partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (156) hide show
  1. packages/ham/bcrham +0 -0
  2. packages/ig-sw/src/ig_align/ig-sw +0 -0
  3. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +155 -73
  5. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  6. test/new-results/test.log +12 -16
  7. test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv +8 -8
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -1
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +8 -8
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -1
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +7 -7
  12. test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -1
  13. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +9 -9
  14. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +8 -8
  16. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out +1 -1
  17. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +9 -9
  18. test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml +1 -1
  19. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out +1 -1
  20. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +8 -8
  21. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out +1 -1
  22. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +4 -4
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml +1 -1
  24. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  25. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +9 -9
  26. test/paired/new-results/partition-new-simu/igh+igl/partition-igh-selection-metrics.yaml +1 -1
  27. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out +1 -1
  28. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +9 -9
  29. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log +3 -3
  30. test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metrics.yaml +1 -1
  31. test/paired/new-results/partition-new-simu/selection-metrics.yaml +1 -1
  32. test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml +1 -1
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  42. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  43. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  44. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  45. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  46. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  47. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  48. test/paired/new-results/run-times.csv +6 -6
  49. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +86 -102
  50. test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml +1 -1
  51. test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml +1 -1
  52. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +84 -100
  53. test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml +1 -1
  54. test/paired/new-results/subset-partition-new-simu/merged-partition.log +50 -54
  55. test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igh.yaml +1 -1
  56. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  57. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  58. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  59. test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igh.yaml +1 -1
  60. test/paired/new-results/test.log +203 -236
  61. test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  62. test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  63. test/ref-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  64. test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  65. test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  66. test/ref-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  67. test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  68. test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  69. test/ref-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  70. test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa +24 -0
  71. test/ref-results/partition-new-simu/iqtree/iclust-0/log +430 -0
  72. test/ref-results/partition-new-simu/iqtree/iclust-0/out.bionj +1 -0
  73. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  74. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +282 -0
  75. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +429 -0
  76. test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist +13 -0
  77. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  78. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +3529 -0
  79. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -0
  80. test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa +16 -0
  81. test/ref-results/partition-new-simu/iqtree/iclust-1/log +373 -0
  82. test/ref-results/partition-new-simu/iqtree/iclust-1/out.bionj +1 -0
  83. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  84. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +279 -0
  85. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +372 -0
  86. test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist +9 -0
  87. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  88. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +2229 -0
  89. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -0
  90. test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa +16 -0
  91. test/ref-results/partition-new-simu/iqtree/iclust-2/log +375 -0
  92. test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj +1 -0
  93. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  94. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +274 -0
  95. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +374 -0
  96. test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist +9 -0
  97. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  98. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +2283 -0
  99. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -0
  100. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -0
  101. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa +24 -0
  102. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +3461 -0
  103. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +10 -0
  104. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -0
  105. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -0
  106. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -0
  107. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  108. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +216 -0
  109. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -0
  110. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba +0 -0
  111. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy +9 -0
  112. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -0
  113. test/ref-results/partition-new-simu/raxml/iclust-0/log +454 -0
  114. test/ref-results/partition-new-simu/raxml/iclust-0/run.sh +3 -0
  115. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa +16 -0
  116. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs +2203 -0
  117. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates +6 -0
  118. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -0
  119. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestModel +1 -0
  120. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -0
  121. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  122. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +217 -0
  123. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -0
  124. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.rba +0 -0
  125. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.reduced.phy +4 -0
  126. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -0
  127. test/ref-results/partition-new-simu/raxml/iclust-1/log +440 -0
  128. test/ref-results/partition-new-simu/raxml/iclust-1/run.sh +3 -0
  129. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa +16 -0
  130. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +2275 -0
  131. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -0
  132. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -0
  133. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -0
  134. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -0
  135. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  136. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +207 -0
  137. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -0
  138. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.rba +0 -0
  139. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -0
  140. test/ref-results/partition-new-simu/raxml/iclust-2/log +420 -0
  141. test/ref-results/partition-new-simu/raxml/iclust-2/run.sh +3 -0
  142. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -0
  143. bin/FastTree-macos +0 -0
  144. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  145. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  146. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  147. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  148. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  149. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  150. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  151. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  152. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  153. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  154. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  155. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  156. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree ADDED
@@ -0,0 +1,279 @@
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+ IQ-TREE 3.0.1 built May 5 2025
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+
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+ Input file name: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa
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+ Type of analysis: ModelFinder + tree reconstruction
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+ Random seed number: 784887
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+
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+ REFERENCES
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+ ----------
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+
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+ To cite IQ-TREE 3 please use:
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+
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+ Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger,
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+ Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn,
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+ Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025)
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+ IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.
