232867 0.240505 0.216529 0.000001 0.239534 +4 0.010273 0.004469 0.131207 0.239534 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab2c7ac3e362001a372dd98cee755b903b89f39c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000722_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.18366585 Before NNI: tree length is 0.18366588 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..1973298b27df688e3a9887fb468679cbb50ba5fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000730_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.59530300 Before NNI: tree length is 0.59530300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..02c84304ff2a98d3563ea35d4bbf41c4d54de873 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000738_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005192 0.058983 0.207461 0.005192 +1 0.005192 0.000001 0.055247 0.203726 0.000001 +2 0.058983 0.055247 0.000001 0.201473 0.055247 +3 0.207461 0.203726 0.201473 0.000001 0.203726 +4 0.005192 0.000001 0.055247 0.203726 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..04cf3c0d1f063aed7fc419bfa8c8ae46a1ae9c69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000739_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23509650 Before NNI: tree length is 0.23509650 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2678c7754b512a24666d45328b6679cce25badfe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000749_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.15659350 Before NNI: tree length is 0.15659350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000750_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000750_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e70bb0332679dcd36eab979f62931db5649928e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.10304080 Before NNI: tree length is 0.10304075 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..79e6549b2d9744fbf5f63486ab3d33f5554ef250 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000760_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.34854225 Before NNI: tree length is 0.34854225 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..36f31c2fa763e2e3d3370b863335789337d7df14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000764_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000502 0.063238 0.288139 0.007347 +1 0.000502 0.000001 0.063740 0.288641 0.006845 +2 0.063238 0.063740 0.000001 0.281260 0.070585 +3 0.288139 0.288641 0.281260 0.000001 0.295486 +4 0.007347 0.006845 0.070585 0.295486 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000785_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000785_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..918004149e3b894613fc255f812805d10f94eee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.55952550 Before NNI: tree length is 0.55952550 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000807_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000807_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2d1547cc36fd2e18fee96d70a5df6350baf923b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.11861830 Before NNI: tree length is 0.11861825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..715fd8b468c1ddd342bfd5376b2779a0fda4e248 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000808_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.029957 0.022294 0.275240 0.012491 +1 0.029957 0.000001 0.019144 0.289930 0.017466 +2 0.022294 0.019144 0.000001 0.282267 0.009803 +3 0.275240 0.289930 0.282267 0.000001 0.272464 +4 0.012491 0.017466 0.009803 0.272464 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad5c99e0dffc231fa90ef6fdd6b923b8a28cd17c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000816_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006653 0.110856 0.043832 0.013307 +1 0.006653 0.000001 0.105285 0.038261 0.006653 +2 0.110856 0.105285 0.000001 0.129782 0.111938 +3 0.043832 0.038261 0.129782 0.000001 0.044914 +4 0.013307 0.006653 0.111938 0.044914 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d75752f2214482b36aff85cb0ad836e05a4ae95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008585 0.105082 0.073385 0.010766 +1 0.008585 0.000001 0.109354 0.077657 0.015037 +2 0.105082 0.109354 0.000001 0.146659 0.106416 +3 0.073385 0.077657 0.146659 0.000001 0.074720 +4 0.010766 0.015037 0.106416 0.074720 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000817_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..41d32131846160fe543e978bd64a399e9f9f4483 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.17504152 Before NNI: tree length is 0.17504150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..58d44e6fa9b5e5b9572fed08e6a98947fb2a1437 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000820_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009946 0.176507 0.258278 0.011653 +1 0.009946 0.000001 0.175920 0.257691 0.007361 +2 0.176507 0.175920 0.000001 0.275568 0.177627 +3 0.258278 0.257691 0.275568 0.000001 0.259398 +4 0.011653 0.007361 0.177627 0.259398 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000821_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000821_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..24643fec83aabbb0036ea63cf87c82395a1598b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.73312525 Before NNI: tree length is 0.73312525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..057f6136b25843632cc8773d9bfaf17954ae81cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000823_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.047273 0.125418 0.149535 0.021239 +1 0.047273 0.000001 0.101222 0.149582 0.059147 +2 0.125418 0.101222 0.000001 0.227727 0.137292 +3 0.149535 0.149582 0.227727 0.000001 0.161409 +4 0.021239 0.059147 0.137292 0.161409 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000825_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000825_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c82f77416cd9e444285970f085925358b52b9d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.27933345 Before NNI: tree length is 0.27933350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..045ce002498c1a5ecff9a0ad610dae65e37fd9d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000826_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033477 0.206649 0.361862 0.019292 +1 0.033477 0.000001 0.214799 0.370011 0.020374 +2 0.206649 0.214799 0.000001 0.363199 0.200614 +3 0.361862 0.370011 0.363199 0.000001 0.355826 +4 0.019292 0.020374 0.200614 0.355826 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..abb15aa91221edb55a70167f119c975a739e949f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000829_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09341450 Before NNI: tree length is 0.09341450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c27e2721ba1e3ce7bd836236fcaeebec684747e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000833_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33404600 Before NNI: tree length is 0.33404600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000834_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000834_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e656e059121bfb8d4b53fa292c97e88018a00579 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.15724450 Before NNI: tree length is 0.15724450 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6855e1c96ec80f171662f81df88d141feee057c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000839_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003999 0.007992 0.000005 0.000005 +1 0.003999 0.000001 0.011991 0.004005 0.003993 +2 0.007992 0.011991 0.000001 0.007987 0.007998 +3 0.000005 0.004005 0.007987 0.000001 0.000011 +4 0.000005 0.003993 0.007998 0.000011 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6d20dbc5fe58027a18963c08de2c210fe0d00c23 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.019413 0.051321 0.030198 0.017121 +1 0.019413 0.000001 0.061956 0.040833 0.005510 +2 0.051321 0.061956 0.000001 0.040485 0.059664 +3 0.030198 0.040833 0.040485 0.000001 0.038540 +4 0.017121 0.005510 0.059664 0.038540 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000842_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cd337d89f49f24acdfb65d4c16ae4d7958e7677 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.07763490 Before NNI: tree length is 0.07763488 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e56137558637591c055bdfe303c3897fc3cb8006 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000850_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.064144 0.000001 +1 0.000001 0.000001 0.000001 0.064144 0.000001 +2 0.000001 0.000001 0.000001 0.064144 0.000001 +3 0.064144 0.064144 0.064144 0.000001 0.064144 +4 0.000001 0.000001 0.000001 0.064144 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6be609b6e375e00f7c67fd4eaa5d0fa89989cb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000851_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.17780600 Before NNI: tree length is 0.17780600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..2be798c96980757f551534c5341e764c311218e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000852_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008686 0.120661 0.264927 0.014687 +1 0.008686 0.000001 0.124002 0.268267 0.011329 +2 0.120661 0.124002 0.000001 0.245244 0.130003 +3 0.264927 0.268267 0.245244 0.000001 0.274269 +4 0.014687 0.011329 0.130003 0.274269 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..78e68c1dfc1498aa97713db05111f4d0d6060803 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000853_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000597 0.111445 0.278225 0.010193 +1 0.000597 0.000001 0.112017 0.278797 0.010765 +2 0.111445 0.112017 0.000001 0.279031 0.105342 +3 0.278225 0.278797 0.279031 0.000001 0.272122 +4 0.010193 0.010765 0.105342 0.272122 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b2783f17d38b0e3a3e5c9260a6a775ff3d66268 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000854_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47477900 Before NNI: tree length is 0.47477900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7409042b242fc765c334205ae3290b2fc5b34bba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000856_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.112619 0.157249 0.014815 +1 0.000001 0.000001 0.112619 0.157249 0.014815 +2 0.112619 0.112619 0.000001 0.159468 0.107841 +3 0.157249 0.157249 0.159468 0.000001 0.152472 +4 0.014815 0.014815 0.107841 0.152472 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c64f1927e445c8bf78379160a600603c9ec160e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000868_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09633400 Before NNI: tree length is 0.09633400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5b088344cbf2a5a7b8502cfb4d6a9cfc6f746d78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000869_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007657 0.060824 0.098360 0.008252 +1 0.007657 0.000001 0.061166 0.098702 0.008593 +2 0.060824 0.061166 0.000001 0.089861 0.057205 +3 0.098360 0.098702 0.089861 0.000001 0.094741 +4 0.008252 0.008593 0.057205 0.094741 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa79987b9ca7455b9b4b1da8817e3b785a57f856 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000877_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33635982 Before NNI: tree length is 0.33635975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..22a2fa4676890865813c379d97871c70dbe8667e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000881_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.38934140 Before NNI: tree length is 0.38934138 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2b4b437c905444fb2a69e927ecb1f8bcf8eb7a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000886_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.32081971 Before NNI: tree length is 0.32081975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d06842614ee8ba1f12a6152309ee1a4a506f2d26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000892_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.72601813 Before NNI: tree length is 0.72601812 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e19e7dea90f07782b6fba2c73fc33a543b0daea4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000897_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.49209129 Before NNI: tree length is 0.49209125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..822ca8586579b82e1936760cde3c2ce087f94284 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000900_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006680 0.243129 0.537572 0.006680 +1 0.006680 0.000001 0.249808 0.544252 0.000001 +2 0.243129 0.249808 0.000001 0.552417 0.249808 +3 0.537572 0.544252 0.552417 0.000001 0.544252 +4 0.006680 0.000001 0.249808 0.544252 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000916_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000916_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7f6be3e936341e4b49738679ed6e8b762ad07b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.26877050 Before NNI: tree length is 0.26877050 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..574d0bcd99df61d9a0ed27c5880f323f661575f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000920_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.108999 0.315206 0.000001 +1 0.000001 0.000001 0.108999 0.315206 0.000001 +2 0.108999 0.108999 0.000001 0.337265 0.108999 +3 0.315206 0.315206 0.337265 0.000001 0.315206 +4 0.000001 0.000001 0.108999 0.315206 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3777056a1f811ef9dd8581efced45704c9c25374 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000926_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24266150 Before NNI: tree length is 0.24266150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..735b950662496e8f8101bcdd70e727c8d9c0a9fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000927_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.24079400 Before NNI: tree length is 0.24079400 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000935_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..55e5f9c6f6f08a080631d5c335fd792c404081fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.28631150 Before NNI: tree length is 0.28631150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d949f6bd5bcdbb501c46e824c7e33ca3fb11136b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000938_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.044147 0.101400 0.000001 +1 0.000001 0.000001 0.044147 0.101400 0.000001 +2 0.044147 0.044147 0.000001 0.095960 0.044147 +3 0.101400 0.101400 0.095960 0.000001 0.101400 +4 0.000001 0.000001 0.044147 0.101400 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..aab4cb5dcdfb3845144afe4d7dbb9b2ac2951c27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000948_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002569 0.070732 0.233368 0.007741 +1 0.002569 0.000001 0.072608 0.235243 0.009616 +2 0.070732 0.072608 0.000001 0.224885 0.073200 +3 0.233368 0.235243 0.224885 0.000001 0.235836 +4 0.007741 0.009616 0.073200 0.235836 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d7a0d479050e24c46ade436b65f516670db32446 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000951_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012523 0.216137 0.336502 0.012523 +1 0.012523 0.000001 0.215201 0.335566 0.000001 +2 0.216137 0.215201 0.000001 0.354914 0.215201 +3 0.336502 0.335566 0.354914 0.000001 0.335566 +4 0.012523 0.000001 0.215201 0.335566 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..639d38cbafc72fac767a19536d25d22a420fcb2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000964_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001456 0.127181 0.249675 0.001487 +1 0.001456 0.000001 0.125726 0.248220 0.000032 +2 0.127181 0.125726 0.000001 0.240631 0.125694 +3 0.249675 0.248220 0.240631 0.000001 0.248188 +4 0.001487 0.000032 0.125694 0.248188 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..56f27ea2660cf8d416d89037ef011c869dca1d42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000967_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000970_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..942893e37e91b3fde744c1b93c00d6d0235b8c7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.25307700 Before NNI: tree length is 0.25307700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..66fd402ce31a694cd376e7dd68c9f1e080286f0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000973_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007113 0.123107 0.215884 0.000001 +1 0.007113 0.000001 0.128095 0.220871 0.007113 +2 0.123107 0.128095 0.000001 0.219620 0.123107 +3 0.215884 0.220871 0.219620 0.000001 0.215884 +4 0.000001 0.007113 0.123107 0.215884 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ec488d2010fb4dd804966e43a06e794bde29cfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000975_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56017352 Before NNI: tree length is 0.56017350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e094a81e3e5eedad7cc060ccbefc399cde012966 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000976_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.043635 0.315797 0.649057 0.040275 +1 0.043635 0.000001 0.331514 0.664775 0.016485 +2 0.315797 0.331514 0.000001 0.642514 0.328154 +3 0.649057 0.664775 0.642514 0.000001 0.661415 +4 0.040275 0.016485 0.328154 0.661415 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d0fa474461b9b92d6f8544d54d5acbcadbbc4d01 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000979_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003062 0.015928 0.274650 0.011562 +1 0.003062 0.000001 0.017018 0.275740 0.012653 +2 0.015928 0.017018 0.000001 0.279221 0.022114 +3 0.274650 0.275740 0.279221 0.000001 0.280836 +4 0.011562 0.012653 0.022114 0.280836 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7216813d45f2b23218d2484839bb8d65b38e78b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000986_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.187009 0.631743 0.000001 +1 0.000001 0.000001 0.187009 0.631743 0.000001 +2 0.187009 0.187009 0.000001 0.679279 0.187009 +3 0.631743 0.631743 0.679279 0.000001 0.631743 +4 0.000001 0.000001 0.187009 0.631743 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0198fecd27c48bd8c6990191bdc3e5f349ffcaaf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000994_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.013862 0.187719 0.425345 0.007530 +1 0.013862 0.000001 0.191557 0.429183 0.014481 +2 0.187719 0.191557 0.000001 0.410495 0.188338 +3 0.425345 0.429183 0.410495 0.000001 0.425963 +4 0.007530 0.014481 0.188338 0.425963 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..044ac240dc01d08082980fa83213f8878179c6ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0000996_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9b1268ee009fe8adadc0228e3a27ed16896f428a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001000_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.016548 0.069190 0.000001 +1 0.000001 0.000001 0.016548 0.069190 0.000001 +2 0.016548 0.016548 0.000001 0.076634 0.016548 +3 0.069190 0.069190 0.076634 0.000001 0.069190 +4 0.000001 0.000001 0.016548 0.069190 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..be50bb51994fc81810c3ebe27f2da3e6c32bdc50 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001008_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.33320235 Before NNI: tree length is 0.33320238 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8aecf827b11ef380d0c0e7b09bf4584e32ae268 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001009_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f67bb77ec43297c922d3eefc95b545f96c3b301 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001020_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25904300 Before NNI: tree length is 0.25904300 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..496f1d1b5755fde832313e882a2830bf498c293b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001023_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012165 0.034157 0.085115 0.010183 +1 0.012165 0.000001 0.034562 0.085519 0.002914 +2 0.034157 0.034562 0.000001 0.077656 0.032579 +3 0.085115 0.085519 0.077656 0.000001 0.083537 +4 0.010183 0.002914 0.032579 0.083537 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..13be9386874656fd3372d3e96f04bcb55fa2a4f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001030_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007720 0.084261 0.105145 0.007720 +1 0.007720 0.000001 0.084853 0.105738 0.000001 +2 0.084261 0.084853 0.000001 0.133991 0.084853 +3 0.105145 0.105738 0.133991 0.000001 0.105738 +4 0.007720 0.000001 0.084853 0.105738 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e2107ab8340a36be9caf25754a5a99b8ed7ac600 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001041_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.005748 0.065122 0.182094 0.000001 +1 0.005748 0.000001 0.063522 0.180494 0.005748 +2 0.065122 0.063522 0.000001 0.180926 0.065122 +3 0.182094 0.180494 0.180926 0.000001 0.182094 +4 0.000001 0.005748 0.065122 0.182094 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..545c49099eb380d1ffc2b140fc58379814804328 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001044_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.22757000 Before NNI: tree length is 0.22757000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a28046c1c04e4df002ebc3d9f1c3130aff209904 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001053_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.529364 1.290908 0.000001 +1 0.000001 0.000001 0.529364 1.290908 0.000001 +2 0.529364 0.529364 0.000001 1.145512 0.529364 +3 1.290908 1.290908 1.145512 0.000001 1.290908 +4 0.000001 0.000001 0.529364 1.290908 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ddef610c73579c05eb94770b0f7f4786d820e557 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001057_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.130914 1.559148 0.632184 0.130914 +1 0.130914 0.000001 1.454878 0.527914 0.000001 +2 1.559148 1.454878 0.000001 1.471621 1.454878 +3 0.632184 0.527914 1.471621 0.000001 0.527914 +4 0.130914 0.000001 1.454878 0.527914 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32ce4425c03b04195db6707157c9f3fe39483d1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001061_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.57461161 Before NNI: tree length is 0.57461162 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..53acb37bd0b0a9f308015c5bd5f5602b1970f53c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001066_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.088171 0.260514 0.000001 +1 0.000001 0.000001 0.088171 0.260514 0.000001 +2 0.088171 0.088171 0.000001 0.273186 0.088171 +3 0.260514 0.260514 0.273186 0.000001 0.260514 +4 0.000001 0.000001 0.088171 0.260514 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001069_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001069_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..57a53abe66fc671a78712c56507e900b3489cf59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.33145029 Before NNI: tree length is 0.33145025 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001080_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001080_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..60a69e8bfea85a3a05e03371b8c5731bab988005 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.83598350 Before NNI: tree length is 0.83598350 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1c19951372a5e88316b8fd94259c850a8c602f53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001084_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.060974 0.206022 0.000001 +1 0.000001 0.000001 0.060974 0.206022 0.000001 +2 0.060974 0.060974 0.000001 0.211953 0.060974 +3 0.206022 0.206022 0.211953 0.000001 0.206022 +4 0.000001 0.000001 0.060974 0.206022 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..63878dc23454b1a58527112d9c107b06f90cfc68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001097_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.23659825 Before NNI: tree length is 0.23659825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0d3d88170b9083df365981855597515b5b66631d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001101_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.155830 0.001628 0.182468 0.154960 +1 0.155830 0.000001 0.157458 0.197143 0.001491 +2 0.001628 0.157458 0.000001 0.184095 0.156587 +3 0.182468 0.197143 0.184095 0.000001 0.196273 +4 0.154960 0.001491 0.156587 0.196273 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..271eb70f6b46da705f8a0c592be005b066617be7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001109_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.017639 0.145942 0.251998 0.015984 +1 0.017639 0.000001 0.135401 0.241457 0.016176 +2 0.145942 0.135401 0.000001 0.290481 0.144479 +3 0.251998 0.241457 0.290481 0.000001 0.250535 +4 0.015984 0.016176 0.144479 0.250535 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d470a6de312734aa12b9fb205a262b5182284ba8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001111_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.002636 0.197739 0.214257 0.036538 +1 0.002636 0.000001 0.195785 0.212304 0.034584 +2 0.197739 0.195785 0.000001 0.289365 0.188644 +3 0.214257 0.212304 0.289365 0.000001 0.205162 +4 0.036538 0.034584 0.188644 0.205162 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..40585977bd73f141a2d8f0337acafa2b024da01a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001114_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009580 0.002288 0.171132 0.002221 +1 0.009580 0.000001 0.007543 0.176387 0.007476 +2 0.002288 0.007543 0.000001 0.168845 0.000067 +3 0.171132 0.176387 0.168845 0.000001 0.168911 +4 0.002221 0.007476 0.000067 0.168911 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71650e5ad885734390174fbb2eb4a1b9940cc302 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001116_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003994 0.113456 0.386167 0.000565 +1 0.003994 0.000001 0.116003 0.388713 0.004559 +2 0.113456 0.116003 0.000001 0.368388 0.114021 +3 0.386167 0.388713 0.368388 0.000001 0.386732 +4 0.000565 0.004559 0.114021 0.386732 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a4773deff99d3b8594adf1ae09fe0e266ddc0207 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001118_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.006815 0.098714 0.015815 +1 0.000001 0.000001 0.006815 0.098714 0.015815 +2 0.006815 0.006815 0.000001 0.102859 0.019959 +3 0.098714 0.098714 0.102859 0.000001 0.108959 +4 0.015815 0.015815 0.019959 0.108959 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..1eb139de618c5b97332f7cf04555bb83673d7189 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001137_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.015620 0.166785 0.512500 0.013184 +1 0.015620 0.000001 0.160018 0.505733 0.012570 +2 0.166785 0.160018 0.000001 0.518329 0.163735 +3 0.512500 0.505733 0.518329 0.000001 0.509450 +4 0.013184 0.012570 0.163735 0.509450 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1bc0a6a8b5438770aff12708fde006e8581c88f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001144_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb5c14cc2eec109da11663eae6cd05faa2c614e0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001156_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28785882 Before NNI: tree length is 0.28785875 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6c899fecd42ff20e5fc187d13bde6b64db8a20fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001162_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.85186971 Before NNI: tree length is 1.85186975 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee2370e02332c021e26b87811b1f0126314a0901 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001163_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.31755039 Before NNI: tree length is 0.31755038 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c74497cc5e24afa082ae461fd7bb828926c1cbaf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001171_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.048551 0.054668 0.333642 0.090945 +1 0.048551 0.000001 0.021876 0.327642 0.084945 +2 0.054668 0.021876 0.000001 0.333760 0.091063 +3 0.333642 0.327642 0.333760 0.000001 0.318451 +4 0.090945 0.084945 0.091063 0.318451 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a299602e0238845019b94cfa8b75048f3b14b0d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001172_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036660 0.097464 0.228704 0.014753 +1 0.036660 0.000001 0.081824 0.213064 0.040197 +2 0.097464 0.081824 0.000001 0.229913 0.101001 +3 0.228704 0.213064 0.229913 0.000001 0.232241 +4 0.014753 0.040197 0.101001 0.232241 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0d0fa25990d1f2e2493d20bc0aa4557503c957ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001181_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.008261 0.027665 0.041887 0.003070 +1 0.008261 0.000001 0.024781 0.039003 0.005289 +2 0.027665 0.024781 0.000001 0.046608 0.024693 +3 0.041887 0.039003 0.046608 0.000001 0.038915 +4 0.003070 0.005289 0.024693 