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+ Submitted.
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+
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+ Please also cite the following paper(s) for the feature(s) that you used:
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+
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+ To cite ModelFinder please use:
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+
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+ Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
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+ and Lars S Jermiin (2017) ModelFinder: Fast model selection for
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+ accurate phylogenetic estimates. Nature Methods, 14:587–589.
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+ https://doi.org/10.1038/nmeth.4285
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+
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+ SEQUENCE ALIGNMENT
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+ ------------------
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+
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+ Input data: 8 sequences with 370 nucleotide sites
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+ Number of constant sites: 368 (= 99.4595% of all sites)
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+ Number of invariant (constant or ambiguous constant) sites: 368 (= 99.4595% of all sites)
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+ Number of parsimony informative sites: 0
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+ Number of distinct site patterns: 7
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+
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+ ModelFinder
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+ -----------
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+
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+ Best-fit model according to BIC: F81
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+
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+ List of models sorted by BIC scores:
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+
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+ Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
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+ F81 -524.779 1075.559 - 0.0353 1076.581 - 0.0459 1126.434 + 0.278
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+ JC -524.779 1075.559 - 0.0353 1076.581 - 0.0459 1126.434 + 0.278
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+ JC -524.779 1075.559 - 0.0353 1076.581 - 0.0459 1126.434 + 0.278
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+ HKY -524.663 1077.325 - 0.0146 1078.508 - 0.0175 1132.114 - 0.0162
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+ K2P -524.663 1077.326 - 0.0146 1078.509 - 0.0175 1132.115 - 0.0162
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+ K2P -524.663 1077.326 - 0.0146 1078.509 - 0.0175 1132.115 - 0.0162
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+ F81+I -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ JC+I -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ JC+I -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ F81+G4 -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ JC+G4 -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ JC+G4 -524.779 1077.559 - 0.013 1078.742 - 0.0156 1132.348 - 0.0144
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+ TPM3u -523.895 1077.791 - 0.0116 1079.147 - 0.0127 1136.493 - 0.00182
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+ TPM3 -523.895 1077.791 - 0.0116 1079.147 - 0.0127 1136.493 - 0.00182
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+ TPM3 -523.895 1077.791 - 0.0116 1079.147 - 0.0127 1136.493 - 0.00182
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+ K3Pu -523.971 1077.941 - 0.0107 1079.297 - 0.0118 1136.644 - 0.00168
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+ K3P -523.995 1077.990 - 0.0105 1079.346 - 0.0115 1136.693 - 0.00164
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+ K3P -523.995 1077.990 - 0.0105 1079.346 - 0.0115 1136.693 - 0.00164
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+ TPM2u -524.023 1078.046 - 0.0102 1079.402 - 0.0112 1136.749 - 0.0016
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+ TPM2 -524.023 1078.046 - 0.0102 1079.402 - 0.0112 1136.749 - 0.0016
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+ TPM2 -524.023 1078.046 - 0.0102 1079.402 - 0.0112 1136.749 - 0.0016
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+ TN -524.028 1078.055 - 0.0101 1079.411 - 0.0111 1136.758 - 0.00159
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+ TNe -524.028 1078.055 - 0.0101 1079.411 - 0.0111 1136.758 - 0.00159
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+ TNe -524.028 1078.055 - 0.0101 1079.411 - 0.0111 1136.758 - 0.00159
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+ F81+F -521.218 1074.437 + 0.0618 1075.978 + 0.062 1137.053 - 0.00137
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+ HKY+I -524.663 1079.325 - 0.00537 1080.681 - 0.00591 1138.028 - 0.000843
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+ HKY+G4 -524.663 1079.325 - 0.00537 1080.681 - 0.00591 1138.028 - 0.000843
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+ K2P+I -524.663 1079.326 - 0.00536 1080.682 - 0.0059 1138.028 - 0.000843
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+ K2P+I -524.663 1079.326 - 0.00536 1080.682 - 0.0059 1138.028 - 0.000843
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+ K2P+G4 -524.663 1079.326 - 0.00536 1080.682 - 0.0059 1138.028 - 0.000843
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+ K2P+G4 -524.663 1079.326 - 0.00536 1080.682 - 0.0059 1138.028 - 0.000843
75
+ JC+R2 -524.779 1079.559 - 0.00478 1080.914 - 0.00526 1138.261 - 0.00075
76
+ JC+I+G4 -524.782 1079.564 - 0.00476 1080.920 - 0.00524 1138.267 - 0.000748
77
+ TIM3 -523.262 1078.523 - 0.00801 1080.064 - 0.00804 1141.139 - 0.000178
78
+ TIM3e -523.262 1078.523 - 0.00801 1080.064 - 0.00804 1141.139 - 0.000178
79
+ TIM3e -523.262 1078.523 - 0.00801 1080.064 - 0.00804 1141.139 - 0.000178
80
+ TIMe -523.336 1078.671 - 0.00744 1080.213 - 0.00746 1141.288 - 0.000165
81
+ TIMe -523.336 1078.671 - 0.00744 1080.213 - 0.00746 1141.288 - 0.000165
82
+ TIM -523.336 1078.671 - 0.00744 1080.213 - 0.00746 1141.288 - 0.000165
83
+ TIM2e -523.390 1078.780 - 0.00705 1080.321 - 0.00707 1141.396 - 0.000157
84
+ TIM2 -523.390 1078.780 - 0.00705 1080.321 - 0.00707 1141.396 - 0.000157
85
+ TIM2e -523.390 1078.780 - 0.00705 1080.321 - 0.00707 1141.396 - 0.000157
86
+ TPM3u+I -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
87
+ TPM3+G4 -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
88
+ TPM3u+G4 -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
89
+ TPM3+G4 -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
90
+ TPM3+I -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
91
+ TPM3+I -523.895 1079.791 - 0.00425 1081.332 - 0.00427 1142.407 - 9.44e-05
92
+ K3Pu+G4 -523.970 1079.940 - 0.00395 1081.481 - 0.00396 1142.556 - 8.76e-05
93
+ K3Pu+I -523.970 1079.940 - 0.00395 1081.481 - 0.00396 1142.556 - 8.76e-05
94
+ K3P+I -523.988 1079.976 - 0.00388 1081.517 - 0.00389 1142.592 - 8.6e-05
95
+ K3P+I -523.988 1079.976 - 0.00388 1081.517 - 0.00389 1142.592 - 8.6e-05
96
+ K3P+G4 -523.996 1079.991 - 0.00385 1081.532 - 0.00386 1142.607 - 8.54e-05
97