0.038915 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..831888edf3eaa8d9893a318ba7b574468eb6d888 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001191_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.11119370 Before NNI: tree length is 2.11119375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..51af88c732e9cd6fa2905a755a25a6baf0cd9891 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001195_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44837725 Before NNI: tree length is 0.44837725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..d89a7012b8f1c8c055078ac8955b7f253a3c9b22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001196_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001216_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001216_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a3a6873124433895452c64cb7676bb8a022dd42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.15510479 Before NNI: tree length is 0.15510475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5329e4ec0b657d67db59e41b925399e71443dd0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001218_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.272335 0.318318 0.026287 +1 0.000001 0.000001 0.272335 0.318318 0.026287 +2 0.272335 0.272335 0.000001 0.367795 0.270206 +3 0.318318 0.318318 0.367795 0.000001 0.316188 +4 0.026287 0.026287 0.270206 0.316188 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..74f411704657d11142c202d61701c81ed42b59e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001220_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7f33235d77102caae180ad9d573cab95b69d5b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001221_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.47063150 Before NNI: tree length is 0.47063150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001226_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001226_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c21b9586ffa63edd18c9381980899c13b9cdeb11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.35287194 Before NNI: tree length is 0.35287200 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa8b1ae7631a5c5afce3ac0f67e7641dbbf02ebe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001242_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.09531000 Before NNI: tree length is 0.09531000 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7a4218e82c43aecd2619da2cb4a6e8c8e0595613 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001248_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.006375 0.079199 0.227545 0.011908 +1 0.006375 0.000001 0.078141 0.226487 0.010849 +2 0.079199 0.078141 0.000001 0.231327 0.075546 +3 0.227545 0.226487 0.231327 0.000001 0.223892 +4 0.011908 0.010849 0.075546 0.223892 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..74bb0543f06b833c66947e85a9e9bfc10cd39d15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001262_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.285618 0.461256 0.089315 +1 0.000001 0.000001 0.285618 0.461256 0.089315 +2 0.285618 0.285618 0.000001 0.382927 0.278310 +3 0.461256 0.461256 0.382927 0.000001 0.453949 +4 0.089315 0.089315 0.278310 0.453949 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..15d3aa12a59596cc73bd10357b541bdf0e0aeffb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001264_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.27499283 Before NNI: tree length is 1.27499275 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fc109380ff89bbd410f13ac3083ca25f874b5e40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001281_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.010006 0.256497 0.008093 +1 0.000001 0.000001 0.010006 0.256497 0.008093 +2 0.010006 0.010006 0.000001 0.257265 0.008510 +3 0.256497 0.256497 0.257265 0.000001 0.255353 +4 0.008093 0.008093 0.008510 0.255353 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9d38d36dcf94e80ed44896f023c6ba6198d29472 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001283_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.050952 0.233414 0.871248 0.008646 +1 0.050952 0.000001 0.240919 0.878752 0.053739 +2 0.233414 0.240919 0.000001 0.890310 0.236201 +3 0.871248 0.878752 0.890310 0.000001 0.874035 +4 0.008646 0.053739 0.236201 0.874035 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e4ec4aa68f8c2915ee1e43422f9d4ef7a53ed601 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001285_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.033590 0.119772 0.318062 0.025359 +1 0.033590 0.000001 0.099574 0.297864 0.026762 +2 0.119772 0.099574 0.000001 0.280824 0.112944 +3 0.318062 0.297864 0.280824 0.000001 0.311233 +4 0.025359 0.026762 0.112944 0.311233 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..7f118f7f9683bd81eb69d60fb0fc01bf5419f5e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001288_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001324 0.776641 0.237388 0.005657 +1 0.001324 0.000001 0.777966 0.238712 0.004333 +2 0.776641 0.777966 0.000001 0.772127 0.782298 +3 0.237388 0.238712 0.772127 0.000001 0.243045 +4 0.005657 0.004333 0.782298 0.243045 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f749659ff997851f0e45b5eb5fd3cb579f81aba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001297_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.44088900 Before NNI: tree length is 0.44088900 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..50ceb35974e8329a4ecd7455cd913eca2c20f8f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001309_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.56418575 Before NNI: tree length is 0.56418575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001321_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001321_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c2e37f9cef0a00add62a4cbc459c75819b01bca9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.44916561 Before NNI: tree length is 0.44916562 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..998f699d08406c16b0aa6301a6a975c3ce2616f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001327_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.036113 0.111410 0.194774 0.035411 +1 0.036113 0.000001 0.140338 0.223701 0.064339 +2 0.111410 0.140338 0.000001 0.198823 0.127217 +3 0.194774 0.223701 0.198823 0.000001 0.210580 +4 0.035411 0.064339 0.127217 0.210580 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..757fb8febb0eb6b050030ddb31395f7eee36dd1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001328_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.058782 0.680629 1.063375 0.094664 +1 0.058782 0.000001 0.705458 1.088203 0.119492 +2 0.680629 0.705458 0.000001 0.992878 0.696191 +3 1.063375 1.088203 0.992878 0.000001 1.078936 +4 0.094664 0.119492 0.696191 1.078936 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a7e75d7a0629c2e25831400539ad66924c99bf54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001334_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.010876 0.038280 0.082351 0.010687 +1 0.010876 0.000001 0.037802 0.081873 0.000480 +2 0.038280 0.037802 0.000001 0.072492 0.037613 +3 0.082351 0.081873 0.072492 0.000001 0.081684 +4 0.010687 0.000480 0.037613 0.081684 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7cf1f4000c5f353e16cf77ccca441beb3c8312c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001339_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.11164942 Before NNI: tree length is 0.11164937 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..3804eb7f2ba1d49ae7d4ecb7655af4a51513f41b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001345_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..acc4eca7dbcc3ea116bff5a2b675e470085cfba1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001351_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.018396 0.266901 0.495804 0.025227 +1 0.018396 0.000001 0.267368 0.496272 0.025695 +2 0.266901 0.267368 0.000001 0.511726 0.254541 +3 0.495804 0.496272 0.511726 0.000001 0.483445 +4 0.025227 0.025695 0.254541 0.483445 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..623b615f5b3971f309f64906724949e4ba4ba49e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001353_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.25678569 Before NNI: tree length is 0.25678575 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001356_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..69041e77722122c2d73d294b1740d9ed4e28a7b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.13776121 Before NNI: tree length is 0.13776125 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f9824e9ccc6d33477b6e247d7899fbd1b02b064 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001370_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03919250 Before NNI: tree length is 0.03919250 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a8f119762f9b46806908bc277d288467a4265f97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001373_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.061850 0.117722 0.010419 +1 0.000001 0.000001 0.061850 0.117722 0.010419 +2 0.061850 0.061850 0.000001 0.100433 0.058299 +3 0.117722 0.117722 0.100433 0.000001 0.114171 +4 0.010419 0.010419 0.058299 0.114171 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c3ebf8011d18b40c91da0eb978eae6447054d673 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001374_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.015884 0.088131 0.000001 +1 0.000001 0.000001 0.015884 0.088131 0.000001 +2 0.015884 0.015884 0.000001 0.084146 0.015884 +3 0.088131 0.088131 0.084146 0.000001 0.088131 +4 0.000001 0.000001 0.015884 0.088131 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7e4b8f44b1ab005ce670aab963876cb52abd2ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001382_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.014753 0.000001 +1 0.000001 0.000001 0.000001 0.014753 0.000001 +2 0.000001 0.000001 0.000001 0.014753 0.000001 +3 0.014753 0.014753 0.014753 0.000001 0.014753 +4 0.000001 0.000001 0.000001 0.014753 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9c782b0c85548e4d4b72b02cca113f4ace510df1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001387_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.000001 0.024369 0.000001 +1 0.000001 0.000001 0.000001 0.024369 0.000001 +2 0.000001 0.000001 0.000001 0.024369 0.000001 +3 0.024369 0.024369 0.024369 0.000001 0.024369 +4 0.000001 0.000001 0.000001 0.024369 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..872788e8f8aed9b5be0f2af28eabc885f332b94b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001391_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.03841800 Before NNI: tree length is 0.03841800 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f2fe1957daa154cb354b938f8329c3db4f99238d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001417_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.187508 0.484513 0.055867 +1 0.000001 0.000001 0.187508 0.484513 0.055867 +2 0.187508 0.187508 0.000001 0.465536 0.137483 +3 0.484513 0.484513 0.465536 0.000001 0.434487 +4 0.055867 0.055867 0.137483 0.434487 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001436_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001436_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..32c68828ee15b96e82777b8f534339cd4f93d9b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.10680700 Before NNI: tree length is 0.10680700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdd2d9607003fe1bed36ba7f80c60fc12f093ed4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001444_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..37dbb9de08f652a59596619bd8c450aee4457e93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001447_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001103 0.036704 0.055148 0.009910 +1 0.001103 0.000001 0.037806 0.056250 0.011013 +2 0.036704 0.037806 0.000001 0.064635 0.045293 +3 0.055148 0.056250 0.064635 0.000001 0.063737 +4 0.009910 0.011013 0.045293 0.063737 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..34db1ee69558e712b642f1fa60880b702f4521d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001448_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007619 0.051423 0.126624 0.005936 +1 0.007619 0.000001 0.058129 0.133329 0.009694 +2 0.051423 0.058129 0.000001 0.140938 0.056446 +3 0.126624 0.133329 0.140938 0.000001 0.131646 +4 0.005936 0.009694 0.056446 0.131646 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..b75b2e2309dd8003680e2531534b6f67a98038eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001457_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.89442145 Before NNI: tree length is 0.89442150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c432dd33181f9bb40c1a725b823141ac211107b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001458_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007308 0.011833 0.369105 0.007785 +1 0.007308 0.000001 0.009561 0.366832 0.005513 +2 0.011833 0.009561 0.000001 0.361286 0.004164 +3 0.369105 0.366832 0.361286 0.000001 0.361436 +4 0.007785 0.005513 0.004164 0.361436 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..544545220cc26ad16d9bb88debdf026d87f5d551 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001466_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.40556210 Before NNI: tree length is 0.40556213 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ee4dcd88a055e523e626ebb94c72139a721e78b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001468_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.001979 0.060430 0.108563 0.010278 +1 0.001979 0.000001 0.060293 0.108426 0.008336 +2 0.060430 0.060293 0.000001 0.105857 0.068593 +3 0.108563 0.108426 0.105857 0.000001 0.116725 +4 0.010278 0.008336 0.068593 0.116725 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..014584151fe276dfefdac95b66caec82ac40afee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001472_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.36192438 Before NNI: tree length is 0.36192438 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..6b48817abef5f994beab5bdec6257273c2772a89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001473_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.189340 0.597580 0.910725 0.124328 +1 0.189340 0.000001 0.697685 1.010830 0.105942 +2 0.597580 0.697685 0.000001 1.255207 0.632672 +3 0.910725 1.010830 1.255207 0.000001 0.945817 +4 0.124328 0.105942 0.632672 0.945817 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..56b033828db6da4ab91a994a6b1cc8173220f9e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001505_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022472 0.023345 0.164458 0.000001 +1 0.022472 0.000001 0.018025 0.159139 0.022472 +2 0.023345 0.018025 0.000001 0.156572 0.023345 +3 0.164458 0.159139 0.156572 0.000001 0.164458 +4 0.000001 0.022472 0.023345 0.164458 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..d847b01d87bfea5e704428dfcfadc0e50a207af8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001506_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034584 0.184404 0.547137 0.008360 +1 0.034584 0.000001 0.182822 0.545554 0.030277 +2 0.184404 0.182822 0.000001 0.524170 0.180097 +3 0.547137 0.545554 0.524170 0.000001 0.542829 +4 0.008360 0.030277 0.180097 0.542829 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001510_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001510_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..8ac6cdd3db6b581876364455e24645c0d4eb701e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001510_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000949 0.107447 0.177446 0.003884 +1 0.000949 0.000001 0.106662 0.176661 0.004071 +2 0.107447 0.106662 0.000001 0.183025 0.110569 +3 0.177446 0.176661 0.183025 0.000001 0.180568 +4 0.003884 0.004071 0.110569 0.180568 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9076d472b36f51c7adfba92268aed0ce7a9a3570 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001515_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.040253 0.282418 0.852233 0.056082 +1 0.040253 0.000001 0.293399 0.863213 0.067063 +2 0.282418 0.293399 0.000001 0.892564 0.278171 +3 0.852233 0.863213 0.892564 0.000001 0.847986 +4 0.056082 0.067063 0.278171 0.847986 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001517_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9bd1eb4e9a3cab6e80b77cda9ed509c04fadbcdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.68047600 Before NNI: tree length is 0.68047600 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..0e1fec40a1e300c82a26302000e6cbdef5b0c223 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001520_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.242620 0.541307 0.019102 +1 0.000001 0.000001 0.242620 0.541307 0.019102 +2 0.242620 0.242620 0.000001 0.522033 0.239626 +3 0.541307 0.541307 0.522033 0.000001 0.538313 +4 0.019102 0.019102 0.239626 0.538313 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..22c5c53fb21320874a1a1200cb6e0ee06593595d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001546_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007576 0.035509 0.047688 0.016074 +1 0.007576 0.000001 0.031442 0.043621 0.012008 +2 0.035509 0.031442 0.000001 0.064022 0.029376 +3 0.047688 0.043621 0.064022 0.000001 0.044588 +4 0.016074 0.012008 0.029376 0.044588 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..40b58774138f853ef968a070166770378e42d5ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001553_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016203 0.016248 0.059059 0.016203 +1 0.016203 0.000001 0.018071 0.072571 0.000001 +2 0.016248 0.018071 0.000001 0.072616 0.018071 +3 0.059059 0.072571 0.072616 0.000001 0.072571 +4 0.016203 0.000001 0.018071 0.072571 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a94ad7bbd373b725b0870c9b0ae79f6f636616a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001569_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.007435 0.000001 0.061088 +1 0.000001 0.000001 0.007435 0.000001 0.061088 +2 0.007435 0.007435 0.000001 0.007435 0.057158 +3 0.000001 0.000001 0.007435 0.000001 0.061088 +4 0.061088 0.061088 0.057158 0.061088 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6d5d112844c436e45f6581ea7193b4df4518b87f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001573_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9f1a138a74c1bcf4f115ba26cb703386b02c1e66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001580_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.28560833 Before NNI: tree length is 0.28560825 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..209a3968366f95f868f3961ec7cd12c5373ba714 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001588_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.022217 0.078551 0.253807 0.009394 +1 0.022217 0.000001 0.087011 0.262267 0.013789 +2 0.078551 0.087011 0.000001 0.251388 0.074188 +3 0.253807 0.262267 0.251388 0.000001 0.249443 +4 0.009394 0.013789 0.074188 0.249443 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..88b134aa4e74d854d9d79c00c1d4b36d2d3b125c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001595_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.026864 0.262636 0.550204 0.026864 +1 0.026864 0.000001 0.251234 0.538802 0.000001 +2 0.262636 0.251234 0.000001 0.564233 0.251234 +3 0.550204 0.538802 0.564233 0.000001 0.538802 +4 0.026864 0.000001 0.251234 0.538802 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc422d644660aca2d19d5e41c66cf7dac206373b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001599_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 2.05363731 Before NNI: tree length is 2.05363725 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..6bfb627652f6ca6b2a73e55de182167964bded09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001601_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.07154474 Before NNI: tree length is 0.07154475 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..54e9e52bb3363120ecbfc532bc06fe103d10fcb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.007088 0.129219 0.161062 0.007088 +1 0.007088 0.000001 0.128512 0.160354 0.000001 +2 0.129219 0.128512 0.000001 0.176508 0.128512 +3 0.161062 0.160354 0.176508 0.000001 0.160354 +4 0.007088 0.000001 0.128512 0.160354 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001606_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..fea1382e8c062acaea613428ab5be2ba5a31f2c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.23658523 Before NNI: tree length is 0.23658525 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c8b5baa76c363e8ab8b0fb287716b79b00e6ff37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001610_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034657 0.509451 0.069666 0.067529 +1 0.034657 0.000001 0.512377 0.072591 0.070454 +2 0.509451 0.512377 0.000001 0.515081 0.501701 +3 0.069666 0.072591 0.515081 0.000001 0.073159 +4 0.067529 0.070454 0.501701 0.073159 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e40947bff9dfcf4bab89d9f444b644416ee41273 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.009447 0.064177 0.010560 0.018449 +1 0.009447 0.000001 0.073623 0.020006 0.010545 +2 0.064177 0.073623 0.000001 0.068249 0.082626 +3 0.010560 0.020006 0.068249 0.000001 0.029009 +4 0.018449 0.010545 0.082626 0.029009 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001611_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..eff7a06f5783dbdcc99900b61138a7d8be76372e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.09071332 Before NNI: tree length is 0.09071325 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..5e2f7cccad1bf5a53a760168958bb797f522b4d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001621_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.046954 0.048089 0.015518 +1 0.000001 0.000001 0.046954 0.048089 0.015518 +2 0.046954 0.046954 0.000001 0.024881 0.053822 +3 0.048089 0.048089 0.024881 0.000001 0.054957 +4 0.015518 0.015518 0.053822 0.054957 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001629_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001629_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..84d729bf969beb8fc855ebae44c406e6978de237 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.53198187 Before NNI: tree length is 0.53198188 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b08daee73d0d3ce891da3dd7f94e5f645934498 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001632_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..e7f762ff986d24cb5b18690292c0e91d7e5f6027 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001637_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.020878 0.012894 0.010799 +1 0.000001 0.000001 0.020878 0.012894 0.010799 +2 0.020878 0.020878 0.000001 0.018698 0.010079 +3 0.012894 0.012894 0.018698 0.000001 0.008620 +4 0.010799 0.010799 0.010079 0.008620 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..258bee016069cc945dc3a0774165f42116202b83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001639_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.034223 0.016834 0.013667 +1 0.000001 0.000001 0.034223 0.016834 0.013667 +2 0.034223 0.034223 0.000001 0.031280 0.031157 +3 0.016834 0.016834 0.031280 0.000001 0.013768 +4 0.013667 0.013667 0.031157 0.013768 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..f763998b403b14e684e5917839c9885a8c83c1c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001647_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.216106 0.390308 0.003107 +1 0.000001 0.000001 0.216106 0.390308 0.003107 +2 0.216106 0.216106 0.000001 0.451078 0.216003 +3 0.390308 0.390308 0.451078 0.000001 0.390205 +4 0.003107 0.003107 0.216003 0.390205 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..ad1e72883676ba43cde00c9bd82eca895501ac92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001684_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.142412 0.375803 0.022016 +1 0.000001 0.000001 0.142412 0.375803 0.022016 +2 0.142412 0.142412 0.000001 0.390659 0.131042 +3 0.375803 0.375803 0.390659 0.000001 0.364433 +4 0.022016 0.022016 0.131042 0.364433 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..54242c4e984c55243940a6a1150b9b5564cdb2f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001687_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012793 0.091225 0.165403 0.011356 +1 0.012793 0.000001 0.089646 0.163824 0.006458 +2 0.091225 0.089646 0.000001 0.177109 0.088210 +3 0.165403 0.163824 0.177109 0.000001 0.162388 +4 0.011356 0.006458 0.088210 0.162388 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd95f526863724cb28fa37d065e8aae639222791 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001689_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 1.00126148 Before NNI: tree length is 1.00126150 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..cf69d7dddafff4f413cb4d14e09af5484263531c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001694_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.012645 0.160470 0.196701 0.044213 +1 0.012645 0.000001 0.164304 0.200534 0.048047 +2 0.160470 0.164304 0.000001 0.250146 0.176541 +3 0.196701 0.200534 0.250146 0.000001 0.212772 +4 0.044213 0.048047 0.176541 0.212772 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..c203d85f2d18945987020680ec2355a53b9df837 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.086608 0.332989 0.007279 +1 0.000001 0.000001 0.086608 0.332989 0.007279 +2 0.086608 0.086608 0.000001 0.324270 0.080655 +3 0.332989 0.332989 0.324270 0.000001 0.327036 +4 0.007279 0.007279 0.080655 0.327036 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001697_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..23336e955712dc7e4ae41fe704542ece7957c88b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.37259700 Before NNI: tree length is 0.37259700 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..71819c76723d6fa3f7d923d0583707628e5cc26d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001701_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003673 0.407693 0.294256 0.012838 +1 0.003673 0.000001 0.405077 0.291641 0.010222 +2 0.407693 0.405077 0.000001 0.443995 0.408195 +3 0.294256 0.291641 0.443995 0.000001 0.294758 +4 0.012838 0.010222 0.408195 0.294758 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001707_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001707_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..77d1f8fed07649202109e60443816eea06091d12 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/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 0.76258372 Before NNI: tree length is 0.76258375 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac210ef4ba886632d0642cb924dcd3946745658a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001708_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.52809100 Before NNI: tree length is 0.52809100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..fa280c139bead58f36b4207767a921a38f7ad349 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001713_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.034399 0.038817 0.934532 0.000001 +1 0.034399 0.000001 0.053002 0.959354 0.034399 +2 0.038817 0.053002 0.000001 0.963772 0.038817 +3 0.934532 0.959354 0.963772 0.000001 0.934532 +4 0.000001 0.034399 0.038817 0.934532 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..a750116734c92a571b4fa571b96f8488af1bfb1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001717_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.000001 0.525414 0.617375 0.000001 +1 0.000001 0.000001 0.525414 0.617375 0.000001 +2 0.525414 0.525414 0.000001 0.553402 0.525414 +3 0.617375 0.617375 0.553402 0.000001 0.617375 +4 0.000001 0.000001 0.525414 0.617375 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..2df04ed1c864dfabba3f18e6c4d0f3a16c64055d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001718_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.79604950 Before NNI: tree length is 0.79604950 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..90d532136b9005d6ea9880f8a55cc25350add571 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001721_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.016464 0.335411 0.590772 0.030721 +1 0.016464 0.000001 0.339640 0.595001 0.034949 +2 0.335411 0.339640 0.000001 0.582257 0.316041 +3 0.590772 0.595001 0.582257 0.000001 0.571402 +4 0.030721 0.034949 0.316041 0.571402 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip new file mode 100644 index 0000000000000000000000000000000000000000..9a5a5ad8a9504d180fe04cfce4efb3b5ef074ea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001725_tree_id.txt.dist.phylip @@ -0,0 +1,6 @@ +5 +0 0.000001 0.003291 0.191270 0.146969 0.000001 +1 0.003291 0.000001 0.188147 0.143845 0.003291 +2 0.191270 0.188147 0.000001 0.160829 0.191270 +3 0.146969 0.143845 0.160829 0.000001 0.146969 +4 0.000001 0.003291 0.191270 0.146969 0.000001 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c03ab1eda7ce5ff575c63aa9cae684f5818431a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001731_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 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/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip_fastme_stat.