+ K3P+G4 -523.996 1079.991 - 0.00385 1081.532 - 0.00386 1142.607 - 8.54e-05
98
+ TPM2u+I -524.023 1080.046 - 0.00374 1081.587 - 0.00375 1142.662 - 8.31e-05
99
+ TPM2u+G4 -524.023 1080.046 - 0.00374 1081.587 - 0.00375 1142.662 - 8.31e-05
100
+ TPM2+I -524.023 1080.046 - 0.00374 1081.587 - 0.00375 1142.662 - 8.31e-05
101
+ TPM2+I -524.023 1080.046 - 0.00374 1081.587 - 0.00375 1142.662 - 8.31e-05
102
+ TPM2+G4 -524.023 1080.046 - 0.00374 1081.588 - 0.00375 1142.663 - 8.31e-05
103
+ TPM2+G4 -524.023 1080.046 - 0.00374 1081.588 - 0.00375 1142.663 - 8.31e-05
104
+ TNe+I -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
105
+ TN+I -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
106
+ TNe+I -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
107
+ TNe+G4 -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
108
+ TNe+G4 -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
109
+ TN+G4 -524.028 1080.055 - 0.00373 1081.596 - 0.00374 1142.671 - 8.27e-05
110
+ HKY+F -521.099 1076.198 - 0.0256 1077.937 - 0.0233 1142.728 - 8.04e-05
111
+ F81+F+I -521.218 1076.437 - 0.0227 1078.175 - 0.0207 1142.966 - 7.14e-05
112
+ F81+F+G4 -521.218 1076.437 - 0.0227 1078.175 - 0.0207 1142.966 - 7.14e-05
113
+ JC+I+R2 -524.782 1081.564 - 0.00175 1083.105 - 0.00176 1144.180 - 3.89e-05
114
+ TPM3u+F -520.242 1076.484 - 0.0222 1078.433 - 0.0182 1146.928 - 9.85e-06
115
+ TVM -523.261 1080.522 - 0.00295 1082.261 - 0.00268 1147.052 - 9.25e-06
116
+ TVMe -523.261 1080.522 - 0.00295 1082.261 - 0.00268 1147.052 - 9.25e-06
117
+ TVMe -523.261 1080.522 - 0.00295 1082.261 - 0.00268 1147.052 - 9.25e-06
118
+ TIM3e+I -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
119
+ TIM3e+I -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
120
+ TIM3+I -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
121
+ TIM3e+G4 -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
122
+ TIM3+G4 -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
123
+ TIM3e+G4 -523.262 1080.523 - 0.00295 1082.262 - 0.00268 1147.053 - 9.25e-06
124
+ TIMe+I -523.336 1080.671 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
125
+ TIM+I -523.336 1080.671 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
126
+ TIMe+I -523.336 1080.671 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
127
+ TIMe+G4 -523.336 1080.672 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
128
+ TIM+G4 -523.336 1080.672 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
129
+ TIMe+G4 -523.336 1080.672 - 0.00274 1082.410 - 0.00249 1147.201 - 8.59e-06
130
+ K3Pu+F -520.390 1076.780 - 0.0192 1078.729 - 0.0157 1147.223 - 8.49e-06
131
+ TIM2e+I -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
132
+ TIM2+I -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
133
+ TIM2e+I -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
134
+ TIM2e+G4 -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
135
+ TIM2e+G4 -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
136
+ TIM2+G4 -523.390 1080.780 - 0.00259 1082.518 - 0.00236 1147.309 - 8.14e-06
137
+ TPM2u+F -520.505 1077.011 - 0.0171 1078.959 - 0.014 1147.454 - 7.57e-06
138
+ TN+F -520.525 1077.050 - 0.0167 1078.999 - 0.0137 1147.493 - 7.42e-06
139
+ HKY+F+I -521.099 1078.198 - 0.00943 1080.147 - 0.00771 1148.641 - 4.18e-06
140
+ HKY+F+G4 -521.099 1078.198 - 0.00943 1080.147 - 0.00771 1148.641 - 4.18e-06
141
+ JC+R3 -524.779 1083.559 - 0.000646 1085.297 - 0.000587 1150.088 - 2.03e-06
142
+ TIM3+F -519.670 1077.339 - 0.0145 1079.511 - 0.0106 1151.696 - 9.08e-07
143
+ SYM -522.627 1081.254 - 0.00205 1083.203 - 0.00167 1151.697 - 9.07e-07
144
+ GTR -522.627 1081.254 - 0.00205 1083.203 - 0.00167 1151.697 - 9.07e-07
145
+ SYM -522.627 1081.254 - 0.00205 1083.203 - 0.00167 1151.697 - 9.07e-07
146
+ TIM+F -519.818 1077.635 - 0.0125 1079.806 - 0.00915 1151.992 - 7.83e-07
147
+ TIM2+F -519.933 1077.866 - 0.0111 1080.037 - 0.00815 1152.222 - 6.98e-07
148
+ TPM3u+F+I -520.242 1078.484 - 0.00817 1080.656 - 0.00598 1152.841 - 5.12e-07
149
+ TPM3u+F+G4 -520.242 1078.484 - 0.00817 1080.656 - 0.00598 1152.841 - 5.12e-07
150
+ TVMe+I -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
151
+ TVM+I -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
152
+ TVMe+I -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
153
+ TVM+G4 -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
154
+ TVMe+G4 -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
155
+ TVMe+G4 -523.261 1082.522 - 0.00109 1084.471 - 0.000888 1152.965 - 4.81e-07
156
+ K3Pu+F+I -520.390 1078.780 - 0.00705 1080.952 - 0.00516 1153.137 - 4.42e-07
157
+ K3Pu+F+G4 -520.390 1078.780 - 0.00705 1080.952 - 0.00516 1153.137 - 4.42e-07
158
+ TPM2u+F+G4 -520.505 1079.010 - 0.00628 1081.181 - 0.0046 1153.367 - 3.94e-07
159
+ TPM2u+F+I -520.505 1079.010 - 0.00628 1081.182 - 0.0046 1153.367 - 3.94e-07
160
+ TN+F+G4 -520.525 1079.050 - 0.00616 1081.222 - 0.00451 1153.407 - 3.86e-07
161
+ TN+F+I -520.525 1079.051 - 0.00616 1081.222 - 0.00451 1153.407 - 3.86e-07
162
+ JC+I+R3 -524.782 1085.564 - 0.000237 1087.513 - 0.000194 1156.007 - 1.05e-07
163
+ TVM+F -519.650 1079.300 - 0.00544 1081.707 - 0.00354 1157.570 - 4.81e-08
164
+ TIM3+F+I -519.669 1079.339 - 0.00533 1081.746 - 0.00347 1157.609 - 4.72e-08
165
+ TIM3+F+G4 -519.669 1079.339 - 0.00533 1081.746 - 0.00347 1157.609 - 4.72e-08
166
+ SYM+I -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
167
+ GTR+I -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
168
+ SYM+I -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
169
+ SYM+G4 -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
170
+ SYM+G4 -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
171
+ GTR+G4 -522.627 1083.254 - 0.000753 1085.425 - 0.000551 1157.611 - 4.72e-08
172
+ TIM+F+G4 -519.818 1079.635 - 0.0046 1082.042 - 0.00299 1157.905 - 4.07e-08
173
+ TIM+F+I -519.818 1079.636 - 0.0046 1082.042 - 0.00299 1157.906 - 4.07e-08
174
+ TIM2+F+I -519.933 1079.866 - 0.0041 1082.273 - 0.00266 1158.136 - 3.63e-08
175
+ TIM2+F+G4 -519.933 1079.866 - 0.0041 1082.273 - 0.00266 1158.136 - 3.63e-08
176
+ GTR+F -519.077 1080.154 - 0.00355 1082.810 - 0.00204 1162.338 - 4.44e-09
177
+ TVM+F+I -519.650 1081.300 - 0.002 1083.955 - 0.00115 1163.483 - 2.5e-09
178
+ TVM+F+G4 -519.650 1081.300 - 0.002 1083.955 - 0.00115 1163.483 - 2.5e-09
179
+ GTR+F+I -519.077 1082.154 - 0.0013 1085.071 - 0.000658 1168.251 - 2.31e-10
180
+ GTR+F+G4 -519.077 1082.154 - 0.0013 1085.071 - 0.000658 1168.251 - 2.31e-10
181
+
182
+ AIC, w-AIC : Akaike information criterion scores and weights.
183
+ AICc, w-AICc : Corrected AIC scores and weights.
184
+ BIC, w-BIC : Bayesian information criterion scores and weights.
185
+
186
+ Plus signs denote the 95% confidence sets.
187
+ Minus signs denote significant exclusion.
188
+
189
+ SUBSTITUTION PROCESS
190
+ --------------------
191
+
192
+ Model of substitution: F81+F
193
+
194
+ Rate parameter R:
195
+
196
+ A-C: 1.0000
197
+ A-G: 1.0000
198
+ A-T: 1.0000
199
+ C-G: 1.0000
200
+ C-T: 1.0000
201
+ G-T: 1.0000
202
+
203
+ State frequencies: (empirical counts from alignment)
204
+
205
+ pi(A) = 0.2374
206
+ pi(C) = 0.2698
207
+ pi(G) = 0.2936
208
+ pi(T) = 0.1993
209
+
210
+ Rate matrix Q:
211
+
212
+ A -1.024 0.3621 0.3941 0.2675
213
+ C 0.3187 -0.9802 0.3941 0.2675
214
+ G 0.3187 0.3621 -0.9482 0.2675
215
+ T 0.3187 0.3621 0.3941 -1.075
216
+
217
+ Model of rate heterogeneity: Uniform
218
+
219
+ MAXIMUM LIKELIHOOD TREE
220
+ -----------------------
221
+
222
+ Log-likelihood of the tree: -521.2183 (s.e. 10.5164)
223