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip_fastme_stat.txt new file mode 100644 index 0000000000000000000000000000000000000000..faeee49ec83d2ff5edfc64ad1e7a0aaab674bea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Distances_SpeciesTree/OG0001732_tree_id.txt.dist.phylip_fastme_stat.txt @@ -0,0 +1,34 @@ + + - FastME 2.1.6.3 - + + +Papers to be cited: + +FastME 2.0 - A comprehensive, accurate and fast distance-based phylogeny inference program. + Vincent Lefort, Richard Desper and Olivier Gascuel, + Molecular Biology and Evolution 32(10), 2798-800, 2015. +BIONJ algorithm: + Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. + Molecular Biology and Evolution, 14(7):685-695 + +------------------------------------------------------------------------------- +Settings for this run: + + I Input data type Matrix + D Number of datasets 1 + M Initial tree building method BIONJ + N NNI postprocessing NNI_BalME + S SPR postprocessing yes + +------------------------------------------------------------------------------- +Dataset 1 + Two tree searches are performed, with NNIs and SPRs respectively. + The resulting tree is the best (shortest) of both. + + Tree length is 0.08418100 Before NNI: tree length is 0.08418100 + Performed 0 NNI(s). + + + Performed 0 SPR(s). + + Explained variance : 1.00000000 diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..836a5f4da47d8d0f5fde1a7b27006eda84370247 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt @@ -0,0 +1,2 @@ +((1_1076:0.00000000,(1_1970:0.00000000,(0_2015:0.00000000,(((0_992:0.00229540,0_1335:0.14500060):0.00377913,1_1072:0.01089969):0.00109931,(4_2144:0.00000000,(1_1064:0.00000000,(0_1245:0.00000000,(4_1289:0.00000000,(1_977:0.00000000,(0_150:0.00000000,(4_1202:0.00000000,(4_566:0.00000000,2_1188:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,4_564:0.00000000,4_1827:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d3ea241c89f212a47c4f7d6e66a2c5fa48a1d0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt @@ -0,0 +1,2 @@ +((((1_80:0.00000000,(4_1300:0.00000000,(1_974:0.00000000,(1_2226:0.00000000,(1_1350:0.00000000,(1_327:0.00000000,(4_2104:0.00000000,0_685:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,4_581:0.00000000):0.00098700,(4_1111:0.00000000,(4_971:-0.00482164,0_2166:0.09516164):0.00482164):0.00098700):0.15460173,(0_1449:0.05673154,0_2164:0.69997046):0.10759912,0_1350:0.09274169); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..05938f3c3b6ac3a97653d2ee692c507ee951718e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt @@ -0,0 +1,2 @@ +((2_2226:-0.02265507,((2_2440:0.16014216,2_2577:0.01641084):0.08779720,2_2557:-0.02489720):0.03162807):0.04192191,((2_2441:0.29584323,2_688:0.47567477):0.36602046,((1_325:0.12568084,(3_1844:0.03139033,4_864:0.02020567):0.11514616):0.05253490,4_1490:0.31001335):0.11818860):0.08849507,1_1715:0.00214371); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1db9ece5eb12aa01b342bff1bcc9f5b1ac7824c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt @@ -0,0 +1,2 @@ +(((3_2235:0.11216389,(2_2354:0.05555261,(0_519:0.00421984,4_522:0.00450616):0.02603239):0.01233836):0.02464242,1_253:0.07817220):0.44894467,((1_1562:0.00126295,4_1776:0.00009905):0.00541692,0_1855:0.00437708):0.07758448,3_861:0.05838252); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a043eff3cbec72e4aecaa1e3d0132d0c0ea369d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt @@ -0,0 +1,2 @@ +((((0_1505:0.01480302,(1_1225:0.01532611,4_1432:0.00921789):0.00776337):0.36350839,((3_1123:0.53626021,2_1211:0.22298879):0.27642981,0_1786:0.64645720):0.14131429):0.37788074,0_1604:0.00021408):0.00986642,4_1534:0.00624150,1_1319:-0.00163650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..537cf9b40766fb6a06eda13461f5fdae5b7a5889 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt @@ -0,0 +1,2 @@ +((2_495:0.11277233,1_1890:0.02172467):0.01843095,(4_2110:-0.00321052,(((3_423:0.81439658,3_633:1.16393842):0.37186589,3_1824:0.37487511):0.31832802,3_437:0.03141573):0.02772414):0.00991827,0_2177:-0.00407695); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..21cdac0ac2c09af47159e8727107c0afadb078e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt @@ -0,0 +1,2 @@ +(0_2236:0.01392864,(((2_421:0.26787438,((2_1803:0.73325550,4_562:1.16960650):0.24232796,3_2381:0.91730269):0.78918974):0.07000540,3_375:0.16747856):0.17454073,4_2178:0.00856487):0.01108813,1_1940:0.01916036); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0adcd0caca4c73bd2f4dd7a91da7e5c1baf4d75e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt @@ -0,0 +1,2 @@ +((((4_90:0.00000000,1_2059:0.00000000):0.00000000,(2_277:0.02610179,0_95:-0.00066179):0.00066179):0.77677782,3_600:0.39614375):0.27961125,3_653:0.00000000,4_1954:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5fc92aa24e00ce6311895697196eb596bc328ecc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt @@ -0,0 +1,2 @@ +((4_1308:-0.00013422,0_1359:0.00413422):0.00013422,(((3_2178:1.20931222,0_164:1.17994078):1.03587084,3_1370:-0.06368284):0.13228547,2_1459:0.00633928):0.05861997,1_1098:-0.00013422); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0dce3aadcbd0b96a82238cd222eb7221765f2138 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt @@ -0,0 +1,2 @@ +((4_249:0.00334650,0_251:0.00048250):0.00863291,(2_100:0.18897131,((2_572:1.45049530,3_507:1.26279670):0.25544114,3_68:0.41616340):0.28058851):0.22004869,1_2215:0.00839211); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4b8b4f8e7ee8bfa7e167150803b1ed6b0278c22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt @@ -0,0 +1,2 @@ +((((0_851:0.01139387,1_582:0.00290412):0.75345837,2_2002:1.06260013):0.35233950,(4_812:0.86043362,3_1900:0.58953737):0.47720050):0.69497075,0_861:0.02612650,1_592:0.04317450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a6e71bb2526b7afe3ecd5eea51cb79f8198db3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt @@ -0,0 +1,2 @@ +((1_1258:0.00200050,0_1536:0.00896550):0.00446675,(((3_1789:1.33546069,3_696:1.69503631):0.58579475,3_626:0.87434475):0.34330212,3_1216:0.18607587):0.18015113,4_1463:0.00423125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9bcca9512f3eb8016999549fd4cf23d392437bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt @@ -0,0 +1,2 @@ +((((1_1703:0.00664034,(0_1986:0.00280441,4_1921:-0.00002441):0.01909816):0.17527966,3_715:0.23809934):0.09273941,3_725:0.70705597):0.67427703,0_1732:0.00349297,2_1064:0.00293503); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdd7fd0feaebdc9a6b54be57774c210c220c588c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt @@ -0,0 +1,2 @@ +((0_1747:0.00762216,4_1669:0.00143484):0.02344403,((3_983:0.14246872,(2_2582:0.71102266,2_381:0.41369034):0.16667328):0.05888703,2_1047:0.27084322):0.05811453,1_1455:0.03247947); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a19a2fb6fc4231ff798391d072aca73b8c84ae67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt @@ -0,0 +1,2 @@ +((((4_1883:0.00327607,0_1944:0.01149893):0.00149267,1_1665:0.00746079):0.03924424,2_818:0.03957108):0.02032753,(4_166:0.81894370,4_165:0.39007030):0.57450385,3_756:0.06378426); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..141119b0aee75b9104d76b32ab52ac51995a8435 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2009:0.00102260,(4_40:0.00830577,0_45:0.00089023):0.00250281):0.09956885,2_339:0.10271446):0.36810510,3_1473:0.31915437,2_1578:0.15227963); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..48a12a64d683462c8094564cb35e3fb22eb49145 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt @@ -0,0 +1,2 @@ +((((0_167:1.35620900,2_2034:-0.29456700):0.39129700,3_1928:0.44712050):0.20511250,0_824:0.01032000):0.00761300,4_783:0.00000000,1_555:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c124fd6cea034cc8f8bef6d9d1db5376b38d2171 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt @@ -0,0 +1,2 @@ +((((0_199:0.00000000,4_199:0.00000000):0.00376662,1_2143:0.00194237):0.00958713,3_120:0.01182137):0.03643063,2_174:0.04419087,3_122:2.45133812); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..018c8ea8324e5d78d7586cb1e4fdaa4eb8746e4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt @@ -0,0 +1,2 @@ +((((4_208:0.00000000,1_2152:0.00000000):0.00000000,0_208:0.00000000):0.15668744,2_157:0.04740756):0.60167566,3_307:0.72564913,2_2156:0.52650587); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d8e57073d454cfbee3953e42ae4ab80437f55e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt @@ -0,0 +1,2 @@ +(((1_83:1.12642419,2_785:0.03646581):0.01229844,3_744:0.03623756):0.01766494,(1_1677:0.01653606,4_1895:0.00826094):0.00151844,0_1957:0.00861506); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..32106449694b5b33cae453e8e0c5b6ae7da21bbb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt @@ -0,0 +1,2 @@ +(((0_2101:-0.15058583,(1_1825:0.17770625,3_501:0.65466475):0.42771580):0.19032916,2_577:0.33351368):0.07398380,1_1826:0.13320558,4_2047:0.06527142); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..078872e5d95fa832abe0637c41309f1469277bb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt @@ -0,0 +1,2 @@ +(4_2069:0.00420819,(((3_474:0.13454819,4_158:2.39922181):0.09205469,2_548:0.05849831):0.06299944,1_1848:0.01371456):0.01002194,0_2123:0.00185681); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..64b962931a68c490af9dbede4bf1adca641c6265 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1946:0.00560969,(4_2184:0.00549603,0_2242:0.00226797):0.00086950):0.03322888,2_416:0.03501343):0.03909647,3_369:0.06960375,2_721:0.49235125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..20eda5299bb7fd6f4d60f6e640e35ae52a7fc0f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt @@ -0,0 +1,2 @@ +((1_1967:1.39443503,(2_1471:0.61606750,3_274:0.55146250):0.53104823):0.34712129,(3_677:0.30923137,3_333:0.20729263):1.00148736,4_106:-0.39217154); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..391113287e64a3c456aeaf814ef4eb882f9abdaa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt @@ -0,0 +1,2 @@ +(1_1956:0.01404125,((3_359:0.12316500,2_405:0.04681400):0.02610225,4_0:0.01693275):0.00789525,0_0:0.00670375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fc649c78b46db0e79e78d6bc965fae273c8b174 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt @@ -0,0 +1,2 @@ +((0_5:0.00543937,(1_1961:0.00117137,4_5:0.00028863):0.00216863):0.03064562,3_353:0.09787812,2_400:0.04376888); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..866ef857a10ce7410a4e3307b543d1a492aec141 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt @@ -0,0 +1,2 @@ +((0_6:-0.00237100,(3_352:0.28838000,2_399:0.06487100):0.09196050):0.00237100,4_6:0.00000000,1_1962:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..09ea17934b69535acc81ad708072dbeb5606cfec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt @@ -0,0 +1,2 @@ +((4_8:0.00024798,(1_1977:0.01394133,0_8:0.00520267):0.00164457):0.07179493,3_2129:0.28412967,2_370:0.07437633); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f39457256d4ceec9cae4bf2ce4df082a3f3f8372 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt @@ -0,0 +1,2 @@ +((2_364:0.07851262,3_346:0.25258237):0.05883138,(1_1983:0.00361612,0_14:0.00942187):0.00215538,4_14:-0.00086838); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3d1a30ae8f150325337f1f95374ecf2f0a138a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt @@ -0,0 +1,2 @@ +((1_1985:0.05015538,(4_16:0.03828838,0_16:0.03629562):0.01567312):0.18180112,3_344:0.57534737,2_361:0.31858062); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b41271172ede4f61d3efad2255562e76984bf62e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt @@ -0,0 +1,2 @@ +(2_199:0.01737812,(0_182:0.08100988,(1_1968:2.28121088,0_31:1.23625813):1.23235362):0.11666313,4_182:0.01121187); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bfd15fb57ee0ecbb9cd1d8140acae482fb08ed73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt @@ -0,0 +1,2 @@ +(((0_35:-0.00033450,1_1999:0.00542250):0.00122700,4_30:0.00695600):0.03733400,2_346:0.07705925,3_288:0.05969075); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..68cafa7422384cb1c0673c38d348a5f5f7f8ec5b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt @@ -0,0 +1,2 @@ +((4_34:0.00000000,(2_342:0.07581700,3_285:0.14985500):0.08173700):-0.00000000,0_39:0.00000000,1_2003:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..65918f41481e1b79c81b46ea14daa60713ad80a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt @@ -0,0 +1,2 @@ +(4_35:0.00504875,((2_341:0.09031975,3_284:0.15297025):0.03957100,0_40:0.03122400):0.02466900,1_2004:0.00411425); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b764017bdc8639395cb01d06c118e42f94cff7a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt @@ -0,0 +1,2 @@ +((4_45:0.00516517,2_329:0.12956983):0.00119657,(1_2014:0.00627592,0_50:0.00309908):0.00230996,3_268:0.01200931); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..22d4531ba774e31d295a8c91375f46a510e2b64b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt @@ -0,0 +1,2 @@ +(((0_52:-0.00043918,1_2016:0.00382318):0.00043918,4_47:0.00000000):0.13267392,2_324:0.17961850,3_265:0.24113450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..46b1912bf88240ccedb22719f4dddb2695757d05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt @@ -0,0 +1,2 @@ +((2_322:0.07151175,3_263:0.40234025):0.08956600,(4_49:0.00286500,1_2018:0.00580600):0.00232300,0_54:0.00944300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8cbdc89cf74b3261191375c9f86acdb8b9a65b80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt @@ -0,0 +1,2 @@ +(1_2025:0.00755811,((2_315:0.06015900,3_258:0.11913700):0.02662956,0_61:0.00887067):0.00137533,4_55:0.00354589); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8d8b3d7865c9896a7424dc62b29127e5b3851b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt @@ -0,0 +1,2 @@ +((1_2027:0.00000000,0_63:0.00000000):0.00401155,(2_312:0.14802767,3_253:0.15225433):0.04508782,4_57:0.00241945); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..19cb54f2f3042d76a388e27280fb2ea1d103e77b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt @@ -0,0 +1,2 @@ +((0_74:0.02081653,(4_68:0.00000000,1_2038:0.00000000):0.01642247):0.07027018,2_300:0.15698267,3_242:0.38749533); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..666ff72c5360afa21e48a9c7b3ba9a9506e7d29e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt @@ -0,0 +1,2 @@ +((1_2041:0.00827975,(4_71:0.00077325,0_77:0.00015175):0.00752275):0.16860875,3_239:0.44382550,2_297:0.22157450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..475c0f3c4514ecfdc0bd5a633f79017ffafd7e33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt @@ -0,0 +1,2 @@ +(((3_236:0.51297675,2_290:0.02588925):0.00461675,0_82:0.01484925):0.01531575,1_2046:0.00124675,4_77:0.00074725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..817beb0b59da49dca031aa86bea9e11bcfb6ec41 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt @@ -0,0 +1,2 @@ +((3_235:0.70070775,(4_78:0.00057775,1_2047:0.00357425):0.04345875):0.05634925,2_289:0.06109900,0_83:0.03162800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a2adda55a9c12a3165fb7343d947c1494d124dfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt @@ -0,0 +1,2 @@ +((0_84:0.00586964,(1_2048:0.00000050,4_79:0.00000050):0.02479486):0.09885755,2_288:0.12148333,3_234:0.32490667); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7da17b34f12cb8af913de6625c369c154fe827ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt @@ -0,0 +1,2 @@ +((4_81:0.00000000,1_2050:0.00000000):0.00000000,(3_232:0.06429150,2_286:0.20444750):0.09737850,0_86:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c6e6b36d592add356bf8d2233c7b5fed48fa42d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt @@ -0,0 +1,2 @@ +((3_226:0.10235150,2_280:0.10072050):0.06690675,(4_87:0.00398725,1_2056:0.00083575):0.00690025,0_92:0.00605025); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1ec91626ba259cdc57b94688d6fc04f45cc673fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt @@ -0,0 +1,2 @@ +(1_2063:0.00291238,(0_99:0.01153637,(3_219:0.18416337,2_272:0.04851563):0.08959512):0.00253513,4_94:0.01602563); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..04c068a2e04115de63b3230d73ee8ae1455ad64e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt @@ -0,0 +1,2 @@ +(((2_271:0.25564225,3_218:0.67627875):0.09958650,0_100:0.03126850):0.00722050,1_2064:0.01830575,4_95:0.02926825); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..120138c27537c090e049df2e399d49bc000d842c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt @@ -0,0 +1,2 @@ +(1_2068:0.00000000,(4_99:-0.00020125,(2_267:0.08912275,3_209:0.05879725):0.14789875):0.00104225,0_104:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ec7fd852b45b5b51a1061fdae3d82502f18dbe6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt @@ -0,0 +1,2 @@ +((3_206:0.60187017,2_264:0.07495483):0.10521451,(1_2071:0.00334266,0_107:-0.00015766):0.00080698,4_102:0.00254069); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f68a1d3a146282687dcdac812c1b19902f533b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2072:0.00000000,4_103:0.00000000):0.00000000,0_108:0.00000000):0.06662200,2_263:0.06081100,3_205:0.36504000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5165af168e701eee020beec5b4186caa41bd0ca4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt @@ -0,0 +1,2 @@ +(((0_109:0.00000050,1_2073:0.00000050):-0.00000000,4_104:0.00000050):0.08513950,2_262:0.04378100,3_204:0.13830300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..67fd5d57fb09e3ec272ea24f1c059b371b93ed7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt @@ -0,0 +1,2 @@ +((4_116:0.01790342,0_111:0.01797858):0.01372494,(2_257:0.12144333,3_190:0.38471867):0.09585591,1_2075:0.01753983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c66557e1fe878afcfec20329c78fb440b0909dd3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt @@ -0,0 +1,2 @@ +(3_183:0.23509556,((1_2083:0.02373050,4_126:0.04389850):0.04831229,0_118:0.05352737):0.03728513,2_249:0.07218044); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1016bc1b00a3cfb73d46765998c9ddd267f3788 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt @@ -0,0 +1,2 @@ +((0_121:0.00729887,(1_2086:0.00283038,4_129:-0.00037537):0.01597862):0.05330613,2_246:0.10669038,3_180:0.20818162); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..da51b3f0ab224f3f678a46f2d59af150508c19c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt @@ -0,0 +1,2 @@ +((2_240:0.00569250,4_135:0.00108950):0.00158350,(1_2092:0.00000000,0_127:0.00000000):0.00239997,3_175:0.17925503); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbaa7ab67e880a8832f152baad3c94e0b9bebdd5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2095:0.00464418,4_138:0.00481782):0.00485221,0_130:0.00377384):0.10445505,3_170:0.14281217,2_236:0.13179683); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b527410ae9b05fd4dca05a38f98e1d97b68c065 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt @@ -0,0 +1,2 @@ +((1_2098:0.00000000,4_141:0.00000000):0.00148794,(2_233:0.40847667,3_167:0.32377133):0.06120969,0_133:0.00278206); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bb80ad479878f129839425687c74121782a38a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2100:0.01497317,0_135:0.07423383):0.07345301,4_143:0.02336853):0.03692447,2_231:0.08983088,3_165:0.08611912); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..82d3f5327493aba64a633051ebf3877fb08c1f30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt @@ -0,0 +1,2 @@ +((0_142:0.00000000,4_150:0.00000000):0.00000000,(2_223:0.08312850,3_162:0.42449950):0.08896950,1_2107:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..144914f3bb39dde13263804327d45add18f74b62 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt @@ -0,0 +1,2 @@ +((4_151:0.00520224,(1_2108:0.01007699,0_143:0.00361001):0.00414749):0.01859043,3_161:0.07207533,2_222:0.03352167); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f87740a9a149d22dda270a949d55f6665ebaed9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt @@ -0,0 +1,2 @@ +(1_2119:0.00314750,(4_169:0.00389650,(2_211:0.02705300,3_156:0.10076500):0.01355350):0.00052650,0_172:0.00194150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..41a76a727801b5c2be7c27f280915785fe559599 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2120:0.00000050,4_170:0.00000050):0.00205675,2_210:0.01893175):0.00199625,0_173:0.00571494,3_155:0.35760406); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9391057a781049c6dfab0b1398a8b5e966df43c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt @@ -0,0 +1,2 @@ +(4_171:0.00000000,((2_209:0.01528850,3_154:0.67969150):0.03512050,0_174:0.01335050):0.02990550,1_2121:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0a103aac2dfb267088d862613f29ed14c7bc7b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt @@ -0,0 +1,2 @@ +(1_2123:0.00409009,((4_173:0.00984550,3_152:0.02676550):0.00751518,0_176:0.00363405):0.00150445,2_207:0.01971491); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..90c1ae09b55bb896b98df6e44101e3c3d024b5c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2124:0.00996683,4_174:0.00797417):0.00943126,0_177:0.01181229):0.00480471,3_151:0.10783863,2_206:0.01982137); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..defb80986ec1e743026d3fde506a6c9d6a032c4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt @@ -0,0 +1,2 @@ +(2_204:0.00739556,((4_176:0.00000000,0_179:0.00000000):0.00087800,1_2126:0.00112100):0.00084500,3_149:0.01689644); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b92da4ce85b4b24cdc097c415d725a662b155d0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt @@ -0,0 +1,2 @@ +(2_196:0.04856815,(4_186:0.00601868,(1_2133:0.00386000,0_186:0.00680000):0.02731389):0.00447032,3_143:0.00256985); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9028f04ac7ad102d6ff37bffb05ea7e111b7b058 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt @@ -0,0 +1,2 @@ +((4_187:0.25667888,(1_2134:0.00000000,0_187:0.00000000):0.01975612):0.01384896,3_142:0.00344067,2_194:0.53548433); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb4f98a37a980adc68e81579fe01dbb715775c1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt @@ -0,0 +1,2 @@ +(((0_194:0.00337213,4_196:0.00538387):0.00942662,3_134:0.02141538):0.00943712,2_180:0.23138463,1_2140:0.01396038); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b7ef38f6558946e04bf50fe8a1828972d26e9ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt @@ -0,0 +1,2 @@ +((2_188:0.19754975,(3_130:0.00662625,0_196:0.00691375):0.06181075):0.00535925,4_198:0.00000000,1_2142:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..881ba78d1ff4334ee8c0f5546f1fe7bd0a0beb0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt @@ -0,0 +1,2 @@ +((1_2146:0.00000050,0_202:0.00000050):0.00586375,(2_171:0.10960325,3_117:0.60426975):0.11889875,4_202:-0.00163625); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe422dd39cfe71e94a1788f2bf9f643c863398d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt @@ -0,0 +1,2 @@ +((4_203:0.00300900,(2_165:0.01556750,3_114:0.08760250):0.01442100):0.00293250,1_2147:0.00000050,0_203:0.00000050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c49574c07c1479ba7f3b3e3725042955e5495efe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt @@ -0,0 +1,2 @@ +((0_207:-0.00834588,(3_109:0.84672788,2_156:0.22870312):0.17089838):0.00834588,4_207:0.03253688,1_2151:-0.00834588); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4a5967568e51234bc8daaa886da6e675c3c1322 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt @@ -0,0 +1,2 @@ +(((4_221:0.01445427,0_220:0.02510773):0.00049367,1_2184:0.00851065):0.00393796,2_143:0.16280417,3_100:0.04311483); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..220679a4e6cae3a66055558d61facaff5168ea40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt @@ -0,0 +1,2 @@ +((3_99:0.06194487,2_142:0.12491512):0.06317438,(1_2185:0.00069437,0_221:0.00185763):0.00465487,4_222:0.00458412); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e60b6afb294d1eb46f0b14e4680e7bd4c33427f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt @@ -0,0 +1,2 @@ +((4_225:0.00697155,(0_224:0.00252752,1_2188:0.00091148):0.00419859):0.07467117,3_94:0.28843317,2_129:0.04922983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b52561e41dc2c910ec25d1de1d2490bbe8602ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt @@ -0,0 +1,2 @@ +((4_229:0.00910662,(0_228:0.01679262,1_2192:0.01052638):0.00407788):0.06277087,3_90:0.79156238,2_125:0.07046263); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c8b61d82b25e1f592b60fa7597feadb445b8be0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt @@ -0,0 +1,2 @@ +(1_2193:0.00000000,(0_229:0.00727525,(2_124:0.02919075,3_89:0.32624425):0.01233975):0.00420075,4_230:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cde26dc80a3f35d08ff80a62f92280ab78205914 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt @@ -0,0 +1,2 @@ +((1_2196:0.01640584,4_233:0.00908116):0.01152747,(3_86:0.78133100,2_119:0.15731000):0.07890459,0_232:0.01207045); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..20b12a116dcbd3a2f7aa281ee374f757e8d0f644 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt @@ -0,0 +1,2 @@ +((0_240:0.02210871,1_2203:-0.00072671):0.00072671,(3_80:0.19830250,2_112:0.04957450):0.08593489,4_240:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..01eeeac71cdddae55a592fc7338328a1cc929225 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt @@ -0,0 +1,2 @@ +(((4_242:-0.00011125,1_2205:0.00401025):0.00567075,0_242:0.00346775):0.07063575,2_110:0.07983850,3_78:0.37343450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..81fefcc0b1db44802a5cae89455a8f6fca823dc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt @@ -0,0 +1,2 @@ +((3_67:0.16989800,2_97:0.18095600):0.07220794,(4_250:0.00000000,0_252:0.00000000):0.00062119,1_2216:0.00283281); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..587d695208ac9bc9dd9103a79582babea0d2824e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt @@ -0,0 +1,2 @@ +(4_255:0.00603230,(1_2221:0.00552067,(2_88:0.04391400,3_59:0.08359000):0.06765589):0.00518333,0_257:0.02022270); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c18dc34e5b3c672338bf79e3d7b07a5f831e08f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt @@ -0,0 +1,2 @@ +(4_257:0.00000000,((3_57:0.27745500,2_86:0.01841800):0.02689194,0_259:0.00065183):0.00191217,1_2223:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b9b20ed4cfac6d42bc86b4d5d537ef991407c5df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt @@ -0,0 +1,2 @@ +(((1_2224:0.01308138,4_258:-0.00016638):0.00016638,0_260:-0.00016638):0.68480037,3_380:0.59788763,2_426:0.69088538); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..240452d725b8df77d03cfc31de73cc7beb5d9c63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt @@ -0,0 +1,2 @@ +((3_55:0.09692100,2_78:0.03714500):0.01998550,(4_259:0.00000000,1_2227:0.00000000):0.00384950,0_261:0.00894150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..484309c85b0905eef6ca079386eae8177ece7501 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt @@ -0,0 +1,2 @@ +(4_264:0.00140976,((3_54:0.21037250,2_71:0.33298850):0.24449070,0_266:0.00111759):0.00217191,1_2232:0.00235324); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..45089ab49c307899f74f4e0dbf581d8505f81c3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt @@ -0,0 +1,2 @@ +((0_269:-0.00021437,(3_51:0.07739538,1_2235:-0.00021437):0.00021438):0.00021437,4_268:-0.00021438,2_66:0.00296538); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa1c5e97d9277d80a26b8e116d12d9676070d78f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt @@ -0,0 +1,2 @@ +((0_271:0.00261544,1_2237:0.00714056):0.00841929,(4_270:0.03067650,2_64:0.00622850):0.00648511,3_50:0.20204667); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7946bd25ecba1428ec34163e1995206a372e1a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt @@ -0,0 +1,2 @@ +((3_49:0.68620162,2_63:0.40458037):0.31899787,(1_2238:0.01418388,0_272:0.02879812):0.01362238,4_271:0.02178612); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc14877d7ab67484e41b6e4fcd441c7032a17ce0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt @@ -0,0 +1,2 @@ +((0_274:0.01273275,(1_2240:0.00494125,4_273:0.00824575):0.05388925):0.06253225,2_61:0.04270675,3_47:0.13158725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a36ddccd423e24b4d17932852ba9fd10d6e15170 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt @@ -0,0 +1,2 @@ +((0_279:0.00001019,(4_285:0.00000000,1_2252:0.00000000):0.00656881):0.01183923,3_36:0.20682217,2_57:0.00483683); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..79feadb0352179da3275c87e3fafb072c663cc7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt @@ -0,0 +1,2 @@ +(0_281:0.00032912,(4_288:0.01043837,(3_34:0.11016912,2_55:0.02472687):0.06823412):0.00766363,1_2255:0.00308387); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b35eb5c6b75bc2359095de994b0ccb45e46c63d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt @@ -0,0 +1,2 @@ +((2_54:0.02219600,3_33:0.07557100):0.04824550,(4_289:0.00000000,1_2256:0.00000000):0.00234750,0_282:0.00234750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f529b12a5b0bbc34b23e3b11b13030dcb5dc2cd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt @@ -0,0 +1,2 @@ +(((1_4:0.02824567,4_294:0.01423933):0.07411509,2_49:0.14922126):0.05931774,0_287:0.16512912,3_27:0.30979888); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a09a165dd4f2dab8a9dbc07d9ca535feadbf2016 