+ Unconstrained log-likelihood (without tree): -533.7213
224
+ Number of free parameters (#branches + #model parameters): 16
225
+ Akaike information criterion (AIC) score: 1074.4366
226
+ Corrected Akaike information criterion (AICc) score: 1075.9776
227
+ Bayesian information criterion (BIC) score: 1137.0526
228
+
229
+ Total tree length (sum of branch lengths): 0.0055
230
+ Sum of internal branch lengths: 0.0000 (0.0914% of tree length)
231
+
232
+ WARNING: 5 near-zero internal branches (<0.0027) should be treated with caution
233
+ Such branches are denoted by '**' in the figure below
234
+
235
+ NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
236
+
237
+ +**XnaiveX
238
+ | (Node1)
239
+ +**13de8675ec
240
+ |
241
+ | +----------------------------------------------------------20a0129b57
242
+ | +**| (Node6)
243
+ | | +----------------------------------------------------------97366cf0d8
244
+ | +**| (Node5)
245
+ | | +**33aaa62e12
246
+ | +**| (Node4)
247
+ | | +**31e052ee14
248
+ | +**| (Node3)
249
+ | | +**91796617a0
250
+ +**| (Node2)
251
+ +**4233d708fe
252
+
253
+ Tree in newick format:
254
+
255
+ (XnaiveX:0.0000010000,13de8675ec:0.0000010000,(((((20a0129b57:0.0027294000,97366cf0d8:0.0027294000)Node6:0.0000010000,33aaa62e12:0.0000010000)Node5:0.0000010000,31e052ee14:0.0000010000)Node4:0.0000010000,91796617a0:0.0000010000)Node3:0.0000010000,4233d708fe:0.0000010000)Node2:0.0000010000)Node1;
256
+
257
+ ALISIM COMMAND
258
+ --------------
259
+ To simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis, you can use the following command:
260
+
261
+ --alisim simulated_MSA -t /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile -m "F81+F{0.237398,0.269755,0.293597,0.199251}" --length 370
262
+
263
+ To mimic the alignment used to produce this analysis, i.e. simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis *and* copying the same gap positions as the original alignment, you can use the following command:
264
+
265
+ iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa --alisim mimicked_MSA
266
+
267
+ To simulate any number of alignments in either of the two commandlines above, use the --num-alignments options, for example mimic 100 alignments you would use the command line:
268
+
269
+ iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa --alisim mimicked_MSA --num-alignments 100
270
+
271
+ For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
272
+
273
+ TIME STAMP
274
+ ----------
275
+
276
+ Date and time: Mon Aug 18 15:31:52 2025
277
+ Total CPU time used: 0.19099 seconds (0h:0m:0s)
278
+ Total wall-clock time used: 0.205656 seconds (0h:0m:0s)
279
+
test/ref-results/partition-new-simu/iqtree/iclust-1/out.log ADDED
@@ -0,0 +1,372 @@
1
+ IQ-TREE version 3.0.1 for Linux x86 64-bit built May 5 2025
2
+ Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
3
+ Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
4
+ Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
5
+
6
+ Host: pkrvmubgrv54qmi (AVX2, FMA3, 15 GB RAM)
7
+ Command: /home/runner/work/partis/partis/bin/iqtree3_intel -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out -o XnaiveX
8
+ Seed: 784887 (Using SPRNG - Scalable Parallel Random Number Generator)
9
+ Time: Mon Aug 18 15:31:52 2025
10
+ Kernel: AVX+FMA - 1 threads (4 CPU cores detected)
11
+
12
+ HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
13
+ HINT: -nt AUTO will automatically determine the best number of threads to use.
14
+
15
+ Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa ... Fasta format detected
16
+ Reading fasta file: done in 7.5741e-05 secs
17
+ Alignment most likely contains DNA/RNA sequences
18
+ Constructing alignment: done in 0.000379799 secs
19
+ WARNING: 3 sites contain only gaps or ambiguous characters.