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt @@ -0,0 +1,2 @@ +(1_7:0.00826163,((2_46:0.15922962,3_24:0.28822338):0.07038513,0_290:0.01727487):0.00981913,4_297:0.00913737); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..536196b977b348aa47f042ab2e482024ea358785 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt @@ -0,0 +1,2 @@ +(0_292:0.04360993,((2_44:0.23730617,3_23:0.53607283):0.18885612,4_299:0.04538887):0.00753413,1_9:0.04463207); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ebee3c91e11da43090a7eada860cade33146a68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt @@ -0,0 +1,2 @@ +((4_302:0.00093152,1_19:0.00025048):0.01113832,(2_24:0.12450267,3_20:0.21894733):0.10691752,0_295:0.01087372); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..04d36013f1eaada121d7cf748099014d0a4856f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt @@ -0,0 +1,2 @@ +(1_24:0.00000000,((3_15:0.14680850,2_19:0.04203850):0.02563566,0_300:0.01255347):0.00657653,4_307:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd39189425eac217e5fade21cd9b29be09864e0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt @@ -0,0 +1,2 @@ +((1_25:0.00859850,4_308:0.00253150):0.00818525,(3_14:0.30109075,2_18:0.08658725):0.08176525,0_301:0.01370875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d807870441a0a8131f81914b6795ee964bc008ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt @@ -0,0 +1,2 @@ +(4_310:0.00028415,(0_303:0.01968058,(2_16:0.04472667,3_12:0.25704033):0.05933853):0.00373992,1_27:0.01044985); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..02ff020e8bb5f207afaf5cf0b31aeba989ff5ed9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt @@ -0,0 +1,2 @@ +(((1_30:0.00000000,0_306:0.00000000):0.00079500,4_313:0.00178900):0.03345600,3_9:0.17918450,2_13:0.04040350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2dfd6c902f1e6fc4b21a5524901eb6371fafe31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt @@ -0,0 +1,2 @@ +(((3_4:0.11532000,2_8:0.02253100):0.02963325,4_318:0.00554275):0.00492825,1_35:0.00386125,0_311:0.00187475); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..087079621e0d01bbbbafd2006e7ff40456f3086c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt @@ -0,0 +1,2 @@ +(4_319:0.00320100,(0_312:-0.00008013,(2_5:0.04541067,3_3:0.08435033):0.03400729):0.00008013,1_37:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed1644464d0b73b65f43360946104903eb8d1cb4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt @@ -0,0 +1,2 @@ +((0_317:0.01147663,(1_42:0.00630288,4_324:0.00573612):0.00121637):0.03200088,2_0:0.09484212,3_1:0.15409288); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d557fd3d88ba70ebbb61f12489ee9d15765469a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt @@ -0,0 +1,2 @@ +((0_318:0.04194650,(4_325:0.01570350,1_43:-0.00296750):0.03127400):0.24129100,3_2431:1.17405050,2_2620:0.27727950); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..452711afab0ec896f85cb35dfbc19e5337ecde0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt @@ -0,0 +1,2 @@ +((1_44:0.00855537,4_326:0.02879363):0.03053912,(3_2428:0.18881838,2_2617:0.17466962):0.14634712,0_319:0.04091488); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b19e2cc355a78a4b13dcd9be6399b37d9ec9a1d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt @@ -0,0 +1,2 @@ +((2_2615:0.09558900,3_2426:0.24042100):0.07496108,(4_327:0.00583886,0_320:0.00683914):0.01794908,1_45:0.00803715); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7efa455a024fb716a2b873bba39be400a684d3f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt @@ -0,0 +1,2 @@ +(1_46:0.01837888,((2_2614:0.18978312,3_2425:0.57144488):0.15653662,0_321:0.01341788):0.04606963,4_328:0.00894312); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a693e5e019432e35371f2ddcf3dd5b298cdfd2d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt @@ -0,0 +1,2 @@ +(((1_49:0.00466412,0_324:0.01787888):0.00921337,4_331:0.00815963):0.14011788,3_2419:0.35353488,2_2568:0.10013012); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3b4d895b927a1a67c6f826930e73b58287990fa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt @@ -0,0 +1,2 @@ +(((3_2418:0.66689233,2_2567:0.09427267):0.11505288,0_325:0.00030465):0.00736435,4_332:0.00771230,1_50:0.01872670); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..19391a2213a0edeace05e7fb6f44a8aba7906bc9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt @@ -0,0 +1,2 @@ +(4_335:0.00258084,(0_328:0.00288781,(2_2564:0.06572867,3_2416:0.13112833):0.02878027):0.00278119,1_53:-0.00019684); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f80f7fc14d9423dad5ed5ff0da40bb6274131e08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt @@ -0,0 +1,2 @@ +(1_54:-0.00014127,((2_2563:0.11153017,3_2415:0.52548883):0.06145421,0_329:0.03050512):0.03710838,4_336:0.00370327); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9a3f5ecbe28e4f85cfed48ad425359e2be1ad11e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt @@ -0,0 +1,2 @@ +(((1_62:0.00000000,4_344:0.00000000):0.00000000,0_337:0.00000000):0.01678900,3_2406:0.12185600,2_2547:0.05560100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..369fb6af8cf27d15e90e06118e436141d3def01c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt @@ -0,0 +1,2 @@ +(1_68:0.00613463,(0_343:0.00744838,(3_2400:0.10518213,2_2541:0.03544087):0.03558812):0.00153062,4_350:0.00768237); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f2da2c74c85561103362593f0514a05e392e5af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt @@ -0,0 +1,2 @@ +((1_69:-0.00835325,2_2540:0.59526725):0.01733325,(3_2399:0.29229250,4_351:-0.00217150):0.01323675,0_344:-0.00411075); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c668bd368811a151e561bcc44870eddca48d4505 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt @@ -0,0 +1,2 @@ +(((1_75:0.00542000,0_350:0.00689200):0.00238050,4_357:0.00518950):0.00728800,2_2535:0.01412400,3_2394:0.07393300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..585c0a6eb8414c8a83ac503e7f9fc21514d95e6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt @@ -0,0 +1,2 @@ +((2_2532:0.01138600,(0_353:0.00000000,4_360:0.00000000):0.03747900):0.89126850,3_1154:1.21972350,2_980:1.15661150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..85ca860fb276c05595a73eaf3cf7c70984185fee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt @@ -0,0 +1,2 @@ +((1_91:0.02039828,(3_2392:0.11160900,2_2520:0.00306600):0.00153300):0.00466472,0_358:0.00000000,4_364:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..51b1cee6cde30abb46e0a4c013a869787857763d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt @@ -0,0 +1,2 @@ +(((0_359:0.00000000,4_365:0.00000000):0.01211325,1_92:-0.00025525):0.02731575,2_2519:0.01709325,3_2391:-0.00125125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..61f9e479e2643c0f0dbb02c0841eca373022fdfd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt @@ -0,0 +1,2 @@ +((4_367:0.00453833,(0_361:0.00904121,1_94:0.00863579):0.00114938):0.02024233,2_2517:0.02590717,3_2389:0.00317683); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b974cf622a5e0870ffcb621fd8a4fd7fe78f2c2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt @@ -0,0 +1,2 @@ +((1_96:-0.00103925,(4_369:0.00000000,0_363:0.00000000):0.00512025):0.00898625,3_1717:0.40181225,2_2515:0.01512575); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..195753dd2a3d8410bd8a6ddc694f8eb89ba567e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt @@ -0,0 +1,2 @@ +(((1_106:0.00000000,4_379:0.00000000):0.00000000,0_373:0.00000000):0.02914300,2_2506:0.02721400,3_2378:0.02911400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5661e18adb7718d53424259e28d2ca83697b537f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt @@ -0,0 +1,2 @@ +(1_109:0.01157538,((3_2375:0.38855800,2_2504:0.17157200):0.10512541,4_382:0.00737923):0.00379077,0_376:0.00958762); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa27f203e084282ece7e8e36b3c878c70b76a12c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt @@ -0,0 +1,2 @@ +(4_385:0.00922350,((2_2501:0.05339400,3_2371:0.13750800):0.06271075,1_112:0.00282125):0.00192925,0_379:0.00533250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..70149bd27d84d24e844ba27c5fbac725198f93ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt @@ -0,0 +1,2 @@ +((4_390:0.00894462,1_116:0.00700138):0.00282512,(3_2363:0.36640137,2_2495:0.00945762):0.01213013,0_384:0.00611388); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..83dd6ffec7ddec0b3c16456b50597ea40a6c2758 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt @@ -0,0 +1,2 @@ +((1_121:0.00000000,4_395:0.00000000):0.00083383,(2_2490:0.00673800,3_2358:0.13961500):0.00703306,0_392:-0.00083383); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..532adb2623815e06891c0c7e65a045f4bf6138be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt @@ -0,0 +1,2 @@ +(((1_128:0.00634950,2_2484:0.06709650):0.00136600,3_2353:0.00380035):0.00823365,4_401:0.00000000,0_398:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b0ae7748b19f8ff1f4037a324b6861db91f928d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt @@ -0,0 +1,2 @@ +((1_133:0.00162913,0_403:0.00433087):0.01327152,(3_2347:0.31498533,2_2477:0.08209867):0.02804992,4_406:0.02574006); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa5eee98d7a91c4afdb0873bba24881d4b9374f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt @@ -0,0 +1,2 @@ +((2_2473:0.12005475,3_2343:0.14604425):0.09348475,(4_410:0.00948050,1_137:0.00201950):0.00241575,0_407:0.00283525); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d3b2113ff7358049179fe3a1b5c9d4b5cb144e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt @@ -0,0 +1,2 @@ +((4_414:0.04632290,1_141:0.04324710):0.02561839,(2_2469:0.18371417,3_2340:0.60971283):0.31767692,0_411:0.03017006); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..85a944c6dd1a81446ead64279838f4508963cfd5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt @@ -0,0 +1,2 @@ +((2_2468:0.01556175,3_2339:0.06121725):0.02619825,(4_415:0.00000000,1_142:0.00000000):0.00063475,0_412:0.00307625); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8063b850dbcbd4aae3a2bbdca5b82efa9f24149b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt @@ -0,0 +1,2 @@ +((0_414:-0.00000000,(3_2337:0.15848200,2_2466:0.03034100):0.04687100):0.00000000,4_417:0.00000000,1_144:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..22994dc8bfd763a9f57d2fa286f9b78a03cf601f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt @@ -0,0 +1,2 @@ +((0_421:0.00426212,(2_2459:0.29290787,3_2330:0.11681313):0.10694937):0.00075588,4_424:0.00266513,1_151:0.00422388); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7e8d00c008ecefd3915099b8c00e55303d4920a6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt @@ -0,0 +1,2 @@ +((1_152:0.00572288,0_422:0.00297712):0.00797562,(3_2329:0.36337712,2_2458:0.09719688):0.06280213,4_425:0.00072038); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a3118db34f79532c6fadcc502728e013602c085 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt @@ -0,0 +1,2 @@ +((1_156:0.01124357,(0_426:0.00733327,4_429:0.01968873):0.00396382):0.11413418,3_2325:0.28443717,2_2454:0.18772883); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8cd81decb8426a1bfa88093aa5a981bb7bf51fdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt @@ -0,0 +1,2 @@ +((0_435:0.00003050,(1_162:0.00172100,4_435:0.00355900):0.01058000):0.10384550,2_2435:0.06434350,3_2319:0.25980050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ac2061687ce7fc5558066794f00ce51233e31e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt @@ -0,0 +1,2 @@ +(0_442:0.00276450,(4_442:0.01159475,(3_2312:0.29497825,2_2429:0.14866675):0.03216375):0.00488475,1_169:0.01165850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..162ac93bb7dfd932d97e546e01df36233ecba12b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt @@ -0,0 +1,2 @@ +((0_443:0.00014263,1_170:0.00313538):0.01303488,(2_2428:0.03914613,3_2311:0.21220387):0.05012337,4_443:-0.00092138); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..57c72cd6cc5c7c8439cca4b339a9b29f97e90a22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt @@ -0,0 +1,2 @@ +(4_447:0.00000000,(0_447:0.00956600,(2_2424:0.15477150,3_2307:0.39868450):0.12011500):0.02304800,1_174:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d49bc42b91a7aa05224d3cd00ad9879d8f1f607b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt @@ -0,0 +1,2 @@ +((1_179:0.00685818,(4_452:-0.00011877,0_452:0.00138377):0.00469559):0.04123854,3_2302:0.45200983,2_2419:0.09036617); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c79e346c5f74e8298172e9e3ab3936a3446fc433 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt @@ -0,0 +1,2 @@ +(((3_2298:0.20098475,2_2415:0.08458625):0.04641025,1_183:0.01359275):0.00739825,4_456:0.00000000,0_456:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5883e1dac31cdb7765a0becfd9de154ed1a40c5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt @@ -0,0 +1,2 @@ +((1_184:0.00869714,(4_457:0.00000050,0_457:0.00000050):0.00410636):0.13936121,2_2414:0.14607750,3_2297:0.49151450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1e06e8dafbac3fcc3dd176978017958ad83c922 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt @@ -0,0 +1,2 @@ +((1_187:0.00000000,4_460:0.00000000):0.00000000,(2_2411:0.22192000,3_2294:0.42185600):0.10857300,0_460:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1d372f40019095b2aa7d8697d45e455dc2ff1a0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt @@ -0,0 +1,2 @@ +((1_189:0.03862400,(4_462:0.01086225,0_462:0.01525975):0.02325000):0.06456500,3_2292:0.53066050,2_2409:0.10742850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd7e9f1826433bc249dd13048d933616061c13ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt @@ -0,0 +1,2 @@ +(((1_192:0.00418075,0_464:0.00680325):0.00294600,4_464:0.01871500):0.04243250,3_2289:0.21875075,2_2407:0.04317425); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..06541e092889f9443927b74c436f8c77cccfb14e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt @@ -0,0 +1,2 @@ +(4_465:0.00006366,((2_2405:0.04919933,3_2288:0.24599067):0.03254728,1_194:0.01583484):0.01451016,0_465:0.00291734); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1f27808d0fa62226df120e0a404f243f417049e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt @@ -0,0 +1,2 @@ +((0_472:0.00860662,(4_471:0.00534412,1_202:0.00700988):0.00097838):0.02086387,3_2282:0.14666838,2_2399:0.02482362); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b3026928cd532d53779b63c905501d81652b80b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2397:0.04123033,3_2280:0.08892967):0.05035346,1_204:0.01061837):0.00246713,4_473:0.00041239,0_474:0.00330261); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..011179502aa18cb6d250a32b08308da544c9ef2a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt @@ -0,0 +1,2 @@ +((3_2274:0.23456150,2_2391:0.19672150):0.21061921,(4_482:0.01007630,1_212:0.02031270):0.01484063,0_483:0.01320279); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4fb1e83cbfcea7686521966af21a224e677bf70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt @@ -0,0 +1,2 @@ +(((0_485:0.00764675,4_484:0.00480925):0.00154250,1_214:0.00876600):0.03549450,2_2389:0.03855875,3_2272:0.06549825); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2edab18d4805823dadd2980a68471948c254ffc6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2386:0.02132962,4_488:0.01579138):0.01094887,0_489:0.01675463):0.17442488,1_218:0.08747088,3_2268:0.13817513); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c289c48ec6140a11d32d228c9e4224c47fab9f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt @@ -0,0 +1,2 @@ +((1_219:0.06670375,0_490:0.06449425):0.04430975,(3_2267:0.12431725,2_2385:0.07730475):0.01763175,4_489:0.07055825); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ea938d0012407c2e8871dfb91d528a88a5f9e24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2382:0.05006875,1_222:0.02733625):0.00279000,4_492:0.05021450):0.00455950,0_493:0.05905725,3_2263:0.05141475); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..54f23f8ebe704b6cd8cd6cb327ea887a76a5e48f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt @@ -0,0 +1,2 @@ +((3_2254:0.14644025,2_2372:0.08766875):0.02706975,(4_503:0.02465900,1_233:0.00570500):0.01272575,0_503:0.02325775); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..10389eada2a36c3289549e83c86fac10a1837560 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt @@ -0,0 +1,2 @@ +((1_239:0.25039400,0_509:-0.01143800):0.07381500,(2_2367:0.27262775,3_2248:0.63488525):0.31187050,4_509:-0.05788000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..26d43dc564d7d1b411e4a99752e15add071dbc67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt @@ -0,0 +1,2 @@ +((0_515:0.00247905,(1_248:0.00342740,4_518:0.00071160):0.00158404):0.11055889,2_2358:0.08874967,3_2240:0.18697033); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..02b7eae2d851f711aca8af3f3e76df614d6cd2b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt @@ -0,0 +1,2 @@ +((2_2356:0.07229617,3_2238:0.13250583):0.07403940,(4_520:0.00431716,0_517:-0.00043316):0.00566584,1_250:0.00478432); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..425faf9504781823e0c8d04dc483dd6b45a00c70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt @@ -0,0 +1,2 @@ +(4_521:0.00466750,(1_251:-0.00004723,(3_2237:0.08585317,2_2355:0.06600583):0.12489442):0.00140473,0_518:0.00849450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..15b02b51a7348ce19fdfd691c91d0b59a5338744 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt @@ -0,0 +1,2 @@ +((1_256:0.01273525,(4_525:0.00000000,0_522:0.00000000):0.02786575):0.28814475,2_2349:0.15009625,3_2232:0.69071375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a12ce5385dcfa973ab319e7255f3378fcc7cfd7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt @@ -0,0 +1,2 @@ +((2_2348:0.00714600,3_2231:0.06669300):0.01652216,(0_523:0.00000050,4_526:0.00000050):0.00020702,1_257:0.00225248); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3188154247bd3821742473385e8f2b05f80da3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt @@ -0,0 +1,2 @@ +((1_259:0.00386763,(0_525:0.00297812,4_528:0.00148687):0.01563038):0.12623088,3_2229:0.42622637,2_2345:0.08408363); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..03f9a4fe6bc24f077d6a8f19952c8c879dce91ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt @@ -0,0 +1,2 @@ +((3_2228:0.21194200,2_2344:0.09591100):0.06221417,(1_260:-0.00037305,4_529:0.00808405):0.00612035,0_526:0.00266770); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..22dab9136c25070a06be51c18378870cdbe33544 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt @@ -0,0 +1,2 @@ +((4_535:0.00667015,(1_266:0.00158930,0_532:0.00630370):0.00327209):0.03465023,2_2337:0.03139117,3_2219:0.12719783); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..be944913c2ffa85e42231f21f0a9d8500594565a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt @@ -0,0 +1,2 @@ +(4_542:0.00313137,(1_273:0.00971363,(3_2211:0.24020888,2_2328:0.11791713):0.10230387):0.00204437,0_539:0.01108663); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6ba8c9864756f1de002be6df84480cb6ccb97c83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt @@ -0,0 +1,2 @@ +((2_2326:0.12459125,3_2209:0.15145475):0.03602275,(4_544:0.00000000,0_541:0.00000000):0.05324788,1_275:0.00747612); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b04df33413ab6d1774efff0da70f0fa09b9ea3f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt @@ -0,0 +1,2 @@ +((0_543:0.16845683,3_2207:0.12704317):0.25901814,(1_277:0.01119562,4_546:0.01459338):0.07940737,2_2324:0.05319119); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee847205c277a95ecf9d8e32facfa36ee6ea7927 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt @@ -0,0 +1,2 @@ +((1_298:0.02430375,(4_557:0.02396275,0_556:0.01928925):0.00319075):0.08123575,3_2194:0.12987075,2_2301:0.11919725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..82427678dfd44c48a033e28b64aaeecdfb1faa0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt @@ -0,0 +1,2 @@ +((2_2299:0.03220917,3_2193:0.11671083):0.03370500,(1_301:0.00192181,4_560:0.00726919):0.00194390,0_559:0.00339430); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fed0c2ecb2471045fbf0aced887f50d284a0b16d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt @@ -0,0 +1,2 @@ +((2_2292:0.09185883,(1_1722:0.12896475,0_587:0.06464925):0.05796475):0.18406550,1_312:0.00237333,4_1949:-0.00012133); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..031f2b204541c317e7cd36db88384e47a51e915e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt @@ -0,0 +1,2 @@ +((3_2141:0.03457950,2_392:0.14353050):0.16016648,(4_570:0.00199583,0_611:0.00151917):0.29905261,3_2140:-0.14403176); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..27e0f09a6a2c0d5549d315ad3ac440b24c914974 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt @@ -0,0 +1,2 @@ +((2_2270:0.08478226,(1_362:0.00242450,4_586:0.00730050):0.00329250):0.00556641,3_2132:0.09008267,0_616:-0.00011167); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa60c5484d0e3a7922fd2feb4f80c913a8b11c92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt @@ -0,0 +1,2 @@ +(((2_369:0.20515217,3_2130:0.07285283):0.05380280,4_588:0.01342589):0.00565511,0_618:0.00611774,1_364:0.00964126); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f42ca609d3f6a641f336d7abb5ec4ccf8cd62121 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt @@ -0,0 +1,2 @@ +((0_622:0.00082850,1_368:0.00168750):0.00308475,(3_2123:0.21773175,2_2265:0.02341325):0.04251025,4_592:0.00575925); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6202ea246020b2a16068d0b373893b7e1fc880c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt @@ -0,0 +1,2 @@ +((2_2264:0.06987025,3_2120:0.49772775):0.04240925,(0_623:0.02261200,4_593:0.01485100):0.01467675,1_369:0.01305075); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f848016c935674c06450e3bdbbfdabf014da6d6d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt @@ -0,0 +1,2 @@ +((0_625:0.04652060,(1_371:0.02040163,4_595:0.00998937):0.04279658):0.23078530,3_2118:0.52356400,2_2262:0.32488700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1ee61acc269c07f0323eb1644271edff80844d0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt @@ -0,0 +1,2 @@ +((1_373:0.00000000,4_597:0.00000000):0.00921247,(2_2260:0.02998867,3_2116:0.05310133):0.00920618,0_627:0.01005553); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c881216140f8d9d934c61026103af5767d000ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt @@ -0,0 +1,2 @@ +(((3_2115:0.13539750,2_2259:0.02046050):0.01119250,1_374:-0.00000000):0.00000000,0_628:0.00000000,4_598:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92d6c34d96766b354b7e3ce1743b5b9c7b463899 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt @@ -0,0 +1,2 @@ +(4_616:-0.00019338,((3_2101:0.04497987,2_2240:0.01443013):0.02298138,1_392:-0.00019338):0.00019337,0_646:0.00152038); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..685f9d6a58b4fda05dcfd8b250380f78349f66ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt @@ -0,0 +1,2 @@ +((4_624:0.00531950,(2_2233:0.03608100,3_2093:0.09050500):0.02602100):0.00011650,1_400:0.00000000,0_654:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e960725c917419b1f95ea5509d1d5fadd617a098 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt @@ -0,0 +1,2 @@ +((0_661:0.00000000,(4_631:0.00000000,2_2220:0.00000000):0.00000000):0.00000000,3_2086:0.00000000,1_407:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d54f15d9571619a55a18f59682bcdbd11968cd7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt @@ -0,0 +1,2 @@ +((4_632:-0.00015062,1_408:0.00120662):0.00015062,(2_2219:0.02244012,3_2085:0.05495687):0.01499263,0_662:-0.00015062); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ea6fdf6bb20ecced8b61d7f8d6353c94332f1b16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2216:0.02833350,3_2084:0.11250950):0.03223416,4_633:0.00051698):0.00302502,1_409:0.00000000,0_663:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..836d9bd97b17d8a88e7688932828c289ace7c963 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt @@ -0,0 +1,2 @@ +((1_411:0.00364500,4_635:0.00108800):0.00471700,(2_2214:0.10386475,3_2081:0.55980125):0.11669850,0_665:0.06955700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9479cba621009f2a91c7cb9031b42d3e41abba15 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt @@ -0,0 +1,2 @@ +(1_416:0.00025775,((3_2078:0.16477800,2_2208:0.02302600):0.04452475,0_670:0.00296225):0.00384825,4_640:0.01452125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a14671e1c10412a1b5c6fefc60ac7c1ae37d25f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt @@ -0,0 +1,2 @@ +((0_673:0.00000000,4_643:0.00000000):0.00000000,(2_2205:0.04679250,3_2076:0.17537050):0.17725850,1_419:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e13cb79a1dc87bb1d7ef59724c4e22a09a2b535a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt @@ -0,0 +1,2 @@ +((1_420:0.00000000,0_674:0.00000000):0.00000000,(2_2204:0.04509250,3_2075:0.19689550):0.02536250,4_644:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0b32d957f70a0ff73c717a96f0fcbf932319d5b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt @@ -0,0 +1,2 @@ +(4_645:0.00224175,(0_678:-0.00001975,(3_2074:0.07522700,2_2203:0.01436900):0.00885275):0.00001975,1_421:-0.00001975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..566ebdaf6e1bb6e1466e5572c01692b5ac42cabe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt @@ -0,0 +1,2 @@ +(4_651:0.00000000,(0_684:0.26989014,(3_2067:0.01464900,2_2195:0.05558600):0.24669271):0.10356586,1_427:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c73793798d1e1dcb21eda4c7b9ea0225b483aff7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt @@ -0,0 +1,2 @@ +((0_690:0.00210997,(4_654:0.00665781,1_430:0.00075319):0.00130991):0.04266615,3_2063:0.18347400,2_2192:0.02684700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8f08ff4cf5a0138be3548b68e94f91b38c39a93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt @@ -0,0 +1,2 @@ +(((4_664:0.00000000,0_700:0.00000000):0.00000000,1_440:0.00000000):0.12722100,3_2053:0.35339400,2_2182:0.05285300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b842b28aadd1454cda228c2299c30ad9502e7a98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt @@ -0,0 +1,2 @@ +((0_703:0.00000000,4_667:0.00000000):0.00728725,(2_2176:0.09952775,3_2049:0.22416325):0.08947375,1_443:0.00521275); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3609ac6382e8c4fbbc2edf720d4a3845d8e702b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt @@ -0,0 +1,2 @@ +((0_708:0.00359309,1_448:-0.00002809):0.01033446,(3_2044:0.27461633,2_2169:0.12222467):0.06778676,4_672:0.00683462); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e3dd5258e415ad3f99926c4d1705698a62d59f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt @@ -0,0 +1,2 @@ +((4_673:0.00182839,(1_449:0.00000000,0_709:0.00000000):0.00595361):0.08540013,2_2145:0.10696933,3_2043:0.32287867); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..90ed7f38a81ac052d47fd57b1451e9070191257a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt @@ -0,0 +1,2 @@ +(((0_715:0.00210562,3_2035:0.00352038):0.00000237,1_455:0.00140363):0.00249137,4_680:-0.00038012,2_2138:0.01168812); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd3126b4a2030e565ed2ba37ae18984711138cdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt @@ -0,0 +1,2 @@ +((2_2129:0.15025512,3_2023:0.38540788):0.13421563,(0_725:0.00723938,1_464:0.01647263):0.00120563,4_689:0.01851387); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1298ac79532cf0bc1cdf85a3c9f96eb1cd20fde1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt @@ -0,0 +1,2 @@ +((2_2127:0.12726313,3_2021:0.29359088):0.08737437,(4_691:0.00055213,1_466:0.01020088):0.04453788,0_727:0.01980013); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d3bf76d409ba9e1e5962c2d341573363bba937d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt @@ -0,0 +1,2 @@ +(1_470:0.00000000,((2_2123:0.06467925,3_2017:0.12599775):0.06095025,4_695:0.00352775):0.00839825,0_731:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e999ce25ad6b7591ffc66f78d47dc86706e3f975 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt @@ -0,0 +1,2 @@ +(((3_2016:0.15188300,2_2122:0.03217300):0.03206350,4_696:0.00413000):0.00341200,0_732:0.00000000,1_471:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e0f12ec1669a6382007141b9af67be449b26987 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt @@ -0,0 +1,2 @@ +((1_475:0.00499737,0_736:0.01206763):0.01107588,(2_2118:0.12979338,3_2012:0.22540462):0.08309088,4_700:0.00186312); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b23ef94a2d5301a79fd5f4c38be42739db6ba1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt @@ -0,0 +1,2 @@ +(4_704:0.00186863,((3_2008:0.10159913,2_2113:0.08313188):0.06616563,1_479:0.00676738):0.00206262,0_740:0.00252237); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdc9c707ef559f9e8aafac9307c5bec943f3c46d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt @@ -0,0 +1,2 @@ +(1_484:0.00620608,(3_2004:0.03715751,(4_711:0.00769217,2_2110:0.00900983):0.00927500):0.00166599,0_744:0.00118592); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0de4dfd5717aa5d2c79b55344aa65e64ba284c71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt @@ -0,0 +1,2 @@ +(0_745:0.00794187,((3_2003:0.18943762,2_2109:0.04167138):0.06973912,1_485:0.00616987):0.00567063,4_712:-0.00057487); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d865224628068ac44f12dbc54b5321b49d790fe7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt @@ -0,0 +1,2 @@ +((1_486:0.00138912,(4_713:-0.00041162,0_746:0.00236262):0.00348788):0.03580338,2_2108:0.04900437,3_2002:0.28148662); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a37e70988aac7c3553133ddb57acf4e5bf4f9b0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2104:0.00786350,3_1998:0.15801050):0.00210650,0_750:-0.00000000):0.00000000,1_490:0.00000000,4_717:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..755fc6a47f6932974f1bfb5acc2a152dd0558910 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt @@ -0,0 +1,2 @@ +(4_718:0.01611126,((2_2103:0.02158117,3_1997:0.23314683):0.01809673,1_491:0.01312068):0.00528582,0_751:0.00420974); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..774bb4dbf5074505e435b60533025d68fb82aec5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt @@ -0,0 +1,2 @@ +((1_492:0.00185859,(4_719:0.00589874,0_752:0.00100526):0.00189351):0.00757573,2_2102:0.00645500,3_1995:0.14051200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fa31497842e5bce7f86be5529761ff693deaf54d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt @@ -0,0 +1,2 @@ +((1_494:-0.00017388,(4_721:0.00017388,0_754:-0.00017388):0.00017388):0.02692037,3_1993:0.18009412,2_2100:0.02952788); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ed506709b6655c0000cc962f5e6d332539c03ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt @@ -0,0 +1,2 @@ +(1_496:0.00388162,((3_1991:0.33851338,2_2098:0.09650963):0.09123713,4_723:0.00777888):0.00553613,0_756:0.01585238); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ccf618945db7dd8c419f6b77d42ac6976e50883 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt @@ -0,0 +1,2 @@ +((4_727:0.01367141,(1_500:0.00000000,0_760:0.00000000):0.01077159):0.05259397,2_2095:0.40706317,3_1987:0.15118583); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..67c0af5ec324d6957129805dbc2a96e823027fbb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt @@ -0,0 +1,2 @@ +(1_501:0.00000000,(4_728:0.00580827,(2_2094:0.08482050,3_1986:0.25533050):0.10270392):0.00891773,0_761:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..759bd2baf148581ad4a79f59425d3bf48c51353e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt @@ -0,0 +1,2 @@ +((4_730:0.00251706,(1_503:0.00000000,0_763:0.00000000):0.00041294):0.01110202,3_1984:0.16057800,2_2092:0.01619400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6b1ee27f078b4f61b485f5b08291d271bb9846a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt @@ -0,0 +1,2 @@ +((1_504:0.00000000,(3_1983:0.04912600,4_731:0.00000000):0.00000000):0.00000000,2_2091:0.00000000,0_764:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..286188c7ade0b831a07608b6fdbd248b53ec30d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt @@ -0,0 +1,2 @@ +((0_765:0.00000000,1_505:0.00000000):0.00000000,(2_2090:0.08224050,3_1982:0.19127350):0.00186950,4_732:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..63253a5cc54d5d3553df0d66c07bc56e187ca8c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt @@ -0,0 +1,2 @@ +((3_1978:0.03851775,2_2086:0.01708025):0.00487400,(4_736:0.00237300,1_509:0.00292000):0.00057200,0_769:0.00101400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c796aba0fafe3b0f0e85e46b14cc36c71675e26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt @@ -0,0 +1,2 @@ +((4_739:0.00507457,(0_772:0.00000000,1_512:0.00000000):0.00041543):0.02693886,2_2082:0.04767533,3_1974:0.05269467); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2de07704daeb2edfb647306ad2476d91b7cea31c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1973:0.07509250,2_2081:0.13113950):0.06002800,4_740:0.00828650):0.00276600,1_513:0.01704625,0_773:0.01753775); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e193dbf655f164c712cd6a629fbe1b7a0f14517 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt @@ -0,0 +1,2 @@ +((3_1972:0.32608425,2_2080:0.13310175):0.13617250,(1_514:0.01358975,4_741:0.01190725):0.04899750,0_774:0.02805850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a6fccf6f3e0381d81385aa1e4471dc1937baa1e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt @@ -0,0 +1,2 @@ +((2_2079:0.09838483,3_1971:0.23695017):0.10965636,(1_515:0.00763600,4_742:0.00263800):0.00475502,0_775:0.01336644); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..61ac2273d2593b635bd1f86f21bea34eeb39cea9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt @@ -0,0 +1,2 @@ +(1_516:0.00605745,((3_1970:0.07224717,2_2078:0.07509083):0.07107723,0_776:0.01481618):0.00370432,4_743:0.01185755); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0759f7cb4ec819b1b2524c81fa55313a54f3ca99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt @@ -0,0 +1,2 @@ +(1_519:0.00145125,((2_2075:0.04329675,3_1967:0.08404025):0.01841225,4_746:0.00305225):0.00118425,0_779:0.00531975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f26ff036f8d707d451c8619495a7d0881af8fae1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2070:0.13998667,3_1960:0.41647733):0.14460077,0_784:0.00308030):0.00537620,1_525:0.00419902,4_753:0.00001198); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ac20dc88514afa35d2e930f5ee6ca83ee44b0c2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt @@ -0,0 +1,2 @@ +((0_786:0.00180300,(1_527:0.00272000,4_755:0.00174900):0.00672100):0.06863600,3_1958:0.16242775,2_2068:0.05410125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f56dac3d3511446624611bbcf45c9859f6ed18b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt @@ -0,0 +1,2 @@ +((0_787:-0.00028850,(2_2067:0.03191775,3_1957:0.11339325):0.03777750):0.00028850,4_756:-0.00028850,1_528:0.00028850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6f323d332a369c17d65fd60068fc34c753a8ba0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt @@ -0,0 +1,2 @@ +((1_529:-0.00047488,4_757:0.00161188):0.00318138,(3_1956:0.20445487,2_2066:0.07720713):0.04148188,0_788:0.00423212); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a09c66ea1ff6e788e15d609f843a7831f49a8b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt @@ -0,0 +1,2 @@ +(0_790:0.00091075,(1_531:0.00150650,(3_1954:0.27763050,2_2064:0.18861450):0.21270850):0.00195950,4_759:0.01703725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92c6725372e385e8e4d036f9b199d96fa60906b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt @@ -0,0 +1,2 @@ +((1_533:0.02911312,(0_792:0.00241088,4_761:0.00345012):0.03873387):0.34475588,3_1952:0.34810688,2_2062:0.27832912); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ed1b71808fdd72ab7520dbb7bbeb75d1a3cba8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt @@ -0,0 +1,2 @@ +(((1_534:0.00015317,4_762:0.00143683):0.00676227,0_793:0.01252239):0.09029692,3_1951:0.21477800,2_2061:0.11864500); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4cef737e9142300b8356e9d815c60ef6ed5caed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt @@ -0,0 +1,2 @@ +((0_801:0.00504162,(4_771:0.00056938,1_542:0.00466762):0.00182587):0.00825337,3_1945:0.13591413,2_2047:0.02023088); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b6bd2d5aa154635b7cca52c8dec520c80a62887 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2045:0.00228600,0_803:0.00311800):0.00161950,3_1943:0.05719498):0.00147352,4_773:0.00329150,1_544:-0.00020550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1f599362bb6dbac8708ce08f1ab7d22018de9d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt @@ -0,0 +1,2 @@ +((0_818:0.00293610,(4_777:0.00000050,1_549:0.00000050):0.00139540):0.05617837,2_2041:0.02480533,3_1940:0.15320767); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cba0d95b8aef14af10c090801bbe0a49cc74fbf0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt @@ -0,0 +1,2 @@ +((4_778:0.00000000,1_550:0.00000000):0.00248633,(2_2040:0.05129983,3_1939:0.02800517):0.01131506,0_819:0.00572167); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..471ca58fb4103e3d2943597ed36980c68243c108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt @@ -0,0 +1,2 @@ +((2_2038:0.28465725,3_1937:0.06231875):0.10718075,(4_780:0.00000000,1_552:0.00000000):0.20465234,0_821:0.13753366); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..356caab0cc6c18a6c19e9fefad31f4b415b4aac7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt @@ -0,0 +1,2 @@ +(((2_2035:0.05072417,3_1929:0.09268483):0.03265228,0_823:0.00506834):0.00746066,1_554:0.00000000,4_782:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..59adc50d94647f7d7d12dcb2e3b05f8aa0e7e2fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt @@ -0,0 +1,2 @@ +(1_557:0.00769550,((3_1926:0.17266750,2_2033:0.20745350):0.07367711,0_826:0.00583683):0.00184667,4_785:0.00578950); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..95a346db592ecd751db62f6d0859321ddee437ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt @@ -0,0 +1,2 @@ +((4_786:0.00513875,(1_558:0.01259250,0_827:0.01427650):0.00556425):0.12994525,2_2032:0.11031850,3_1925:0.41141350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..da38eef20d5df9a41d0508a65824164df65870df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt @@ -0,0 +1,2 @@ +(((0_829:0.00000000,1_560:0.00000000):0.00483250,4_788:-0.00074250):0.01589200,3_1923:0.11266150,2_2030:0.02320750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4fca3b82cc236fc3a0ee33242bed0e71ee8f30f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt @@ -0,0 +1,2 @@ +(0_830:0.00000000,(1_561:0.00435425,(3_1922:0.05825675,2_2029:0.01625125):0.01647425):0.00770375,4_789:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6700e1f216b969b24896cebf0392b5af42ae86aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt @@ -0,0 +1,2 @@ +(4_790:0.00000000,((3_1921:0.14935883,2_2028:0.01225817):0.02592749,1_562:0.00785097):0.00586903,0_831:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..13c3e9b902f898d24e8cd9d01361cb8b1a7d708d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt @@ -0,0 +1,2 @@ +((1_566:0.00235262,0_835:0.00096338):0.00459163,(3_1917:0.14924013,2_2024:0.05254187):0.04725963,4_794:0.01008837); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ea6524a6a8e15b7e3829b9a2eb8a73d8c978529 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt @@ -0,0 +1,2 @@ +((4_795:0.00138487,(1_567:0.00156737,0_836:0.00642663):0.00750663):0.04802562,2_2023:0.08101962,3_1916:0.30703437); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a41bacfac3ad8767da7418f7d9cb7b4540f90878 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt @@ -0,0 +1,2 @@ +((0_838:0.03891413,(3_1914:0.67809063,2_2021:0.13995537):0.09421687):0.00914587,1_569:0.01488738,4_797:0.01527263); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1110dac2d6ebf7177e5b26026c21aedbd485e6b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt @@ -0,0 +1,2 @@ +((1_572:0.01295277,(0_841:0.00845723,4_800:0.00994477):0.00732976):0.02854504,2_2018:0.06148917,3_1911:0.27157483); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1dbecab816a680cf3fc8cdf2e6e0cb894713cdd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt @@ -0,0 +1,2 @@ +(((0_845:0.00000000,1_576:0.00000000):0.00000000,4_804:0.00000000):0.00769450,2_2014:0.00751550,3_1907:0.03864650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0276c6145139bb8476b9a415cd5a3b5f188f8a20 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt @@ -0,0 +1,2 @@ +((0_846:-0.00009228,(2_2013:0.03961675,3_1906:0.17330825):0.00308425):0.00717578,1_577:0.00000050,4_805:0.00000050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb9cb47872d4af2b3df5d7abff30a7ed2008f4c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt @@ -0,0 +1,2 @@ +(((1_579:0.00760552,4_807:0.01353448):0.00037273,0_848:0.01630614):0.12762222,2_2011:0.10521133,3_1904:0.56094067); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..51f08fbc3f799ffcfb128eebb5faa540458f9c70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt @@ -0,0 +1,2 @@ +(0_849:0.00710275,(3_1903:0.30522250,(2_2010:0.04458175,4_808:0.02303725):0.08374500):0.05590550,1_580:0.00688325); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8c9ee90e7db6d45e51434c3e278396c6169d1c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt @@ -0,0 +1,2 @@ +((3_1893:0.16400118,(1_598:0.01391200,4_818:0.01318500):0.06900550):0.12363582,0_870:0.00000000,2_1996:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a160648f3de1bf0998de4bd66d9fb7c068b1fc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt @@ -0,0 +1,2 @@ +(((1_599:0.00097325,4_819:0.00107775):0.00136850,0_871:0.00935200):0.02368900,3_1892:0.09462075,2_1995:0.02000325); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a60efcca3f2519db5f37203401bcc8e2982625d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt @@ -0,0 +1,2 @@ +(4_822:0.00716217,((2_1992:0.06915500,3_1889:0.30953100):0.06847517,0_874:0.00738152):0.01345848,1_602:0.00894583); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..867ff85166135e0f83da7d7bc8c2e744244dd916 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt @@ -0,0 +1,2 @@ +(1_604:0.00434713,((2_1990:0.04287513,3_1887:0.04060088):0.00897738,0_876:0.00694213):0.00280888,4_824:0.00432988); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a8b9f8dff9a58b934fb7e3614c9bf6ace86a8f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt @@ -0,0 +1,2 @@ +(((1_608:0.00000000,4_828:0.00000000):0.00000000,0_880:0.00000000):0.05202400,2_1986:0.00511300,3_1883:0.15097500); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bd95f3635bd6846bf435069a20f2819b3deabfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt @@ -0,0 +1,2 @@ +(4_829:0.00000000,((2_1985:0.05289167,3_1882:0.28602433):0.07084851,1_609:0.00622053):0.00615447,0_881:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0368d67558d0a107f3e4b465a71245778dd57935 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt @@ -0,0 +1,2 @@ +((1_610:0.00512858,(0_882:0.00000000,4_830:0.00000000):0.00516242):0.08972453,2_1984:0.07634800,3_1881:0.25693900); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..989442d8220b2e03358c03896e58d6bea0cf5ed3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt @@ -0,0 +1,2 @@ +(4_836:0.00147995,((2_1977:0.08358633,3_1875:0.11230167):0.03016957,1_616:0.00046771):0.00027129,0_888:0.00073805); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c9498f9ce12cb8e609d27507854d843aac05c378 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt @@ -0,0 +1,2 @@ +((3_1871:0.25044433,2_1973:0.06579567):0.03696679,(4_840:0.00000000,0_892:0.00000000):0.00053063,1_620:0.01028037); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb5d56bed8aeda73ca43e7c07b059aacb72e333d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt @@ -0,0 +1,2 @@ +(((4_842:0.01774238,0_894:0.02803062):0.02055688,1_622:0.04189213):0.14982887,2_1970:0.09392387,3_1868:0.34566213); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1954a57be8379a0fd8e36738a589bbb83873868 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt @@ -0,0 +1,2 @@ +(((1_627:0.00438715,0_899:0.00159785):0.00121917,4_848:0.00535432):0.01933528,3_1860:0.10891083,2_1965:0.01860617); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..77fd9429e5f830f7aa606b17e84c5461b680edfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt @@ -0,0 +1,2 @@ +((0_900:0.00442050,(3_1859:0.10053600,2_1963:0.04491300):0.03223750):0.00080150,4_849:0.00000000,1_628:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e5adc0fcb427cfc4d593de1c8bdd05af8340111 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt @@ -0,0 +1,2 @@ +((1_632:0.02184475,(0_904:0.03238250,4_853:0.00386950):0.01471025):0.12544025,2_1959:0.04611200,3_1855:0.85160600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bdb445cb5e944d3125d2ebd9b4574037a0ea5dbb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1957:0.11242388,3_1853:0.21805913):0.10517762,1_634:0.02202888):0.00738263,4_855:0.01811637,0_906:0.01262362); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fbacb198e33d4a88f1482b4731a84a69a35341e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt @@ -0,0 +1,2 @@ +((0_907:0.00000000,4_856:0.00000000):0.00901125,(2_1955:0.34029325,3_1852:0.45517075):0.09769375,1_635:0.02630975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..165a8d42b513eb6de714363acaa07e652eed2cab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt @@ -0,0 +1,2 @@ +((4_859:0.02102200,(1_637:0.00290150,0_909:0.00499250):0.03062350):0.05040550,2_1953:0.10742500,3_1849:0.17703100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c50b51fa0a2a7a0060d036cd4b8f9be8c11cb39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1889:0.04282187,3_1840:0.19982813):0.04217087,1_644:0.00086162):0.00307438,4_868:0.00801438,0_922:0.00500863); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..22134a63c7ce051145c1f9ee4b64162dba8fde61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt @@ -0,0 +1,2 @@ +((0_927:0.00265275,(1_649:-0.00000575,4_873:0.00091275):0.00007275):0.00435675,3_1835:0.07749100,2_1885:0.01540700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3da2180fd16a853db2c070f36fdb19246f40ab7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1883:0.08968355,1_650:0.01153845):0.01212142,3_1831:0.12592211):0.01893083,4_874:0.01655650,0_928:0.00468250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0117ff655bde5a8c7a3bcd6b7ef5cc2a5a4baf6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt @@ -0,0 +1,2 @@ +((4_877:0.00807650,(3_1827:0.15840917,2_1880:0.04229183):0.04101800):0.00376700,0_931:0.01467877,1_653:0.01109223); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..68bc724827b3a59fe4892baa3369d0be7e3f82c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt @@ -0,0 +1,2 @@ +(((4_878:0.00309453,1_657:0.01727947):0.00353366,0_935:0.01266381):0.08999232,3_1825:0.25920567,2_1878:0.10399333); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dbb8d1d79dd5a46112fbb9755b9371a6001b74d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt @@ -0,0 +1,2 @@ +((2_1877:0.13404625,3_1823:0.29982475):0.08764900,(4_879:0.00509450,0_936:-0.00051350):0.01486100,1_659:0.02516200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f772a979871583e9cf1375d8bd4ae13e8e2ec7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt @@ -0,0 +1,2 @@ +(4_882:-0.00021162,((3_1820:0.06505562,2_1874:0.01284437):0.01821313,1_662:-0.00021163):0.00021162,0_939:0.00256462); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0aa2c8f8f743c9c5c527b8709656e16d80f7b111 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt @@ -0,0 +1,2 @@ +((0_942:0.00000000,1_665:0.00000000):0.00000000,(2_1870:0.29369000,3_1817:0.02575200):0.01460300,4_885:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d127bef130523706db4ee46087ca65684492d622 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt @@ -0,0 +1,2 @@ +(((0_945:0.00000000,4_888:0.00000000):0.01669400,1_668:0.00634600):0.02609300,2_1867:0.01917000,3_1813:0.00755800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..293e1cfcfa3770030ecfc9e2c912f62a3194cdb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt @@ -0,0 +1,2 @@ +((0_948:-0.00000550,(1_671:0.00399350,4_891:-0.00000550):0.00000550):0.00000550,3_1810:-0.00000550,2_1864:0.00798650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..73c0bbee0b41e55fd0377533365d93eca0e097e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt @@ -0,0 +1,2 @@ +(1_679:0.00000073,((2_1856:0.22713217,3_1802:0.12639183):0.05648380,4_899:0.00384289):0.00135311,0_956:0.00310627); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b81ce28e03197c971c1d2d0e4dba34d5ff4c128 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt @@ -0,0 +1,2 @@ +(((0_958:0.00000000,4_901:0.00000000):0.00000000,1_681:0.00000000):0.02553450,2_1855:0.05554150,3_1800:0.16495550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cb6a4b0c6d5f1fecf873e11d8a7da5cee9305f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt @@ -0,0 +1,2 @@ +((0_959:0.00000000,1_682:0.00000000):0.01053645,(3_1799:0.20466850,2_1854:0.12010650):0.11207035,4_902:0.01541255); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..918f09fd91a5f86568d3ba685c3a424ea1e89e83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt @@ -0,0 +1,2 @@ +((0_976:0.01981313,1_699:0.01636687):0.01211862,(2_1834:0.00468462,4_920:0.01572438):0.00232213,3_688:1.36090387); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e7aa7af8c9e8afd64666760e8c950fe41fdbdac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt @@ -0,0 +1,2 @@ +((4_921:0.00864725,0_977:0.00220175):0.00279625,(3_1724:0.13302600,2_1833:0.06776800):0.01415725,1_700:0.00446675); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..90dccc41986bacca280a91298434fdb93dc68b3d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt @@ -0,0 +1,2 @@ +((3_1726:0.49800587,2_1831:0.11350612):0.09803987,(0_979:0.00939587,1_702:0.00358713):0.07433488,4_923:0.03642562); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..351b4c6848996cf19caec1fe661b2637251fd961 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt @@ -0,0 +1,2 @@ +((4_924:0.01671905,(1_703:0.00880569,0_980:0.00105431):0.00809471):0.20113683,2_1830:0.51742617,3_1725:0.97699183); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d14ef4df59ef5a051d6391dc915cfd96c9cac3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt @@ -0,0 +1,2 @@ +((4_925:0.00046134,(0_981:-0.20720139,1_705:0.52471339):0.22478705):0.08155576,1_704:0.41306017,2_764:1.27653983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d005fc04b771d73693a769bd196d3bcf6e85554 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1704:0.00785662,4_934:-0.00014763):0.00010312,2_1815:0.01284238):0.00012262,0_990:0.00329963,1_714:0.01043437); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e709d9d1dc55b28ffd5b03322f5a593c6f33d026 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt @@ -0,0 +1,2 @@ +((4_936:0.00235038,0_994:0.02641562):0.00111312,(1_716:0.00702288,2_1813:0.00479312):0.02566562,3_1702:0.00260388); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..00afbea5fead6a346e3e0de9ceec090bc89b683a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt @@ -0,0 +1,2 @@ +(4_944:0.00796162,((2_1809:0.02834413,3_1695:0.23876987):0.05367537,1_725:0.00437513):0.00230637,0_1003:0.00092738); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f404ba77846ee5c28375c20dc5b3272b88322029 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt @@ -0,0 +1,2 @@ +((4_947:0.00716388,(1_728:0.00118033,0_1006:0.00328867):0.01147350):0.07740229,2_1805:0.10798983,3_1692:0.30200717); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..912b62b7f408500400f9b5c7f8163703bb5df9d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt @@ -0,0 +1,2 @@ +((3_1690:0.20452117,2_1801:0.09140283):0.12441946,(4_949:0.00672531,1_730:-0.00040631):0.00595517,0_1008:0.00712915); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ec3961cd8d2172661e0b2a69ebf6db7422f15fdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt @@ -0,0 +1,2 @@ +(0_1009:0.00000000,(4_950:0.00160800,(2_1800:0.05644350,3_1689:0.16195750):0.04793600):0.00183400,1_731:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ba92c43fc0450408f9ed7f02fd95bdad646136f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt @@ -0,0 +1,2 @@ +((1_740:0.00028144,0_1012:0.00315156):0.00591369,(3_1686:0.18146767,2_1797:0.06463633):0.05504713,4_959:0.01032195); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..630331bf51e5f2493c249a5ef4f52eb8b257ad24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt @@ -0,0 +1,2 @@ +((3_1685:0.22661800,2_1796:0.09311600):0.05821800,(4_960:0.01100350,1_741:0.00004650):0.00437050,0_1013:0.00533000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad02f32b57409aab6322ba856db434debe9000cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt @@ -0,0 +1,2 @@ +(4_961:0.02286079,((2_1795:0.12741317,3_1684:0.37001483):0.07479024,1_742:0.04351822):0.00683278,0_1014:0.01360421); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3508e18f066ce3b33c6585574bfcd9263fc63c91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt @@ -0,0 +1,2 @@ +(0_1015:0.00996387,(1_743:0.00901813,(2_1794:0.08185163,3_1683:0.20963837):0.06918837):0.00841137,4_962:0.00617812); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6a2c5beb6806c4f9942c76b86fa2a3ac7aeaa78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt @@ -0,0 +1,2 @@ +(0_1017:0.00103185,((2_1792:0.04195883,3_1681:0.08640117):0.04496648,4_964:0.00105595):0.00204005,1_745:0.00309215); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbdc606df06a913d16e71ee2d3e13d4b6dd09d23 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt @@ -0,0 +1,2 @@ +((2_1784:0.10680325,3_1671:0.27129875):0.10632575,(1_764:0.00000000,4_985:0.00000000):0.00494425,0_1036:0.00271875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2de74ea42bd7d3c446c023695ab19669ba9eb261 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt @@ -0,0 +1,2 @@ +(1_765:0.00000000,((2_1783:0.03811750,3_1670:0.15600350):0.02331278,0_1037:0.01282184):0.00382516,4_986:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..94d1f6d747a1758d0bb286e895712e8d5b310753 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt @@ -0,0 +1,2 @@ +(((4_987:0.00000000,1_766:0.00000000):0.00937476,0_1038:0.00186124):0.23898408,2_1782:0.45132767,3_1669:0.37533733); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..51e0c81ec1bc81f07a99b6414443f746f7aed1de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt @@ -0,0 +1,2 @@ +(4_989:0.00000000,((3_1667:0.21378775,2_1780:0.02875025):0.02069625,0_1040:0.00494325):0.00115475,1_768:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a69d146d2a1c7ccc6bd51888660a685310165358 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1775:0.23187600,3_1663:0.04011100):0.05149600,1_772:0.00000000):0.00000000,4_993:0.00000000,0_1044:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e4e67c70ce6e4b24e0bdd460d76a53fefdffa17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt @@ -0,0 +1,2 @@ +(1_776:0.00025712,(0_1048:0.00173513,(3_1659:0.19380712,2_1770:0.46174988):0.10472988):0.00041038,4_997:0.00174288); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..71a50ddb639e56a08c6974f2a6986e3744aa0e5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1760:0.00962200,3_1650:0.03453600):0.00484100,0_1057:0.00000000):0.00000000,4_1006:0.00000000,1_785:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..41f9e3ddf7fcde9d9cfadcd671cd934873e46814 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt @@ -0,0 +1,2 @@ +(1_786:0.00191182,(0_1058:0.00761953,(3_1649:0.45357133,2_1759:0.26857367):0.26893284):0.02169947,4_1007:-0.00065482); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d36e4fc197383d99bbe61d4fa4db49640dc40ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt @@ -0,0 +1,2 @@ +(0_1073:0.00114488,((3_1635:0.11875687,2_1743:0.04417313):0.02969612,1_801:0.00313888):0.00625912,4_1023:0.00130413); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a9ba754bddc302c14dd69694fed77df5e4bee705 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1634:0.18182600,2_1742:0.05642500):0.05787900,1_802:0.00000000):-0.00000000,0_1074:0.00000000,4_1024:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4b33504b8d1b021fd6f31eecd5a0280bda9c87d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt @@ -0,0 +1,2 @@ +((1_803:0.00445163,(0_1075:0.01098968,4_1025:-0.00051168):0.00579405):0.03666498,3_1633:0.21543433,2_1741:0.04588567); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..60a03f0e0e573e261c70436196ff8d42133bc293 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1632:0.08350233,2_1740:0.02260967):0.03685832,1_804:0.00269195):0.00334405,0_1076:0.00000000,4_1026:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cda6841aa291c1e317a0c2a4068775f7611ef039 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt @@ -0,0 +1,2 @@ +(((1_805:0.00000000,0_1077:0.00000000):0.00000000,4_1027:0.00000000):0.01625850,2_1739:0.01743950,3_1631:0.02357950); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4a7040159cbf4fa6d7e3682d407aeb12223a13d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1734:0.22359225,3_1627:0.39897375):0.08924875,4_1031:0.00778975):0.00164375,1_809:0.00000050,0_1081:0.00000050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a418f91dbd5f75331428d020dbd11356cd4199a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt @@ -0,0 +1,2 @@ +(1_812:0.00000000,((2_1731:0.07645617,3_1624:0.25991183):0.05283563,4_1034:0.00053340):0.00291160,0_1084:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dff983ae62b31b55d1be65fa0ada41d52e53d6f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1728:0.04175663,3_1621:0.10900537):0.03201937,0_1087:-0.00014337):0.00014338,4_1037:0.00484237,1_815:-0.00014337); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..56eaf73cbba19efa0586e690f03df880c026218e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt @@ -0,0 +1,2 @@ +((4_1038:0.00652255,(2_1727:0.08778033,3_1620:0.54704567):0.10111518):0.00780845,1_816:0.00000000,0_1088:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4578a73ac01f1ac77db365abff8c29cbd2e45075 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt @@ -0,0 +1,2 @@ +((0_1089:-0.00048437,(4_1039:0.00584337,1_817:-0.00048437):0.00048437):0.05715187,3_1619:0.19270912,2_1726:0.09495788); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cc7a70800f3a5132ff73fc27f7b4e64a44f2372e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt @@ -0,0 +1,2 @@ +((2_1722:0.03112487,3_1615:0.19376013):0.03697113,(1_821:0.00222237,0_1093:0.00034663):0.00228963,4_1043:0.00510437); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3d79dfe844090c5631974437422511fe187c8a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt @@ -0,0 +1,2 @@ +((1_823:0.00000000,4_1045:0.00000000):0.01424726,(2_1720:0.00265300,3_1613:0.03780200):0.00291400,0_1095:0.00125174); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..19ed026e275d23815e5ecf7c46869af1970687ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt @@ -0,0 +1,2 @@ +(((1_824:0.00000000,4_1046:0.00000000):0.00579372,0_1096:0.00672928):0.09213326,2_1718:0.11727450,3_1612:0.23763950); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..82f887fd20d172645b664664fe841a060bb34b7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt @@ -0,0 +1,2 @@ +(4_1054:0.00000000,((3_1604:0.19009817,2_1711:0.06504183):0.07151003,0_1104:-0.00070742):0.01005342,1_832:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9e88fb93010c769fda1a1377305ead82769c607 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt @@ -0,0 +1,2 @@ +((4_1061:0.00000000,0_1111:0.00000000):0.00000000,(2_1701:0.01353400,3_1598:0.09482500):0.01177700,1_839:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b926e1d79ccf55eb4f338b6f03784683d8af7af1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt @@ -0,0 +1,2 @@ +((1_840:0.00011797,(0_1112:0.00000000,4_1062:0.00000000):0.00114603):0.04069266,3_1597:0.13270333,2_1700:0.03015067); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..902553fbcfe1714c34c30db325b9a0cecfbe9de0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1116:0.00243075,4_1066:0.00060825):0.00607925,1_844:0.00459575):0.04481575,2_1697:0.06594525,3_1593:0.30177875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6702225a3f9fb9a94d6b442d78442d9e69c0e14e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1691:0.03360450,3_1588:0.09451450):0.01707450,1_849:0.00000000):0.00000000,4_1071:0.00000000,0_1121:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8fced530164a55e1787e3491603588673b30b8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1690:0.03480350,3_1587:0.06920450):0.07396650,4_1072:0.00000000):0.00000000,1_850:0.00000000,0_1122:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..605e4e36c7883815b4186a5dd51dd9c97826998f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt @@ -0,0 +1,2 @@ +((0_1124:0.00574475,(4_1074:0.00000000,1_852:0.00000000):0.00395225):0.04999825,2_1688:0.03854375,3_1585:0.25317525); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d09c17a5eb9c5aeae2f51d6b19980276f3143dd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt @@ -0,0 +1,2 @@ +((4_1080:-0.00380037,(3_1579:0.49847313,2_1682:0.01986388):0.02173737):0.03984787,0_1130:0.01604737,1_858:0.00448163); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bd4ade769aa1216b21330e16b1f5200db7b558ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt @@ -0,0 +1,2 @@ +((0_1133:0.01120613,4_1083:0.00189287):0.00184662,(2_1679:0.05340888,3_1576:0.16146412):0.02883513,1_861:0.00114738); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f32a3b6d409003e932901a4dbf6c08a128fcb6dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt @@ -0,0 +1,2 @@ +((2_1673:0.07321550,3_1571:0.39101550):0.05547898,(4_1088:0.00000000,0_1138:0.00000000):0.00928157,1_866:0.00462543); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2021e4c2e5b50f7b484568923782062a1af9752 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1089:0.00161487,0_1139:-0.00030987):0.01067188,1_867:0.01359613):0.05293637,2_1672:0.04208963,3_1570:0.20084837); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..75f9ad2180e11af4a5aecb756213fd263780efab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt @@ -0,0 +1,2 @@ +(4_1101:0.11970737,((2_1663:0.77781263,3_1560:0.74278437):0.52267688,0_1147:0.08975062):0.02918987,1_876:0.08384963); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4136a235f6edb3535d5c0539624bf9370aeef94 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt @@ -0,0 +1,2 @@ +((1_878:0.00039862,0_1149:0.01096537):0.00484687,(4_1103:0.00306687,3_1558:0.13046912):0.00477738,2_1661:0.03105713); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..20f92f207cd4098b5fc10f07fca3f1cbd2161542 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1555:0.06463800,2_1659:0.01199600):0.00455200,0_1151:0.00000000):-0.00000000,1_880:0.00000000,4_1105:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9d4e51262c3635151d600402ef0b2da967fcdcd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt @@ -0,0 +1,2 @@ +(2_1658:0.01227659,((4_1106:0.00000000,0_1152:0.00000000):0.01754025,1_881:0.00769875):0.00384325,3_1554:0.10754541); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc6e3ec977135bbe6b5f42f9cc1f563bfd916051 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt @@ -0,0 +1,2 @@ +(1_882:0.00107025,(4_1107:0.00539175,(3_1553:0.09856050,2_1657:0.01108750):0.00421825):0.00259625,0_1153:0.01138475); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..39edf39b930773887ddefe7edfe922e693bda1ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt @@ -0,0 +1,2 @@ +(1_883:0.01217150,(3_1552:0.12299975,(2_1656:0.03082100,4_1108:0.01134200):0.01196475):0.00971375,0_1154:0.01709850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..06eebab0b3d079fb136f980769fc2c38c25a2fa9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt @@ -0,0 +1,2 @@ +(4_1114:0.00316912,(1_885:0.00666587,(2_1653:0.00334963,3_1550:0.02965738):0.01333213):0.00079113,0_1157:0.02085188); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e5bb95df032d19241a3a37a9283b67376f167477 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt @@ -0,0 +1,2 @@ +(0_1159:-0.00074875,((2_1651:0.01418575,3_1548:0.02485325):0.01151575,1_887:-0.00074875):0.00074875,4_1116:0.00074875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0054563bb7547320f0ef417cd4918ab2ea347396 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt @@ -0,0 +1,2 @@ +((3_1547:0.19630737,2_1650:0.05435963):0.04883487,(0_1160:0.01028837,4_1117:0.00990262):0.00239487,1_888:0.01111462); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2dd09abe3bbe24d28b705bbee5caf0672e1be41d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt @@ -0,0 +1,2 @@ +((4_1123:0.00004313,0_1166:0.00083387):0.00347487,(3_1541:0.07302288,2_1645:0.01842112):0.02728838,1_894:0.00267863); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..51cd4ab7f8f242686f0d6166bb8f4d635de76bb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt @@ -0,0 +1,2 @@ +(4_1124:0.00525997,((2_1644:0.02192450,3_1540:0.15638350):0.03284128,0_1167:0.00161634):0.00040616,1_895:-0.00041197); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5863ef82e168faa338c82a8935da0e412ec62ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt @@ -0,0 +1,2 @@ +((4_1125:0.00000000,0_1168:0.00000000):0.00198375,(3_1539:0.25209975,2_1643:0.05596725):0.06993675,1_896:0.00610225); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff36ebdbb5bce86f21120a79e4b6d5b75e5aaf50 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1537:0.16976250,2_1641:0.05575550):0.08050550,4_1127:0.00000000):0.00000000,1_898:0.00000000,0_1170:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3acbd8fc31bd53553fca6f37b068bf6dec9f9b31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt @@ -0,0 +1,2 @@ +((2_1638:0.04644000,3_1534:0.15185800):0.04786705,(4_1131:0.00142456,0_1173:0.00500644):0.00601526,1_901:0.00043161); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5e9e1e10bf7717af60cb567e2d581c7edb0d670f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt @@ -0,0 +1,2 @@ +((0_1181:0.03099358,(4_1139:0.00045292,1_909:0.00086308):0.02631735):0.19426145,2_1630:0.22082683,3_1527:0.43834417); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6cb925f54ae73f611445034c275d0fc81d9a65f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt @@ -0,0 +1,2 @@ +((0_1184:0.00356350,(4_1142:0.00000050,1_912:0.00000050):0.00415600):0.02414350,3_1524:0.07743750,2_1627:0.05655350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..17c4f3adce7a552acdf117b54c719e7d605047bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt @@ -0,0 +1,2 @@ +((1_913:0.01284022,(4_1143:0.00583915,0_1185:0.00577085):0.00805180):0.12078238,3_1523:0.17035267,2_1626:0.14188733); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a52486b53848394ea26e5f12cb5fbbd2b107107 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt @@ -0,0 +1,2 @@ +((0_1189:0.01600550,(4_1147:0.00137950,1_917:-0.00012750):0.01521900):0.04459150,3_1519:0.24563925,2_1622:0.09347975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba1645e733a55037c9f0312e5796b3466a1fb81e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt @@ -0,0 +1,2 @@ +((1_922:0.00070950,(4_1152:0.00000000,0_1194:0.00000000):0.00023750):0.01753300,3_1514:0.06040550,2_1617:0.02093550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbc3dd30861588d60864e94dd1f2894f441cb0b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt @@ -0,0 +1,2 @@ +((0_1195:0.00000050,4_1153:0.00000050):0.00367350,(2_1616:0.03197700,3_1513:0.14894900):0.02947100,1_923:0.00207400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c61d1ca986255f41eae698d4f2de78d6c6d321c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1198:0.00000000,4_1156:0.00000000):0.00000000,1_926:0.00000000):0.03472700,2_1612:0.06254300,3_1509:0.13029900); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b8224d5c6e8e5cc380a7d8e5ec6cdde59519b86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt @@ -0,0 +1,2 @@ +((4_1157:0.00000000,(3_1508:0.08990250,2_1611:0.02564350):0.02205950):-0.00000000,0_1199:0.00000000,1_927:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba1e66e3e2891df22f3af1b2bda85c81c0311769 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1158:0.00000000,1_928:0.00000000):0.00000000,0_1200:0.00000000):0.05422350,3_1507:0.05546250,2_1610:0.01573550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a5c20ae9d95923524e3dcc2b1f43ff1aa56d72e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt @@ -0,0 +1,2 @@ +((3_1505:0.59081183,2_1608:0.07675717):0.17212241,(1_930:0.00000000,4_1160:0.00000000):0.00670726,0_1202:0.00312074); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9583e302bc9954ae5a121c40f5af458c14de573 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt @@ -0,0 +1,2 @@ +(4_1164:0.00088188,((2_1603:0.04093563,3_1500:0.05364037):0.02471763,0_1207:0.00929437):0.00461313,1_935:-0.00000888); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..440934775882baeda83f30f3a88f2aef8e8cce75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt @@ -0,0 +1,2 @@ +((0_1209:-0.00032325,(4_1166:0.00000000,1_937:0.00000000):0.00282625):0.00534025,2_1600:-0.00032925,3_1498:0.00282925); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa7b4fe288a4d6d8031eb58c9e9c348962a5ac8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt @@ -0,0 +1,2 @@ +((4_1167:0.00000000,(3_1497:0.59043250,2_1599:0.18938550):0.26975650):0.00000000,0_1210:0.00000000,1_938:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c6d7ffff08bd3fa38dfcb3aefa0603da0de0fdf9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt @@ -0,0 +1,2 @@ +(((1_939:0.00000000,4_1168:0.00000000):0.00398100,0_1211:0.00337000):0.05579200,2_1598:0.06742850,3_1496:0.12663450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..43d8a2e31cf2f3ede6fc5f3e103c56ee9ba659b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1495:0.27232867,2_427:1.19929233):0.24226333,0_1212:0.11759199):0.01332201,1_940:0.00000000,4_1169:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bf08c2ebc29b0abcf762ebd8f11144d1870cf1f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt @@ -0,0 +1,2 @@ +((1_943:0.00350850,0_1215:-0.00015850):0.00218350,(2_1594:0.03750275,3_1491:0.06451625):0.01829750,4_1172:0.00116800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..38464ee66b58a19538a3a0278b0e980540253e57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1184:0.00000000,1_955:0.00000000):0.00000000,0_1227:0.00000000):0.04858600,2_1582:0.08204400,3_1477:0.07221000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d04ef6a06fc03068b4963199f61deafc1aa00baa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt @@ -0,0 +1,2 @@ +(1_957:0.00000000,(0_1229:0.01233925,(3_1475:0.23339325,2_1580:0.09469675):0.09233675):0.00579775,4_1186:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5490b2a7e41285e884d6eaf8d6c94ba756460779 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt @@ -0,0 +1,2 @@ +(4_1188:-0.00059725,((2_1577:0.14638325,3_1472:0.36475075):0.12550625,1_959:-0.00059725):0.00059725,0_1231:0.00671925); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..78a633a5192697ffd080bf4ff8e54905dc4d9ffa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1233:0.00731212,4_1190:0.00043388):0.00032588,1_961:0.00244312):0.12293238,3_1470:0.20106288,2_1575:0.08145813); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..682368f09b8e533c6281378f93a4d8f838afc632 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt @@ -0,0 +1,2 @@ +((3_1469:0.70926733,2_1573:0.13484467):0.14769489,(4_1191:0.00000000,1_962:0.00000000):0.00852833,0_1234:0.01642867); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c6dd3f6921091a5ddd1445a5fe44cc6100338ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1193:0.00000000,1_964:0.00000000):0.00000000,0_1236:0.00000000):0.25560350,3_1467:0.45760350,2_1571:0.12277550); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4d8bbbc9a9acc01667bf0033f82149e306169b0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt @@ -0,0 +1,2 @@ +(((1_966:0.00000000,4_1195:0.00000000):0.01555575,0_1238:0.01392625):0.09063825,3_1465:0.39397425,2_1569:0.06184475); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b4cb7db8b57457786c988b0de161a034182e7aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt @@ -0,0 +1,2 @@ +(((1_967:-0.00006063,0_1239:0.00196963):0.00074238,4_1196:0.00269962):0.02610387,3_1464:0.12551663,2_1568:0.03122838); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..12d7987c56dedef01715ecd0e25028af454796c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1564:0.07547175,3_1460:0.31742125):0.05868875,0_1250:0.00044875):0.00176625,1_982:0.00000000,4_1207:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae591d231e466cfd953e72266a838266baaf0470 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt @@ -0,0 +1,2 @@ +(((1_984:0.00000000,4_1209:0.00000000):0.00000000,0_1252:0.00000000):0.12996400,2_1562:0.06112100,3_1458:0.44301600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6fa0ff9eb3b23d7999ee80d800253bef18f17778 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1455:0.20422550,2_1559:0.05541850):0.04453850,1_987:0.00000000):0.00000000,0_1255:0.00000000,4_1212:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ee40521d34c56863369d28141706f62717e67bc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt @@ -0,0 +1,2 @@ +(((1_993:0.00000050,4_1218:0.00000050):0.00426375,0_1261:0.01383775):0.05362975,2_1553:0.04441775,3_1449:0.18410425); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f749616747ee0ee8e0f8dc2c70c1b3416f1b75d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt @@ -0,0 +1,2 @@ +(0_1263:0.01175601,((1_995:0.01119083,4_1220:0.01655017):0.33026759,3_1447:0.23314828):0.19842522,2_1551:0.01152399); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7582d99318cac5a416462e09233306945a443662 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt @@ -0,0 +1,2 @@ +((0_1270:0.00070729,(4_1225:0.00797131,1_1000:0.00227769):0.01417823):0.02597974,2_1544:0.02482433,3_1440:0.16050067); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4f23e67ad1c9f9a5c3e2f786d08de44de9bf6be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt @@ -0,0 +1,2 @@ +(4_1228:0.03221161,((2_1540:0.03739283,3_1436:0.14086817):0.05470571,0_1273:0.03058764):0.01211636,1_1003:0.02424639); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..577c27fa9c6dd7f33729d68134af303f6ce49ac8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt @@ -0,0 +1,2 @@ +((1_1006:0.00354919,(4_1231:0.00726050,0_1276:0.00872350):0.00536596):0.03963970,2_1537:0.09221250,3_1433:0.19826850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f39593e7280b13d39bda688d4bba3f69ae498a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt @@ -0,0 +1,2 @@ +((1_1007:0.00118325,(4_1232:-0.00050525,0_1277:0.00162425):0.00105775):0.00150875,3_1432:0.01161100,2_1536:0.02486000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..65d26afc15c759941f228cba48082f6bdcdf15d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1008:0.00034137,0_1278:0.00229463):0.02052163,4_1233:0.01372138):0.03849912,3_1431:0.15294188,2_1535:0.13642312); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9976691ec9f578e0413bbae4d8ad54ad185b7366 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt @@ -0,0 +1,2 @@ +((1_1009:0.00784825,(0_1279:0.00000000,2_1534:0.00000000):0.00096275):0.00110825,4_1234:0.00552175,3_1430:0.11006125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6ac7da20eb52440da4e4a4ac791e1416a3ddc99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt @@ -0,0 +1,2 @@ +((4_1235:0.03078775,(1_1010:0.00254475,0_1280:0.01084925):0.01855625):0.02092475,2_1533:0.05790775,3_1429:0.94587125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ba587f48e79e5b64f59e82bb11ca076d2c8e045 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt @@ -0,0 +1,2 @@ +(1_1017:0.01243687,(0_1287:0.01416663,(3_1422:0.26592237,2_1526:0.05350762):0.03974387):0.00410937,4_1242:0.00242613); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d94c9d93e28e804dd5ce64120083988a1e292f21 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt @@ -0,0 +1,2 @@ +(1_1019:-0.00003235,((3_1420:0.18549700,2_1524:0.08289500):0.05212957,0_1290:0.00432871):0.00302379,4_1244:0.00278035); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9be6ea2e1e82348fcc29b21b64608ccfafd879e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt @@ -0,0 +1,2 @@ +(1_1025:0.00809225,(4_1250:0.00509850,(2_1518:0.09439675,3_1414:0.11385225):0.02021800):0.00639700,0_1296:0.00137175); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..51c6bcbc4638faebfe87630a0bef5d14ff0d7cd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt @@ -0,0 +1,2 @@ +((3_1409:0.26077367,2_1513:0.10432533):0.12881757,(0_1301:0.01510541,4_1255:0.01291859):0.00193482,1_1030:0.01303933); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0dc0ce1ee40209cabc0dd2b176efca4df39dbf73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt @@ -0,0 +1,2 @@ +((0_1302:0.01663250,1_1031:0.01883450):0.00338525,(2_1512:0.16539175,3_1408:0.43995425):0.10460425,4_1256:0.02809725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..114d8f0f7d6d8183afc3ec2c95ea833ab16a83c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1305:0.00401200,1_1034:0.00088800):0.00384850,4_1259:0.00352100):0.06127500,2_1509:0.05281725,3_1405:0.16394875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..62dad46bd263985de7d235262ab2a440ed5dfd3d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1403:0.43202200,2_1507:0.08630700):0.06928447,1_1036:0.00442640):0.00307660,0_1307:0.00811698,4_1261:0.00506702); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb94ef924cccfc94bbcd43915a8633265c3e0d3c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt @@ -0,0 +1,2 @@ +(0_1313:-0.00060775,((3_1397:0.65088750,2_1502:0.15689550):0.11711300,1_1042:0.04235250):0.01707400,4_1267:0.00489875); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..45b169a14923646a962aaaf9b007d95b156eade9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt @@ -0,0 +1,2 @@ +(4_1268:0.00000000,(1_1043:0.00320321,(3_1396:0.14790533,2_1501:0.04323067):0.01937340):0.00807779,0_1314:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6084803ec27009afa3f73ad363a26b0995340f79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt @@ -0,0 +1,2 @@ +((4_1272:0.00661777,(1_1047:0.02744393,0_1318:0.00671107):0.00370733):0.12760878,2_1497:0.10789467,3_1392:0.27066133); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92186027ce230eb3b468bacf42b51bd6a5504855 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt @@ -0,0 +1,2 @@ +((0_1322:0.00000000,4_1276:0.00000000):0.00094500,(2_1492:0.01268567,3_1388:0.11354633):0.00621667,1_1051:0.00118700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ef325d9455d1f3d1e0b59fb2c47802845ccb08aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt @@ -0,0 +1,2 @@ +(4_1279:0.00057233,((2_1489:0.05242283,3_1384:0.22586317):0.07886947,0_1325:0.00477391):0.00369509,1_1054:0.00489867); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8085bdc5ec00f7d294965b7fd9d84443831d249 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt @@ -0,0 +1,2 @@ +(2_1487:0.00330813,(0_1327:0.00253813,(4_1281:0.00320263,1_1056:0.00123637):0.00312537):0.00297787,3_1382:0.10895988); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b3e12114fbc5f2e6c05459b57b070200ceceadd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt @@ -0,0 +1,2 @@ +((3_1381:0.21994200,2_1486:0.02018300):0.02264975,(1_1057:0.00571900,0_1328:-0.00024000):0.01152825,4_1282:0.00783675); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d34787feafc58e655dc02aeb83c65fa5a054f060 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt @@ -0,0 +1,2 @@ +(1_1059:0.00053175,(0_1330:0.01274830,(3_1379:0.46271000,2_1484:0.11933600):0.07707010):0.01589320,4_1284:0.00479925); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc8fbf2f5218d2759096b3fc98098e4e439f4cd0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt @@ -0,0 +1,2 @@ +(0_1333:0.00000000,((3_1376:0.20889483,2_1481:0.05803417):0.06141828,1_1062:0.00389134):0.01428466,4_1287:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b63ea7557be961f44a2bd1b1ffb47dd5f43893c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt @@ -0,0 +1,2 @@ +((1_1094:0.00196925,4_1304:0.00054875):0.00128750,(2_1462:0.19745625,3_1374:0.10139175):0.01138550,0_1355:0.00351150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a39494234e84e3a80cf4bce357707a60a6ea0c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt @@ -0,0 +1,2 @@ +(4_1306:-0.00028300,((2_1461:0.08699400,3_1372:0.25119900):0.06250400,0_1357:-0.00028300):0.00028300,1_1096:0.00512500); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b921e29d15556fe8e27ea7fe7ed9446552c2b92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1307:0.00000000,0_1358:0.00000000):0.00000000,1_1097:0.00000000):0.02216700,2_1460:0.01016100,3_1371:0.11239300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ba70734d2ac0d4f982bac20362a50c3ce976428 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt @@ -0,0 +1,2 @@ +((1_1110:0.01050997,(0_1370:0.00560830,4_1319:0.00914470):0.02054223):0.02197723,2_1451:0.04933650,3_1359:0.18057650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fdaf49750b484318f77b86ab874d7d9064d70be1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt @@ -0,0 +1,2 @@ +(1_1115:0.00000050,((2_1446:0.14513450,3_1354:0.34329750):0.12495792,0_1375:0.06630427):0.01406423,4_1324:0.00000050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..00f8ebd48b0dd3964a6768460e3d78bfef7e5299 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt @@ -0,0 +1,2 @@ +(4_1326:0.00329352,((2_1444:0.05070233,3_1351:0.20412067):0.05486603,0_1377:0.00336109):0.00341591,1_1118:0.00293448); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d4f88fabbfbb1af8ee11dd9e65d685586eae6f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1330:0.00000000,0_1381:0.00000000):0.00000000,1_1122:0.00000000):0.03408300,2_1439:0.04455700,3_1347:0.21142100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..176779ea57b09044ff376269b8eb93531bcaefe5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1438:0.04145100,3_1346:0.12252000):0.03780700,0_1382:0.00052600):0.00595700,1_1123:0.00000000,4_1331:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cb8ab70dc8e6308cbe860869f9c1f51f3efbf1d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt @@ -0,0 +1,2 @@ +((4_1333:0.00299338,(0_1384:0.00225728,1_1125:0.00016872):0.00178103):0.04071176,3_1344:0.15090383,2_1436:0.06282617); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ad269cdbb7e5e0f739bf405eef8add541d9eba5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt @@ -0,0 +1,2 @@ +(1_1130:0.00000000,((3_1339:0.31779433,2_1431:0.04383567):0.09965285,0_1389:0.00643254):0.00074746,4_1338:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d1e266169dbb38cfd35fe949b3d22b4e5d02373a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt @@ -0,0 +1,2 @@ +(0_1390:0.00000000,((3_1338:1.29030100,2_1430:0.35051900):0.38045950,4_1339:0.00784600):0.08206800,1_1131:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8580a858a6916afc14ee30526068f3d04298d610 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt @@ -0,0 +1,2 @@ +((3_1325:0.25772400,(1_1141:0.08378600,2_1421:0.27853000):0.06555100):0.10009200,4_1349:0.03116875,0_1400:0.01429825); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b62e7eeff5ceedbcbc3e5ae65f951e990169f4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt @@ -0,0 +1,2 @@ +((1_1144:0.13818537,(0_1403:0.01217867,4_1352:0.02494533):0.09548246):0.08126763,2_1419:0.05092800,3_1322:0.32051400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f2af7ff8a70d659a5cee123689fe8662d74b4dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt @@ -0,0 +1,2 @@ +((3_1319:0.01197600,(1_1147:0.00000000,4_1355:0.00000000):0.00000000):0.00000000,0_1406:0.00000000,2_1416:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5a98efa0955d1d02ea59c27298faae98f1459744 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt @@ -0,0 +1,2 @@ +((0_1408:0.01333501,(4_1357:0.00000050,1_1149:0.00000050):0.01958649):0.19726817,3_1317:0.49584217,2_1414:0.26215883); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2addcceacb95013237daa785a671207b5b414b54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt @@ -0,0 +1,2 @@ +(4_1359:-0.00008150,(0_1410:-0.00099691,(2_1412:0.07260967,3_1315:0.33429533):0.03089803):0.01164841,1_1151:0.01062650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..188f3d427c000f6eb7492a982cd6c7c49efb5410 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt @@ -0,0 +1,2 @@ +((4_1360:-0.00200110,1_1152:0.01742010):0.00926714,(2_1411:0.14738817,3_1314:0.49059083):0.18913202,0_1411:0.00253096); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a953b0466b22faca164ff123c9a39decfd46f01 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt @@ -0,0 +1,2 @@ +((4_1364:0.01016975,1_1156:0.00283925):0.01006772,(3_1309:0.30480050,2_1407:0.05730950):0.04854653,0_1415:0.00111667); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..870cdbed72aec79aed0cb2a7c620c3ef0213e050 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt @@ -0,0 +1,2 @@ +((0_1428:0.00197263,(3_1296:0.28804937,2_1396:0.12010362):0.11598088):0.00255537,4_1377:0.00248463,1_1169:0.00411637); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b83fde5507f6e3e859bf97b8ffee36a9fe8a9afe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1378:0.00000000,0_1429:0.00000000):0.00798975,1_1170:0.00711025):0.06950825,3_1295:0.17696675,2_1395:0.17817625); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dafe8963b024bc72e3f8d81b6dabe45ad3cfe5a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt @@ -0,0 +1,2 @@ +((0_1432:0.01334438,(4_1381:0.00435113,1_1173:0.00242887):0.00921962):0.15574612,2_1392:0.20457837,3_1292:0.47258963); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fd9a70691cd7f3c6e9927b511b38fb42b768ef2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1434:0.00423563,4_1383:-0.00083663):0.00083662,1_1175:-0.00083663):0.06857512,2_1390:0.08384588,3_1290:0.24726712); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a658c2fbc98045770c6e8660016d5a462dbde480 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt @@ -0,0 +1,2 @@ +((1_1178:0.00143748,(3_1286:0.41513350,2_1387:0.11422850):0.08340099):0.00078852,4_1386:0.00373749,0_1459:0.00372551); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f1b15179d66299302fb32eb32338bc7e64033d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt @@ -0,0 +1,2 @@ +((4_1388:0.05215669,(0_1461:0.00000000,1_1180:0.00000000):0.06051331):0.11115956,3_1285:0.50468567,2_1385:0.27502333); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7155175331f5df13ebe71ad3c5784c9437c9adf3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt @@ -0,0 +1,2 @@ +((0_1462:0.00828550,1_1181:-0.00088950):0.01733000,(2_1384:0.24331650,3_1284:1.03731150):0.12892250,4_1389:0.00027600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..330b90210ad06ab34ab889e95da4e65e5c2e57d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt @@ -0,0 +1,2 @@ +(0_1464:0.00144550,((2_1382:0.07556300,3_1282:0.49129900):0.07442850,4_1391:0.00822350):0.00837400,1_1183:0.00008750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b1f79c867a18655843287348a63d41ffdbd0e4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt @@ -0,0 +1,2 @@ +(1_1185:0.00180337,(0_1466:0.00948225,(2_1380:0.08047183,3_1280:0.29398817):0.05484825):0.00529875,4_1393:0.00389463); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ac8dd43edd619661bfcaec332d90f771d8e4524 