20
+ Alignment has 8 sequences with 370 columns, 7 distinct patterns
21
+ 0 parsimony-informative, 2 singleton sites, 368 constant sites
22
+ Gap/Ambiguity Composition p-value
23
+ Analyzing sequences: done in 6.192e-06 secs
24
+ 1 XnaiveX 0.81% passed 100.00%
25
+ 2 13de8675ec 0.81% passed 100.00%
26
+ 3 20a0129b57 0.81% passed 99.96%
27
+ 4 31e052ee14 0.81% passed 100.00%
28
+ 5 33aaa62e12 0.81% passed 100.00%
29
+ 6 4233d708fe 0.81% passed 100.00%
30
+ 7 91796617a0 0.81% passed 100.00%
31
+ 8 97366cf0d8 0.81% passed 99.95%
32
+ **** TOTAL 0.81% 0 sequences failed composition chi2 test (p-value<5%; df=3)
33
+
34
+
35
+ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
36
+ Perform fast likelihood tree search using GTR+I+G model...
37
+ Estimate model parameters (epsilon = 5.000)
38
+ Perform nearest neighbor interchange...
39
+ Optimizing NNI: done in 0.000308676 secs using 59.61% CPU
40
+ Estimate model parameters (epsilon = 1.000)
41
+ 1. Initial log-likelihood: -519.628
42
+ Optimal log-likelihood: -519.601
43
+ Rate parameters: A-C: 0.00010 A-G: 3.78712 A-T: 0.00010 C-G: 0.00010 C-T: 0.00010 G-T: 1.00000
44
+ Warning! Some parameters hit the boundaries
45
+ Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
46
+ Proportion of invariable sites: 0.497
47
+ Gamma shape alpha: 998.448
48
+ Parameters optimization took 1 rounds (0.001 sec)
49
+ Time for fast ML tree search: 0.003 seconds
50
+
51
+ NOTE: ModelFinder requires 0 MB RAM!
52
+ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
53
+ No. Model -LnL df AIC AICc BIC
54
+ 1 JC 524.779 13 1075.559 1076.581 1126.434
55
+ 2 JC+I 524.779 14 1077.559 1078.742 1132.348
56
+ 3 JC+G4 524.779 14 1077.559 1078.742 1132.348
57
+ 4 JC+I+G4 524.782 15 1079.564 1080.920 1138.267
58
+ 5 JC+R2 524.779 15 1079.559 1080.914 1138.261
59
+ 6 JC+R3 524.779 17 1083.559 1085.297 1150.088
60
+ 14 JC+I+R2 524.782 16 1081.564 1083.105 1144.180
61
+ 15 JC+I+R3 524.782 18 1085.564 1087.513 1156.007
62
+ 23 JC 524.779 13 1075.559 1076.581 1126.434
63
+ 24 JC+I 524.779 14 1077.559 1078.742 1132.348
64
+ 25 JC+G4 524.779 14 1077.559 1078.742 1132.348
65
+ 45 F81 524.779 13 1075.559 1076.581 1126.434
66
+ 46 F81+I 524.779 14 1077.559 1078.742 1132.348
67
+ 47 F81+G4 524.779 14 1077.559 1078.742 1132.348
68
+ 67 F81+F 521.218 16 1074.437 1075.978 1137.053
69
+ 68 F81+F+I 521.218 17 1076.437 1078.175 1142.966
70
+ 69 F81+F+G4 521.218 17 1076.437 1078.175 1142.966
71
+ 89 K2P 524.663 14 1077.326 1078.509 1132.115
72
+ 90 K2P+I 524.663 15 1079.326 1080.682 1138.028
73
+ 91 K2P+G4 524.663 15 1079.326 1080.682 1138.028
74
+ 111 K2P 524.663 14 1077.326 1078.509 1132.115
75
+ 112 K2P+I 524.663 15 1079.326 1080.682 1138.028
76
+ 113 K2P+G4 524.663 15 1079.326 1080.682 1138.028
77
+ 133 HKY 524.663 14 1077.325 1078.508 1132.114
78
+ 134 HKY+I 524.663 15 1079.325 1080.681 1138.028
79
+ 135 HKY+G4 524.663 15 1079.325 1080.681 1138.028
80
+ 155 HKY+F 521.099 17 1076.198 1077.937 1142.728
81
+ 156 HKY+F+I 521.099 18 1078.198 1080.147 1148.641
82
+ 157 HKY+F+G4 521.099 18 1078.198 1080.147 1148.641