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1187:0.00930838,0_1468:0.00916263):0.02045213,4_1395:0.00960337):0.20633212,2_1378:0.09603338,3_1278:0.48404562); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..902042a9e090f17a0acb3ebb04890923b1b1f52b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt @@ -0,0 +1,2 @@ +(4_1398:0.00387000,(0_1471:0.00362125,(2_1375:0.07324600,3_1275:0.01528900):0.00476175):0.00162125,1_1190:0.00014400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b4f62376613d68688b45b6dc73e2d73df3f8627f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt @@ -0,0 +1,2 @@ +((2_1372:0.04094783,3_1264:0.50379017):0.04169797,(1_1194:0.00000000,0_1474:0.00000000):0.01463959,4_1401:0.02161941); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..695404de26ba653264302f2fe4e8073e02c788f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt @@ -0,0 +1,2 @@ +(1_1196:0.00265825,(4_1403:0.00412725,(2_1370:0.04149050,3_1262:0.18983650):0.02992825):0.00406375,0_1476:0.00371675); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4939133ebd238019dfa8a33a03cebada500ba361 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt @@ -0,0 +1,2 @@ +((3_1259:0.19586300,2_1367:0.10472200):0.07040200,(4_1406:0.00000000,1_1199:0.00000000):0.00003700,0_1479:0.00155100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e5c10eef30876dde8909829314b09c57d8dc941 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1409:0.02951175,1_1202:0.00218425):0.00524500,0_1482:0.00825600):0.04386250,2_1364:0.22611750,3_1256:0.98690450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..46c8086310972117f74ca2eacd3d6e572ddce2f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt @@ -0,0 +1,2 @@ +(0_1489:-0.00071413,(1_1209:0.06463812,(2_1357:0.14495037,3_1249:0.39885362):0.07264788):0.06290737,4_1416:0.00313812); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1eb0c224140e13f7678fb310648744fa5741be3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt @@ -0,0 +1,2 @@ +(0_1492:0.00000000,(4_1419:0.01374275,(3_1246:0.17475475,2_1354:0.05948425):0.02941175):0.02269825,1_1212:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9653c7d2c6f46d0ed992ece785628f962246434b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1245:0.54427800,4_1420:0.02822100):0.01457850,1_1213:0.03466761):0.02283889,0_1493:-0.00845750,2_1353:0.63040850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1360e0779e046c8c8ab9d1cf4d6273b7b813efdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt @@ -0,0 +1,2 @@ +((1_1220:0.00739200,(4_1427:0.00228775,0_1500:0.00052025):0.01928600):0.06525750,2_1346:0.06381725,3_1238:0.11223775); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fb3b4163f53c8f2f21818718bc3fce4a61137a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt @@ -0,0 +1,2 @@ +((0_1501:0.00400275,(4_1428:0.00000000,1_1221:0.00000000):0.00558925):0.00771575,3_1237:0.12513725,2_1345:0.01354575); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e82c2578a27f84f8a279335e49f85b5180d79e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt @@ -0,0 +1,2 @@ +(1_1227:0.00365154,((2_1340:0.04147633,3_1232:0.15034867):0.04790043,0_1507:0.00371029):0.00742121,4_1434:0.00918646); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b6f736845d2e738c11ff637f5896cc136656e341 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt @@ -0,0 +1,2 @@ +(0_1508:0.00000000,((2_1339:0.00543533,3_1231:0.05122467):0.02923388,4_1435:0.00657863):0.00193237,1_1228:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7d0cb7d217c7e8cd169154dc2f5dcf0d1870a1ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt @@ -0,0 +1,2 @@ +((3_1228:0.16257000,2_1336:0.05735500):0.03016700,(1_1231:0.00118625,4_1438:0.00344975):0.00259100,0_1511:0.00502300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b87d7712d3ebed9b6e8d3e7592a51280cbf03689 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1241:-0.00132450,4_1448:0.00433250):0.00132450,0_1521:-0.00132450):0.12095100,2_1324:0.65569025,3_1218:0.11643675); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8d09b20d3563045cc4b6376a04d4a0e4e3766c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt @@ -0,0 +1,2 @@ +((3_1217:0.17493462,2_1323:0.08522937):0.13382037,(1_1242:0.00297238,4_1449:-0.00036138):0.00329388,0_1522:0.00237462); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7fa8d16ae38f2522efcf8634ab8d0f14021787dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt @@ -0,0 +1,2 @@ +((4_1450:0.00619025,(2_1321:0.10986450,3_1215:0.11976550):0.04288775):0.01183125,1_1243:0.00533375,0_1523:0.00535225); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..35fc67201249d49d16a28939c6b33573f62480c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt @@ -0,0 +1,2 @@ +((1_1262:0.00203198,(4_1467:0.00000000,0_1540:0.00000000):0.00363902):0.08009049,3_1191:0.15866983,2_1302:0.19645717); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..848c05e1f3e354647a21805506662846f4a35bfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1175:0.01592633,2_1266:0.06448467):0.00279815,4_1476:-0.00003356):0.00003356,0_1549:0.00000000,1_1271:0.00762800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2c8612318980acfc24ca58552e33d298338462b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt @@ -0,0 +1,2 @@ +(0_1576:0.01712995,(1_1291:0.00705658,(3_1150:0.28855417,2_1241:0.06658983):0.05488603):0.00462642,4_1505:0.00618305); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d383be3aeb8cceaa7894461fed3f44ff9d7ecb30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt @@ -0,0 +1,2 @@ +((3_1147:0.33469063,2_1237:0.32337237):0.33989463,(1_1294:0.00375462,4_1508:0.02416837):0.00928662,0_1579:0.00959438); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c76bd919fb6f1ae81c0e1978120e5012005dbe0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt @@ -0,0 +1,2 @@ +((4_1512:0.02378512,(0_1583:0.00010963,1_1298:0.00820837):0.02802288):0.06381237,2_1233:0.08611963,3_1143:0.35317938); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6261f9854befbfc95ae92365324a4bafece17328 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt @@ -0,0 +1,2 @@ +((0_1585:0.02188185,4_1514:0.13392015):0.06392902,(3_1141:0.57258700,2_1231:0.41546900):0.27941929,1_1300:0.03297502); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d7294b7a2be4a25d6656b6aba59e8432596dc32 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1592:0.00359277,1_1307:0.03252023):0.00620961,4_1522:0.02560889):0.04387812,2_1222:0.05772983,3_1134:0.14109317); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8411093c44c02c51a30e1e7f1f4499f999034551 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt @@ -0,0 +1,2 @@ +((1_1309:0.00513886,(4_1524:0.00900126,0_1594:0.00278274):0.00218337):0.05665248,3_1132:0.25989683,2_1220:0.06212817); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fda59dda2628e13cfb2043108f2d857ee728ee2a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt @@ -0,0 +1,2 @@ +((0_1595:0.00242288,(3_1131:0.07840717,2_1219:0.01310283):0.01004446):0.00348462,4_1525:0.00856522,1_1310:0.00322978); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..757b923e6f47ca2a92084504992f8f967f9259ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1128:0.08809833,2_1216:0.01349067):0.02367099,1_1313:0.00472996):0.00073004,0_1598:0.00685558,4_1528:0.00270642); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e78fb53b6180cbbec79d106e186f093c0cba413 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1124:0.01358425,2_1212:-0.00002325):0.00002325,1_1318:-0.00002325):0.00002325,0_1603:0.00813525,4_1533:-0.00002325); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3c83cb45e27292ca2bf966ce04fda701e90bb84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt @@ -0,0 +1,2 @@ +(0_1607:0.00470610,((2_1208:0.08216567,1_1322:0.00221233):0.00490541,4_1537:0.00830024):0.00173676,3_1120:0.00762290); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b42b8c09f2c7679cfbaa9cf258081590b1d15a2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt @@ -0,0 +1,2 @@ +(4_1542:0.00301801,((2_1203:0.01899783,3_1115:0.13122417):0.01209832,0_1612:0.00748845):0.00675705,1_1327:0.00968399); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ad313e1b44191394d850902af267e55a6054c40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt @@ -0,0 +1,2 @@ +((3_1112:0.10587400,1_1331:0.00619000):0.00760125,(0_1616:0.00325700,4_1546:0.00657800):0.00270075,2_1183:0.01285975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f43f9a07a4bd302e0e5b417f5f1829f18db8238d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt @@ -0,0 +1,2 @@ +((3_1111:0.33107850,(4_1547:0.03039483,0_1617:0.01334517):0.00638800):0.00443300,2_1182:0.10657047,1_1332:0.02141053); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7efe7118831b267f597cecbc8798b16f54492848 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1336:0.01501976,4_1551:0.00867224):0.00429710,0_1621:0.01426929):0.09093124,3_1107:0.43837500,2_1178:0.10413600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8269ba9a83642610566abef7a0e57739eed7cb8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1555:0.00099712,1_1340:0.00314688):0.00198062,0_1626:0.01260937):0.03235413,2_1173:0.02362788,3_1103:0.06304512); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..92cf5678e8b8119ec067229c16d7c173a751e105 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt @@ -0,0 +1,2 @@ +((4_1557:-0.00043075,(1_1342:0.00343575,0_1628:-0.00043075):0.00043075):0.07533725,2_1171:0.04670200,3_1101:0.20323900); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..569efb08396aa382a4f70cac36de3b7895ecdf5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt @@ -0,0 +1,2 @@ +((4_1563:0.08487410,(1_1348:0.05066826,2_1165:0.68236874):0.02884304):0.11022919,3_1096:0.22676600,0_1634:0.04713400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..58ecc2067be1043af88012bb8978ddcc6a9b543a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt @@ -0,0 +1,2 @@ +((3_1094:0.04273337,2_1163:-0.00120437):0.01492687,(0_1636:-0.00005988,4_1565:0.00518088):0.00005988,1_1353:-0.00005988); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b271d54f7932a665380019a4a08efb94ff48de2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt @@ -0,0 +1,2 @@ +((0_1637:0.00975850,(4_1566:0.00386325,1_1354:0.01290975):0.00283100):0.09186550,3_1093:0.32235000,2_1162:0.07041600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..542a5a83986072d33b62aec4014cf1da61831227 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt @@ -0,0 +1,2 @@ +((1_1357:0.00000000,0_1640:0.00000000):0.00000000,(3_1090:0.03546050,2_1159:-0.00044950):0.02085850,4_1569:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc2dd0e76347141acda92f4241414bc123f2c281 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt @@ -0,0 +1,2 @@ +((4_1570:0.00000000,(3_1089:0.03300600,0_1641:0.00000000):0.00000000):0.00000000,1_1358:0.00000000,2_1158:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..29b6e5c5460897632652bb83af0622558ab35769 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt @@ -0,0 +1,2 @@ +((2_1157:0.00000000,(4_1571:0.00000000,3_1088:0.02263300):0.00000000):0.00000000,1_1359:0.00000000,0_1642:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bab999267283c07aaf697873bb3dcf4f8201c9c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1085:0.11487483,2_1154:0.02501217):0.03138441,0_1645:0.00066272):0.00958278,1_1362:0.00383317,4_1574:0.00382983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..822c407621d3208cc5026ccbe8863d84c0e69bb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1150:0.01348050,3_1081:0.07735950):0.05557850,0_1649:0.00000000):0.00000000,4_1578:0.00000000,1_1366:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..317e2888eae511fa4a1f64ff06eba128f5909027 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt @@ -0,0 +1,2 @@ +((3_1079:0.07829323,(4_1580:0.00000000,1_1368:0.00000000):0.01095377):0.01035041,0_1651:0.04804433,2_1148:0.00871567); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d720ad3291c0be3340b19afc5f14e81bfc166233 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt @@ -0,0 +1,2 @@ +(2_1147:0.00392863,((0_1652:-0.00002262,3_1078:0.03158362):0.00002262,1_1369:-0.00002263):0.00002263,4_1581:-0.00002263); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f175f5c9ffdbe07b3df24b2052f0f6fc91bdaeb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1582:0.00000000,1_1370:0.00000000):0.00000000,0_1653:0.00000000):0.01076150,2_1146:0.01222450,3_1077:0.01636650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d73967909a9963e9cdbed172aff6724200d8898 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt @@ -0,0 +1,2 @@ +((4_1583:-0.00000000,(3_1076:0.03411700,2_1145:0.01753800):0.02197400):0.00000000,1_1371:0.00000000,0_1654:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e9b3d7585a8cf2208db7198df1ebd5a7e48f0a1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1373:0.00000000,0_1656:0.00000000):0.00000000,4_1585:0.00000000):0.01492350,2_1143:0.00197850,3_1074:0.14155250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0bc921181ac14865c5ca785fd52f173a9a5bc100 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt @@ -0,0 +1,2 @@ +((1_1374:0.00000000,(3_1073:0.10167100,2_1142:0.02222800):0.00574900):0.00000000,0_1657:0.00000000,4_1586:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..37db268325fd2715554a18d6ba2782ca7c78aee7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt @@ -0,0 +1,2 @@ +((1_1375:-0.00000000,(3_1072:0.01077250,2_1141:0.00176150):0.01072150):0.00000000,4_1587:0.00000000,0_1658:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..38576a982b67bae1b4d5a59299eaa32dd19ffe8b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt @@ -0,0 +1,2 @@ +((0_1659:0.01574164,(4_1588:0.00000000,1_1376:0.00000000):0.00237936):0.02278321,2_1140:0.01140533,3_1071:0.04442167); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4c199dba4e337f9f4b16430d97a7f2484312396f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt @@ -0,0 +1,2 @@ +((0_1661:0.00000000,(1_1378:0.00000000,2_1138:0.00000000):0.00000000):0.00000000,4_1590:0.00000000,3_1069:0.00522200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..928554350a2c94dc9b1e7112ebf6ebd8543f254d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1665:-0.00003000,1_1382:0.01112400):0.00003000,4_1594:-0.00003000):0.00921650,2_1134:0.01218400,3_1065:0.02245500); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..64466a1eaa6d55ec3b3cae6bccdd88d44e5dfab2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1667:0.00000000,4_1596:0.00000000):0.00990150,1_1384:0.00654650):0.15606650,2_1132:0.09888450,3_1063:0.28848250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6083adc607ab5aebacb9aa2813adac73ad16eacd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt @@ -0,0 +1,2 @@ +((4_1597:0.00000000,0_1668:0.00000000):0.05055456,(2_1131:0.10622167,3_1062:0.46761633):0.18253315,1_1385:-0.00176456); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..43c27e3682fb32870a14a5ab4cc72d7a448e6d5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt @@ -0,0 +1,2 @@ +((1_1386:0.00330650,0_1669:-0.00009450):0.00009500,(2_1130:0.00538550,3_1061:0.01599450):0.00884450,4_1598:-0.00009450); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0eee907bbd49f0860668f67523fac38b12a10f63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt @@ -0,0 +1,2 @@ +((1_1387:0.00131386,(0_1670:0.00000000,4_1599:0.00000000):0.00016114):0.02522079,2_1129:0.01849750,3_1060:0.02848750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69a70e3b857e37521cf1cecac548128eec0360d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1671:0.00000000,4_1600:0.00000000):0.00000000,1_1388:0.00000000):0.00163950,3_1059:0.00490750,2_1128:-0.00163950); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f15d03aae1d49864d1f38167d8b18b0a0827fad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt @@ -0,0 +1,2 @@ +((0_1676:0.00525075,(1_1393:0.00000000,4_1605:0.00000000):0.00109825):0.01527725,3_1053:0.06265475,2_1123:0.00634125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c66020261d09cf9cd094c84122300b8830be6ecc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt @@ -0,0 +1,2 @@ +((4_1606:0.00171250,(0_1677:-0.00022925,1_1394:0.00474425):0.00167900):0.01149750,2_1122:0.00677950,3_1052:0.08748050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9b3985f5ee5b8d620a31a89530daf65b50fcb7ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt @@ -0,0 +1,2 @@ +((1_1397:0.00085748,(0_1680:0.00000000,4_1609:0.00000000):0.00882552):0.03137049,3_1049:0.27046267,2_1119:0.07015833); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7eaf4b857cf5eea82c74050787ab8792bb6aa474 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1047:0.15470850,2_1117:0.03153750):0.05525025,4_1611:0.01026625):0.00804675,0_1682:0.00951275,1_1399:0.00798225); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..05a605caa8a9635040b09d8419e3a7de5aa275ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1683:0.01023002,4_1612:0.01423398):0.01391353,1_1400:0.01537117):0.10317446,3_1046:0.21387267,2_1116:0.13877533); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8fb848acc284e90928dd458ad15d1047cdfb8f08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt @@ -0,0 +1,2 @@ +((0_1684:0.00654429,4_1613:0.00019271):0.00276295,(2_1115:0.21729850,3_1045:0.43199250):0.25931196,1_1401:0.01284095); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..75f2db339372f0daac217c4f4a0a4c373a63a1bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1039:0.09890600,2_1109:-0.00221200):0.03837000,4_1618:0.00000000):0.00000000,0_1689:0.00000000,1_1406:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..df79d61e5facdb03ed9bb878f5f38e23d16c1a7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt @@ -0,0 +1,2 @@ +((0_1694:0.00000000,(3_1030:0.07754600,2_1104:0.02587200):0.00916600):-0.00000000,1_1411:0.00000000,4_1623:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bcdfb4734483226e35f22a1a5c54bc6e07e3885f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt @@ -0,0 +1,2 @@ +((1_1412:0.00000050,0_1695:0.00000050):0.01230270,(2_1103:0.01289950,3_1029:0.28468550):0.00209250,4_1624:0.00585580); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..31db63a2e84e91db4aaad42e8fe39ae7b5f08466 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt @@ -0,0 +1,2 @@ +((1_1416:-0.00032475,4_1628:0.01463775):0.00032475,(2_1099:0.05133800,3_1025:0.25856400):0.06881225,0_1699:-0.00032475); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0465f00445bee9c236b8e3baebecf5184f2ef83c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt @@ -0,0 +1,2 @@ +((4_1632:0.00462294,(0_1703:0.00000000,1_1420:0.00000000):0.00725806):0.03128298,2_1095:0.08940767,3_1021:0.64747733); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4aaed7d0eac7662a191f62d7b7d76e9dde01a3e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt @@ -0,0 +1,2 @@ +((4_1633:0.00151425,(0_1704:0.00000000,1_1421:0.00000000):0.00533675):0.03643225,2_1094:0.04036975,3_1020:0.06457525); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0dcd8d3f743541b0e5f058c0eb8f40ea6734535 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt @@ -0,0 +1,2 @@ +((0_1705:0.00155588,(1_1422:0.00064468,4_1634:0.00120832):0.00050536):0.05222130,3_1019:0.08368433,2_1093:0.13104567); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..86d0aeb2a57ae05610bfd55ecd0c1c05e4fc6727 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1018:0.21805150,2_1092:0.05331250):0.05566425,4_1635:0.00675975):0.00228175,0_1706:0.00383900,1_1423:0.00266900); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..49760424de8b6a5d05b03971496305af4682585c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt @@ -0,0 +1,2 @@ +(0_1714:0.00000000,((2_1084:0.07290100,3_1011:0.14985300):0.07972050,4_1643:0.01763200):0.00311600,1_1431:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb50bd7e80b7622fbc02b035809209fab24935b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt @@ -0,0 +1,2 @@ +(1_1432:-0.00013875,((3_1009:0.06709475,2_1083:0.04465125):0.04316475,0_1715:0.01117275):0.00669425,4_1644:0.00604675); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a23f70852accda9f9413604cd64b7ea00698e89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt @@ -0,0 +1,2 @@ +(4_1648:0.00683887,((2_1079:0.11434117,3_1004:0.29622783):0.11977863,0_1719:0.01977539):0.00349961,1_1436:0.00144113); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c1206a571189b136f9e4acbfa25d6b0c5e7a07e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1652:0.00170687,0_1723:0.00110112):0.00908138,1_1440:0.00599013):0.07797688,2_1076:0.15046312,3_1000:0.71248787); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bfc948c6a05d3b7baba08143acdba248d32d107d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt @@ -0,0 +1,2 @@ +(0_1724:0.00396188,(4_1653:0.01212662,(2_1075:0.07296088,3_999:0.11915713):0.07776387):0.00427238,1_1441:0.00280013); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..559379d17cc7c5606fc26460eea629bb6a39615b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt @@ -0,0 +1,2 @@ +((4_1656:0.00844050,1_1444:-0.00022650):0.00022650,(2_1072:0.05762150,3_996:0.14749950):0.04351850,0_1727:-0.00022650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4bdb1e3566f368f11104e9c1087ac55903a598a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt @@ -0,0 +1,2 @@ +(3_982:0.35927861,(4_1670:0.00005805,(1_1456:0.00251783,0_1748:0.00479017):0.00293685):0.00209895,2_1046:0.00200739); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf3e05dbd4c95d1b99fe08e7add6851292bd3033 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt @@ -0,0 +1,2 @@ +(1_1465:0.01483650,((3_972:0.22673250,2_1033:0.20727250):0.29558700,4_1679:-0.00064100):0.00051050,0_1757:0.01494850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..30526cf4734d1480cd0a2ce755393b062b51a4b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt @@ -0,0 +1,2 @@ +(0_1758:0.00459275,(1_1466:0.03387725,(3_971:0.22002775,2_1032:0.06670525):0.06950175):0.00964425,4_1680:0.00121325); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9162174ac368392f5af3bdc1bf0036e6b31bc69e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt @@ -0,0 +1,2 @@ +((0_1767:0.00000000,4_1689:0.00000000):0.01642182,(2_1022:0.16154183,3_962:0.46587317):0.11657589,1_1475:0.02706318); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e190d004e15bcc00f9dc7c69b6e544b6a3a63238 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt @@ -0,0 +1,2 @@ +((2_1021:0.24285933,3_961:0.56874767):0.10067967,(0_1768:0.00839797,4_1690:0.01046603):0.01736106,1_1476:0.06703292); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ffdd64c1b90c2fe95b44a56ddcd37466da3b5d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1478:0.01894888,0_1770:0.01359512):0.00689763,4_1692:0.01275288):0.14299562,2_1019:0.14324912,3_959:0.30300688); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2418c56ab964389115d90691d03f4992f6b5c75a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt @@ -0,0 +1,2 @@ +(0_1775:0.02512388,((2_1013:0.14933512,3_955:0.54307888):0.10013913,4_1697:0.04101088):0.01579812,1_1483:0.00509812); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c672c69c0fd16f710fe3cc72fa0a90c446fa5158 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt @@ -0,0 +1,2 @@ +(((2_1010:0.00413650,3_952:0.06487450):0.00299750,0_1778:-0.00000000):0.00000000,4_1700:0.00000000,1_1486:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..18386f798eddd24c5a0e26e32d81892e4d0e1e6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt @@ -0,0 +1,2 @@ +((0_1779:0.01201750,(4_1701:0.00000000,1_1487:0.00000000):0.03267650):0.11805700,2_1009:0.18778350,3_951:0.41963350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6bfd8602d16aeccd1c5ac8dbd96a9f78be00bc32 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt @@ -0,0 +1,2 @@ +(((0_1781:0.00000000,4_1703:0.00000000):0.00000000,1_1489:0.00000000):0.01368450,3_949:0.06495850,2_1007:0.06913350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..adc41f5ae4de4d17b3c91238e4251c5685a6266b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt @@ -0,0 +1,2 @@ +((4_1704:0.00712455,(0_1782:0.00149340,1_1490:0.00592260):0.00511316):0.03886874,2_1006:0.04194350,3_948:0.30954350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2633ed211de90b4cd64a3f83146293aa8161529a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt @@ -0,0 +1,2 @@ +((0_1784:0.00000000,1_1492:0.00000000):0.00391500,(2_1004:0.15116500,3_946:0.15330400):0.20481200,4_1706:0.00005200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..29e9c9e5ef4c1c5cf45512ebea034fad524f8f40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt @@ -0,0 +1,2 @@ +((3_942:0.50346117,2_999:0.18070683):0.14971539,(0_1789:-0.00452082,1_1496:0.01894282):0.02556787,4_1710:0.03492394); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e48d00a6733bba0f11675b0f07fb0b227e78b99c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt @@ -0,0 +1,2 @@ +((2_997:0.17553750,3_940:0.60003950):0.22057844,(0_1791:0.00669221,4_1712:0.01189979):0.01107264,1_1498:0.01511887); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7787c12c8e78354cf752cdc5ecc1aae03eba3618 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt @@ -0,0 +1,2 @@ +((0_1795:0.00100879,(1_1502:0.01210554,4_1716:0.00338346):0.00634672):0.05479092,3_936:0.05831800,2_993:0.08939800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..15db94c8dd3f445f2b2c9827dfcffed2c2f70f00 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt @@ -0,0 +1,2 @@ +(4_1720:0.00620713,(1_1506:0.00497138,(3_930:0.16577038,2_985:0.22431063):0.14370162):0.00546812,0_1799:0.00300687); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aae114318e936d5590b96c4ad8271c52b1a92b8b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt @@ -0,0 +1,2 @@ +(3_925:0.14884290,((4_1724:0.00000000,0_1803:0.00000000):0.01389575,1_1510:0.00857625):0.00171975,2_977:0.00772910); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f94aee518e988e47cc3b15c57ab1dbd44b4a5cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt @@ -0,0 +1,2 @@ +(4_1725:0.00202625,((2_976:0.08071875,3_916:0.44345125):0.08560200,1_1511:0.01650100):0.01174950,0_1804:0.00633375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b17114b0bce3b0d99877be2e550a77955446b9b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1518:0.00198600,0_1811:0.01685000):0.02781050,4_1732:0.05156850):0.12961600,3_908:0.52914475,2_969:0.30146725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f149e757463b81aa4f08693f310b7f6e668b87c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt @@ -0,0 +1,2 @@ +(((3_906:0.17887962,2_968:0.06535438):0.07257612,4_1733:0.02225387):0.03791913,0_1812:0.00164238,1_1519:0.00520362); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e2b5f587d312585261c974cf07a00799808b44cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt @@ -0,0 +1,2 @@ +(2_962:0.00311267,((4_1738:0.00283717,1_1524:0.00337083):0.01290768,3_901:0.04925253):0.00187047,0_1817:0.00605933); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e23c3276281d0def29c674cfa1dd07372afc87c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt @@ -0,0 +1,2 @@ +((2_954:0.02107625,3_893:0.30313075):0.05014925,(0_1824:0.00000000,4_1745:0.00000000):0.01686675,1_1531:0.00680325); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..df6fd9df1e1d65a253189c5b970fb9d2b7dff40b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt @@ -0,0 +1,2 @@ +((4_1751:0.00348706,(0_1830:0.01084510,1_1537:0.01807390):0.00874473):0.02127263,2_948:0.02751833,3_887:0.24377567); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..f04daca75edeba7256795b266bd2f9321a1e9989 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1760:0.00318067,0_1839:0.03104733):0.00852310,1_1546:0.00331682):0.06944121,2_939:0.09759817,3_880:0.40982483); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5456e06eca45102ae49a5655bad673654ade070b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt @@ -0,0 +1,2 @@ +(4_1763:0.00068763,((3_877:0.16895087,2_936:0.09812913):0.07813513,1_1549:0.00744637):0.00143862,0_1842:0.00101637); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..be0c07cfb75623200eb5b8f366781c9741031f13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt @@ -0,0 +1,2 @@ +((3_874:0.57515486,(1_1552:0.07712708,2_933:0.92972592):0.01190473):0.02130333,0_1845:0.01675517,4_1766:0.00495583); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..66a6b97abbfab096964df880cd08c7e4816c1674 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt @@ -0,0 +1,2 @@ +((0_1847:-0.00048523,(3_872:0.00821800,2_931:0.00625400):0.01209759):0.00048523,4_1768:0.00870800,1_1554:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..490ff5c29cabc9d8507df9dd5455fc061d6cdd2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt @@ -0,0 +1,2 @@ +((1_1555:0.00000000,(0_1848:0.00000000,4_1769:0.00000000):0.00000000):0.00000000,2_930:0.00000000,3_871:0.05638400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..66a00e8f5bf544bea99f7e2adf8cb17167addcc8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt @@ -0,0 +1,2 @@ +(((4_1779:0.00497062,2_922:0.02440537):0.00151638,3_858:0.03810062):0.00376587,0_1858:0.00582112,1_1565:0.00175488); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c708750455cbeb3f5a8c4d22aa2d287d034534e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt @@ -0,0 +1,2 @@ +((0_1863:0.00000000,(3_853:0.01126750,2_917:0.24504350):0.03834050):0.00000000,1_1570:0.00000000,4_1784:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed2033355d72bad5c018e102a183f813779e796b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt @@ -0,0 +1,2 @@ +(0_1864:-0.00137184,((2_916:1.52308250,3_849:0.08115450):0.09047732,1_1571:0.00637345):0.01433955,4_1785:0.04006884); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8c7333cc34d4d731f8b15c497ab475921464c84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt @@ -0,0 +1,2 @@ +(1_1576:0.00476700,(0_1869:0.00629250,(3_1561:1.14056125,2_910:0.08092375):0.07760550):0.00367250,4_1789:0.00277800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a757e00765276ff4b328511d729e856fa2af7de4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt @@ -0,0 +1,2 @@ +(((3_843:0.12305025,2_908:0.13044675):0.14693000,1_1577:-0.00062450):0.00062450,0_1870:-0.00062450,4_1790:0.00815250); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b10bee584b90ce1b76b612d3d8610145d325bbed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt @@ -0,0 +1,2 @@ +((1_1581:0.01421575,(2_905:0.23416750,3_840:0.18444150):0.13193125):0.01371375,0_1874:0.00572350,4_1794:0.00496350); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1cd4da216023455165d28b78a767bafab00421b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt @@ -0,0 +1,2 @@ +((1_1583:0.00662875,(4_1796:0.00000000,0_1876:0.00000000):0.00619825):0.12397675,2_903:0.20155975,3_838:0.19365725); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3692df32f196ce6e5b6e1be57b8ea3ee33bca123 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt @@ -0,0 +1,2 @@ +((1_1588:0.03392688,(3_834:0.33512050,2_898:0.42833750):0.15537879):0.00182112,4_1801:0.00000000,0_1881:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..47967ad0c99b58bff462f17f43e34f7c42e2d642 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt @@ -0,0 +1,2 @@ +(0_1882:0.00827900,(3_833:0.02406200,(1_1589:0.00000000,4_1802:0.00000000):0.00544100):0.00235550,2_894:0.02406100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a09f06bbd505c4a4609701a358eefd9fe80c5f10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt @@ -0,0 +1,2 @@ +((2_893:0.07958837,3_832:0.01020463):0.00107487,(1_1590:0.00086287,4_1803:0.00205012):0.00838238,0_1883:0.00902362); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd54c2b88e5bc199c146aefcb4920985b4ee571f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt @@ -0,0 +1,2 @@ +(2_892:0.02095119,(0_1884:0.00283198,(1_1591:0.00155517,3_831:0.01207683):0.00308016):0.00102802,4_1804:0.00509181); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..318dc1b9362abb22830144b8172e429094e6fcc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt @@ -0,0 +1,2 @@ +((3_826:0.00578762,(0_1891:1.14837787,3_278:1.64784713):1.02769437):0.00498087,4_1813:0.01379588,2_886:0.01381712); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..86ed5fc13092e99a0644cad9d7200f6c1e65ce74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt @@ -0,0 +1,2 @@ +(((3_422:0.94109800,3_815:0.78648200):0.36212629,4_1830:-0.06896114):0.08206264,0_1903:0.00489150,2_874:0.34648150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..671df72f35852861a0432f08c916ab25891ac4c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt @@ -0,0 +1,2 @@ +((3_814:0.88483865,(0_1906:0.01433844,4_1833:0.00493556):0.00508232):0.00794592,2_873:0.01150933,1_1611:0.06781967); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f89871eb321959402f4b911f3961dac40d40232 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt @@ -0,0 +1,2 @@ +((0_1909:0.01135096,(1_1614:0.00671010,4_1836:0.00527490):0.00719550):0.02926887,3_812:0.49622617,2_870:0.04044983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4a71afb7a66633272477133a054876e80f0ab59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt @@ -0,0 +1,2 @@ +((1_1617:0.00000000,4_1839:0.00000000):0.00482000,(2_867:0.04305500,3_809:0.31651800):0.05912350,0_1912:0.00616200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..10df0cb8105f6db90905cba100e84505a878085e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt @@ -0,0 +1,2 @@ +(4_1840:0.00830325,(1_1618:0.06053350,(2_865:0.37915275,3_808:0.55663725):0.19710750):0.00699600,0_1913:0.03155975); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4757472588b053de7d4f102fde5b76de726dbc24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt @@ -0,0 +1,2 @@ +(((3_791:0.00754500,2_854:0.08489400):0.00092750,1_1628:0.00210805):0.00492395,0_1923:0.00000000,4_1850:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..20c0ca7b87e544eed846f848d44d686574858040 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt @@ -0,0 +1,2 @@ +((0_1929:0.00687877,(1_1634:0.01330617,4_1856:0.00048283):0.00203245):0.03360613,3_1720:0.21332183,2_848:0.03806617); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..81fa76ccb577a2557c1ee188613254a2a058cd82 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt @@ -0,0 +1,2 @@ +(4_1864:0.01799238,((2_840:0.59974587,3_777:0.44035413):0.11407812,1_1642:0.00910787):0.00156713,0_1937:0.01370562); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7b5bef62618d7b9b44c0ce835dc8c5cde28d5ecf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt @@ -0,0 +1,2 @@ +((0_1938:0.01913310,(4_1865:0.00000000,1_1643:0.00000000):0.00773090):0.10517020,2_839:0.13833250,3_776:0.42590050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0c2821dfd079a21dfbfe6b6cd19bb530872719b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt @@ -0,0 +1,2 @@ +((1_1663:0.01021763,(0_1942:0.00355338,4_1881:0.01553263):0.00660338):0.04594287,3_758:0.21566462,2_820:0.03475238); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..30ec0eb27aaa7c92fbe6f98b0da8c3c1aa4280c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt @@ -0,0 +1,2 @@ +(1_1666:0.02160730,((2_817:0.25911567,3_755:1.44147933):0.25695372,0_1945:0.03866216):0.01232234,4_1884:0.02349670); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..614be63236e91ad2acc49d3fbc1ca748f58ce66a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt @@ -0,0 +1,2 @@ +((4_1886:0.00635025,(0_1947:0.00409300,1_1668:-0.00042100):0.00140675):0.01390875,2_815:0.02596475,3_753:0.01982125); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..185bd39e7487275d7538381a99c9e7649a8078e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt @@ -0,0 +1,2 @@ +((3_745:0.01446087,(2_786:0.02552638,1_1676:0.01205962):0.00182863):0.00638312,4_1894:0.00008437,0_1956:0.01597663); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..090815f4edee22222b2b9099b1e73c6479a49a06 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt @@ -0,0 +1,2 @@ +(0_1966:0.00113511,((2_774:0.02054017,3_735:0.01945083):0.00487235,4_1904:0.00278555):0.00137245,1_1686:0.00163189); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..79c50ccbde3c0f799fca12a45b2eec8bc6ab8336 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt @@ -0,0 +1,2 @@ +(2_765:0.04978528,(3_731:0.00646838,(0_1973:0.00087033,1_1691:0.00179267):0.00448246):0.00132862,4_1909:0.00498872); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..56becb8e845cb13e598e206a1eb94eacb096b22b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt @@ -0,0 +1,2 @@ +((2_752:0.10699637,3_722:0.18500663):0.16945662,(0_1991:0.00075462,1_1708:0.00822437):0.00662413,4_1926:-0.00146113); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3aec8c2988e0aceaf66e2a4df0a6db02134a9d65 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt @@ -0,0 +1,2 @@ +(1_1711:-0.00033055,((2_693:0.09766933,3_708:0.09612267):0.16151796,4_1929:0.16496387):0.00093563,0_1994:0.00698655); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..35c54a760332e0c0f9292ea431a79cb8120cb955 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt @@ -0,0 +1,2 @@ +(((2_746:0.11522100,3_710:0.13391900):0.14723600,0_1995:0.01358700):0.00653000,1_1712:0.00000000,4_1930:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b275934761d651cc997e3fcc24b251c25246664d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt @@ -0,0 +1,2 @@ +(0_1997:0.00416675,(4_1934:0.04923600,(3_705:0.52228325,2_742:0.25975775):0.14646100):0.05820800,1_1714:0.00584625); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6893993c7956ae3944d8ba6ddd188c5def26b4e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt @@ -0,0 +1,2 @@ +(((3_470:0.27872029,2_541:0.27477971):0.01669196,2_724:0.09999315):0.08383624,0_2010:0.00402533,4_1939:0.00402867); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..72c20222d4e9718ee136a503a525c40e787fefc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt @@ -0,0 +1,2 @@ +(((3_597:0.01829764,0_2019:0.01899636):0.00481981,2_686:0.31375674):0.00738002,4_1958:0.00590517,1_1734:0.00637583); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c3a109ec1cce844cf31b5fbef51a7c6f021ff99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt @@ -0,0 +1,2 @@ +((3_591:0.00535725,(4_1964:-0.00005675,2_680:0.01007875):0.00326225):0.00753675,1_1740:0.00000000,0_2024:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..52e1e77b1ab8c212164154b174296502dd570711 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt @@ -0,0 +1,2 @@ +((0_2034:0.01860037,(3_581:0.02815112,4_1974:0.15796288):0.01244163):0.02284663,2_665:0.14398937,1_1753:0.03322962); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2909b8f8cd3fc6831218d877e2a421293aeb1720 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt @@ -0,0 +1,2 @@ +((4_1982:0.00268100,(1_1759:0.00000000,0_2041:0.00000000):0.00405800):0.31376450,2_659:0.18272450,3_575:0.72002150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebeeadb31fc564beb06ee4ea5b9336d46b27984a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt @@ -0,0 +1,2 @@ +((1_1764:0.00000000,0_2046:0.00000000):0.00292200,(2_654:0.56345750,3_571:0.80596050):0.05190550,4_1987:0.00013800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bdbeb6a7d35a275fd529ee1eeaf5bb52a3fdec74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt @@ -0,0 +1,2 @@ +((4_1989:0.01911182,(1_1766:0.01920649,0_2048:0.00895951):0.00548095):0.00847908,3_569:0.34096417,2_651:0.03747983); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..180fd68f6122ce15543e2150010c3d3308b40119 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt @@ -0,0 +1,2 @@ +(4_1993:0.00546750,((3_564:0.06833225,2_647:0.01808475):0.01946725,0_2054:-0.00012675):0.00011775,1_1773:0.00268650); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cbeeae92f6a51a2f4bc4b745880703a8bb590e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt @@ -0,0 +1,2 @@ +(((3_563:0.60707088,2_645:0.17638113):0.11796313,4_1995:0.05855387):0.00157063,1_1775:0.01148637,0_2056:-0.00251737); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed0fe692030c878de1b39f64f5a13ef14848ad7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt @@ -0,0 +1,2 @@ +((4_1996:0.01248925,1_1776:0.01181675):0.01199275,(2_644:0.07558325,3_562:0.33051275):0.06673825,0_2057:0.00369625); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..93bb714ce289d58920c6dc08fa29d9d337938dd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1779:0.00000000,4_1999:0.00000000):0.01501550,3_559:0.02640850):0.01578000,0_2060:0.01884600,2_641:0.05439100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a059ad6e750a95d9c2b0cd977f2a2d2cc3016b56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt @@ -0,0 +1,2 @@ +((1_1783:0.00591487,(3_555:0.24818113,2_637:0.10770888):0.03505163):0.00925713,4_2003:0.01034263,0_2064:0.04014938); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..adc19a9fd5d0fa1a1eadb9c7ca0f8225692aa9df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt @@ -0,0 +1,2 @@ +((3_552:0.02938713,(4_2005:0.00894162,0_2066:0.00839138):0.01703738):0.01296688,1_1785:0.01030763,2_635:0.02294137); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..4fac187eff7d4f26983a8bfe1c15b657d919ae28 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt @@ -0,0 +1,2 @@ +((0_2068:0.00684942,(2_633:0.00215680,3_550:0.00178820):0.00231203):0.00253753,4_2007:0.00090867,1_1787:0.00007933); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ade6ecdf5fed47b3fbc5f9805643278c3ae042c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt @@ -0,0 +1,2 @@ +((0_2070:0.00041763,1_1789:0.01325238):0.00358438,(3_548:0.03389487,2_631:0.00762213):0.00039787,4_2009:0.02698113); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7dd99893028c832e1952d9088e9c5c0b2308a1f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt @@ -0,0 +1,2 @@ +((0_2077:0.00361415,(4_2016:0.00000000,1_1796:0.00000000):0.00417585):0.09450872,3_541:0.20039600,2_616:0.05827400); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..39149ad6fce4c76341471fca72440c36265c1f58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt @@ -0,0 +1,2 @@ +(4_2019:0.01882815,((2_698:0.27210233,3_537:0.06684367):0.05166548,1_1799:0.01039343):0.00685957,0_2080:0.01646685); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..62dd501acf83eeafc96e94f8c203a6c38590aa44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt @@ -0,0 +1,2 @@ +(1_1800:0.00509121,(3_536:0.00451247,(2_611:0.05381450,0_2082:0.03050550):0.15432399):0.00644953,4_2020:-0.00003221); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..98a2a1b8be2d0c1221d5a39eb6dfef09e5efaacd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt @@ -0,0 +1,2 @@ +((1_1806:0.00444113,(0_2087:0.00736962,4_2026:0.00716737):0.00189587):0.06848838,3_529:0.05631138,2_603:0.07794962); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b7ae22a887b2a28cd7e6854a1290feeaadfb84f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt @@ -0,0 +1,2 @@ +((1_1812:0.01380450,(4_2032:0.00683400,0_2088:0.00617500):0.00842750):0.06564650,3_520:0.33100900,2_595:0.08197900); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..69f613df1cc976f3dcf218056c6a756c2e9ce2a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt @@ -0,0 +1,2 @@ +(((2_594:0.07863367,3_519:0.31202533):0.04708502,4_2033:0.00532307):0.01669293,1_1813:0.00000000,0_2089:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..a790d9ffb7063a8d5aa533ad88cd4008c6d17189 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt @@ -0,0 +1,2 @@ +(((2_582:0.25464087,3_505:0.45708113):0.22336712,0_2097:0.00941838):0.02714112,1_1821:0.01785812,4_2041:0.01175488); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..76d7cdfb3d07bb58c23c518501f723bb02e4b7cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1834:0.00422746,0_2109:0.00574654):0.00257916,4_2055:0.00469300):0.07975679,2_564:0.07173633,3_491:0.26835767); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..26171192cda3fbc934404c8870ae9d4c492feb0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt @@ -0,0 +1,2 @@ +(0_2112:0.00000000,(4_2058:0.00066293,(2_561:0.03894450,3_489:0.28532550):0.04104714):0.00661607,1_1837:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c69cbb42cc14515a72d0043728e909584ee28f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt @@ -0,0 +1,2 @@ +(0_2117:0.00314416,(4_2063:0.00666978,(3_484:0.16527917,2_556:0.27871583):0.12280909):0.00302372,1_1842:0.00052884); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d186954138b48700bde53f6c88ecdff71a56bb96 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt @@ -0,0 +1,2 @@ +((0_2125:0.01197960,(1_1850:0.00660587,4_2071:0.02223913):0.00984927):0.07880121,2_545:0.08376850,3_472:0.31484750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9300a274736143bd4773c47bfa54392e24761d4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt @@ -0,0 +1,2 @@ +(((1_1864:0.00000000,4_2085:0.00000000):0.00000000,0_2140:0.00000000):0.29469350,2_478:0.23072050,3_1273:0.32268150); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2ac5fd524a43eccb019d75ad1327ccca03fa147f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt @@ -0,0 +1,2 @@ +((4_2090:0.00000000,1_1869:0.00000000):0.00000000,(3_452:0.90502500,2_521:0.15886000):0.11674400,0_2145:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ff42e6e47ead34591c208caea5111c159e84c7c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt @@ -0,0 +1,2 @@ +((3_450:0.41880883,2_507:0.16344817):0.14691797,(1_1879:0.01034638,0_2155:0.00611762):0.01892773,4_2095:0.00567522); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b7f767b852452254d570c09d6a129d56db0df6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt @@ -0,0 +1,2 @@ +((1_1892:0.00008375,(4_2112:0.00000000,0_2179:0.00000000):0.00320725):0.08549775,2_487:0.10256525,3_424:0.05826375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9693d51eef00e9277ebe26d927f16e3d48f006ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt @@ -0,0 +1,2 @@ +(0_2180:0.00178312,((2_697:0.20858837,4_2153:0.29268162):0.40095288,1_1893:0.00069263):0.00108187,4_2113:0.00713287); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..280f47c786ca51fbe7299e9bd349a87f4d87d1bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt @@ -0,0 +1,2 @@ +((1_1896:0.00210949,(4_2116:0.00092585,0_2183:0.00363315):0.00282958):0.09985074,3_2037:0.52283900,2_484:1.12563500); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6c12fed83669bd9aa019aab28a6fa6596a7c713 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt @@ -0,0 +1,2 @@ +((3_420:0.02404680,(2_481:0.11437093,1_1899:0.03969007):0.00921162):0.00506787,0_2186:0.00366550,4_2119:0.00606050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c420f20983cab4838f5b1d3a0969ba67aa133e38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt @@ -0,0 +1,2 @@ +((0_2193:0.00028663,(4_2125:0.00075462,1_1904:0.00746738):0.00176537):0.00459737,2_459:0.03103613,3_415:0.29174387); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..d3135ec5695dbb82aca546a77715fe9949347972 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt @@ -0,0 +1,2 @@ +(((3_413:0.02261700,2_457:0.02715700):0.03440600,4_2127:0.00000000):0.00000000,0_2195:0.00000000,1_1906:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e559010e636f75cfed2467b37c5db9e6302dff83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt @@ -0,0 +1,2 @@ +((1_1907:0.00000000,(3_412:0.03646550,2_456:0.03873850):0.02947050):-0.00000000,0_2196:0.00000000,4_2128:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2882194f436ea26caf36dbb723576dbb42d4e02e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt @@ -0,0 +1,2 @@ +((1_1913:0.00185828,4_2142:0.00158072):0.00081135,(3_477:0.28908917,2_443:0.00654383):0.00775673,0_2209:0.00707164); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ed75914aa387d7b5f31e80e8e5ccf201e58efc3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt @@ -0,0 +1,2 @@ +(0_2221:0.00127625,((3_389:0.01646167,2_436:0.01164433):0.00190462,4_2161:0.00346986):0.00166114,1_1923:0.00099775); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2428b705fd77d94e7fb0460fb08ef94daf40c5d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt @@ -0,0 +1,2 @@ +((1_1926:-0.00016320,(2_434:0.00013067,3_388:0.12901233):0.00324060):0.00016320,0_2224:0.00512900,4_2164:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf4d7edefb39a94fa460179c007dc0afd568bb0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt @@ -0,0 +1,2 @@ +((1_1934:0.00000050,0_2231:0.00000050):0.00000000,(2_428:0.00091000,3_381:0.03820200):0.02225050,4_2172:0.00000050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fb283fe0bbd2711be4ab8677e8b10eee63424739 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt @@ -0,0 +1,2 @@ +(4_2174:-0.00045744,((3_379:0.28948717,2_425:0.08653183):0.06532377,0_2232:0.01155481):0.00276019,1_1936:0.00730844); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f0bf35032faa1451536c4370bc5afdf342e5837 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt @@ -0,0 +1,2 @@ +(1_1937:0.02097800,((3_378:0.49616100,2_424:0.32103900):0.22464112,0_2233:0.06720537):0.03173863,4_2175:0.07871800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..511e1929e977926e328b10a0a932b9ea2bddb774 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt @@ -0,0 +1,2 @@ +((0_2234:0.00873650,(1_1938:0.00195025,4_2176:0.00534975):0.00362500):0.10764150,3_377:0.26446300,2_423:0.09129200); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8f33623f032eb8783ca62db46f0bc3aa3531ca86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt @@ -0,0 +1,2 @@ +(0_2238:0.00159335,((3_373:0.11902483,2_419:0.03129417):0.03394978,1_1942:0.00748885):0.00358965,4_2180:0.00050065); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7288f6e66f98bc803ea71394270ebd0323d64241 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt @@ -0,0 +1,2 @@ +(0_2240:-0.00030437,((3_371:0.30823163,2_418:0.20024638):0.04295213,4_2182:0.00470788):0.00247712,1_1944:0.00122838); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..467a31b6b8bf363945cbdeebb8a6b45679462383 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt @@ -0,0 +1,2 @@ +(((4_2193:0.00000050,1_1955:0.00000050):0.00000000,0_2251:0.00000050):0.02968900,3_360:0.02230850,2_406:0.01444750); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0be28bb708be9200f11fa77ed1fa460a35ffd7a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt @@ -0,0 +1,2 @@ +((2_2601:0.33542479,(2_596:0.04497025,3_521:0.06159975):0.11279125):0.13467921,1_1810:0.00000000,4_2030:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e4c0d7b6ae0901d8e92029b0da8e9f5a45fe4c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt @@ -0,0 +1,2 @@ +((1_2079:0.00000000,4_120:0.00000000):0.01306850,(2_81:0.59653100,3_125:0.53828500):0.89134850,2_254:0.01548050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..71985e86cf2a895e475a9a47a15edb2c09a9c086 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt @@ -0,0 +1,2 @@ +(((3_1792:0.12513275,3_639:0.02036525):0.08781375,2_372:0.10160825):0.68822575,3_1185:0.27315025,3_316:0.74239375); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b8b01771488b2b2b7be73c80e558e191f4d89e54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt @@ -0,0 +1,2 @@ +((4_9:0.03426950,1_1978:-0.00239550):0.00239550,0_9:0.00000000,2_368:0.22041800); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..0da4c62e99cf33564837ad43142c28bf6049c346 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt @@ -0,0 +1,2 @@ +(0_44:0.00796298,(4_39:0.00078325,1_2008:0.00025675):0.00602025,3_282:0.15522402); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..aa74d38ddda35ee2623627271e881664b35613c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt @@ -0,0 +1,2 @@ +(2_337:0.15978406,(1_2011:0.00573125,4_42:0.00641575):0.00512375,0_47:0.01401494); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebede0855d6655bc15cc0b702e3b87fcbeb998b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt @@ -0,0 +1,2 @@ +((4_153:0.03891975,2_220:0.22517525):0.04697925,1_2110:0.00518114,0_145:0.00367086); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1dc8beb65018a37268b3714455bb002aa5cacb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt @@ -0,0 +1,2 @@ +(2_215:0.16927071,(0_169:0.02575125,1_2113:0.01518375):0.03328925,4_161:0.04575329); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..02025b57c360f671e799df35d038969688788e56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt @@ -0,0 +1,2 @@ +((2_158:0.37739100,0_209:0.69109600):0.23009100,4_209:0.00000000,1_2153:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f9ede7fa5329357403b0bca819db0c1233eab10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt @@ -0,0 +1,2 @@ +((1_2229:0.00000000,0_263:0.00000000):0.00000000,2_75:0.45316000,4_261:0.00000000); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..765c585bdc1e3e40951e669b852452c89e9199b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt @@ -0,0 +1,2 @@ +((0_277:0.02208650,2_59:0.15235150):0.01994450,4_283:0.01598253,1_2250:0.00287247); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ddf85d3979b0e43af16349caf5f48a6da763f2a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt @@ -0,0 +1,2 @@ +(4_298:0.03107486,(0_291:0.06690125,2_45:0.26370275):0.03430375,1_8:0.01142614); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..bc374a161e2eb24569fa83803cccfe5dfb09207c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt @@ -0,0 +1,2 @@ +(2_728:0.00499750,(2_716:-0.00130025,0_600:0.07277825):0.27229675,2_731:0.08479850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..3bf2a1d07d820f6e33290df8e87fa3b647fa7de2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt @@ -0,0 +1,2 @@ +((2_388:0.00000000,3_2145:0.00000000):0.00000000,4_574:0.00000000,0_607:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..947cb66b387c720515e448890ad1d51a5a814119 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt @@ -0,0 +1,2 @@ +((0_610:0.00896275,2_391:-0.00020075):0.00018975,3_2142:0.00732600,4_571:0.00293100); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..431ebea326e3c72fd226204c6bb9f75d7db1517a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt @@ -0,0 +1,2 @@ +((3_2133:0.10456775,1_361:-0.03195675):0.07907725,0_615:1.08293225,4_584:-0.03009825); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..b91336c32c8c8ea8b4e2d2950ff476273e6b097a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt @@ -0,0 +1,2 @@ +(0_637:0.00213000,(1_383:0.00000000,4_607:0.00000000):0.00264600,2_2250:0.03916700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..c4b5ad0a354885c24222a8e917213b9183da8a24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt @@ -0,0 +1,2 @@ +(0_639:0.00737100,(1_385:0.00000000,4_609:0.00000000):0.00190700,2_2247:0.02828300); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..72dd4fbaa4240a6ba41c915161c0d92b41d275e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt @@ -0,0 +1,2 @@ +(1_387:0.01074230,(2_2245:0.13887400,0_641:0.01786800):0.00487650,4_611:0.01076470); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6a3e7319b9bd103b59352c3b6a77b7af33c7d873 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt @@ -0,0 +1,2 @@ +(2_2141:0.55630557,(1_453:0.03559800,4_677:0.05170100):0.01163850,0_713:0.03023643); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..fefb6fd2435d0c00b2c6694b15d37efd3cb419ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt @@ -0,0 +1,2 @@ +(4_1918:0.02035383,(0_1983:0.07782225,1_1700:0.03032075):0.00213075,2_754:0.20017617); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab0097ebdda578f05932d145a1c82bbc05fdaf4f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt @@ -0,0 +1,2 @@ +(0_1987:0.00249000,(3_714:0.31653475,4_1922:0.00275525):0.00193075,1_1704:0.00651700); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..9dbd975d8a54f03511985b53f5c2541d83b5b412 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt @@ -0,0 +1,2 @@ +(1_1705:0.00499932,(0_1988:0.00290425,4_1923:0.00095475):0.00420825,3_713:0.19433068); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..8a9014b0fd3853926bd010b31ac6f5062ce319bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt @@ -0,0 +1,2 @@ +((0_1993:0.20502175,4_1928:-0.04975475):0.43149725,2_748:0.44234550,1_1710:0.34470250); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..6f6c98ab98f748c5aac964e6dd0ed3130116e926 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt @@ -0,0 +1,2 @@ +((1_1758:0.00000000,0_2040:0.00000000):0.01048300,4_1981:0.01347300,2_660:0.43192600); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..37d5712d18c795742acca61182a1feb90c15d9d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt @@ -0,0 +1,2 @@ +(1_1819:-0.00063786,(2_586:0.32477025,4_2039:0.00065175):0.00368775,0_2095:0.00802986); 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+ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..756305fe19df20544736c0bb96f712ed7666f04b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt @@ -0,0 +1,2 @@ +((2_882:0.02453550,3_822:0.01104150):0.00286300,4_1817:0.01192452,1_1597:0.01212148); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..82664e210d3b0a086308c494a415743355d2692e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt @@ -0,0 +1,2 @@ +((1_1652:0.00000000,4_1870:0.00000000):0.04890250,3_768:0.06254350,2_830:0.05935050); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..5c32243ce66baa57af09be918122d28f5a1515f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt @@ -0,0 +1,2 @@ +(1_1736:0.00000000,(2_684:0.01250000,3_595:0.02988100):0.00446200,4_1960:0.00000000); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7f94d5b50db3716b086d187d0cc540760e4ff684 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt @@ -0,0 +1,2 @@ +((4_2027:0.07395025,1_1807:0.00578275):0.12906125,3_524:0.00938732,2_599:0.03330268); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..2507198855e8c348b254ebb88f85dc1aecfe2858 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt @@ -0,0 +1,2 @@ +(3_522:0.17425850,(1_1809:0.00000000,4_2029:0.00000000):0.10525950,2_597:0.41098850); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..44fa9a91423b6051d29106fe3db71ec78867b43a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt @@ -0,0 +1,2 @@ +((1_1900:0.01549000,3_419:0.03514500):0.09448050,4_2120:0.08140305,2_1299:1.31491995); + diff --git a/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cabf393d8c02706624de37ee8224e1b6f64a964 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_750/comparative-genomics_20260519_131022/orthofinder_input/OrthoFinder/Results_May19/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt @@ -0,0 +1,2 @@ +(3_1369:2.32367150,(3_681:-0.00252650,3_704:0.03852450):0.16378600,3_644:0.09611750); +