83
+ 177 TNe 524.028 15 1078.055 1079.411 1136.758
84
+ 178 TNe+I 524.028 16 1080.055 1081.596 1142.671
85
+ 179 TNe+G4 524.028 16 1080.055 1081.596 1142.671
86
+ 199 TNe 524.028 15 1078.055 1079.411 1136.758
87
+ 200 TNe+I 524.028 16 1080.055 1081.596 1142.671
88
+ 201 TNe+G4 524.028 16 1080.055 1081.596 1142.671
89
+ 221 TN 524.028 15 1078.055 1079.411 1136.758
90
+ 222 TN+I 524.028 16 1080.055 1081.596 1142.671
91
+ 223 TN+G4 524.028 16 1080.055 1081.596 1142.671
92
+ 243 TN+F 520.525 18 1077.050 1078.999 1147.493
93
+ 244 TN+F+I 520.525 19 1079.051 1081.222 1153.407
94
+ 245 TN+F+G4 520.525 19 1079.050 1081.222 1153.407
95
+ 265 K3P 523.995 15 1077.990 1079.346 1136.693
96
+ 266 K3P+I 523.988 16 1079.976 1081.517 1142.592
97
+ 267 K3P+G4 523.996 16 1079.991 1081.532 1142.607
98
+ 287 K3P 523.995 15 1077.990 1079.346 1136.693
99
+ 288 K3P+I 523.988 16 1079.976 1081.517 1142.592
100
+ 289 K3P+G4 523.996 16 1079.991 1081.532 1142.607
101
+ 309 K3Pu 523.971 15 1077.941 1079.297 1136.644
102
+ 310 K3Pu+I 523.970 16 1079.940 1081.481 1142.556
103
+ 311 K3Pu+G4 523.970 16 1079.940 1081.481 1142.556
104
+ 331 K3Pu+F 520.390 18 1076.780 1078.729 1147.223
105
+ 332 K3Pu+F+I 520.390 19 1078.780 1080.952 1153.137
106
+ 333 K3Pu+F+G4 520.390 19 1078.780 1080.952 1153.137
107
+ 353 TPM2 524.023 15 1078.046 1079.402 1136.749
108
+ 354 TPM2+I 524.023 16 1080.046 1081.587 1142.662
109
+ 355 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
110
+ 375 TPM2 524.023 15 1078.046 1079.402 1136.749
111
+ 376 TPM2+I 524.023 16 1080.046 1081.587 1142.662
112
+ 377 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
113
+ 397 TPM2u 524.023 15 1078.046 1079.402 1136.749
114
+ 398 TPM2u+I 524.023 16 1080.046 1081.587 1142.662
115
+ 399 TPM2u+G4 524.023 16 1080.046 1081.587 1142.662
116
+ 419 TPM2u+F 520.505 18 1077.011 1078.959 1147.454
117
+ 420 TPM2u+F+I 520.505 19 1079.010 1081.182 1153.367
118
+ 421 TPM2u+F+G4 520.505 19 1079.010 1081.181 1153.367
119
+ 441 TPM3 523.895 15 1077.791 1079.147 1136.493
120
+ 442 TPM3+I 523.895 16 1079.791 1081.332 1142.407
121
+ 443 TPM3+G4 523.895 16 1079.791 1081.332 1142.407
122
+ 463 TPM3 523.895 15 1077.791 1079.147 1136.493
123
+ 464 TPM3+I 523.895 16 1079.791 1081.332 1142.407
124
+ 465 TPM3+G4 523.895 16 1079.791 1081.332 1142.407
125
+ 485 TPM3u 523.895 15 1077.791 1079.147 1136.493
126
+ 486 TPM3u+I 523.895 16 1079.791 1081.332 1142.407
127
+ 487 TPM3u+G4 523.895 16 1079.791 1081.332 1142.407
128
+ 507 TPM3u+F 520.242 18 1076.484 1078.433 1146.928
129
+ 508 TPM3u+F+I 520.242 19 1078.484 1080.656 1152.841
130
+ 509 TPM3u+F+G4 520.242 19 1078.484 1080.656 1152.841
131
+ 529 TIMe 523.336 16 1078.671 1080.213 1141.288
132
+ 530 TIMe+I 523.336 17 1080.671 1082.410 1147.201
133
+ 531 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
134
+ 551 TIMe 523.336 16 1078.671 1080.213 1141.288
135
+ 552 TIMe+I 523.336 17 1080.671 1082.410 1147.201
136
+ 553 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
137
+ 573 TIM 523.336 16 1078.671 1080.213 1141.288
138
+ 574 TIM+I 523.336 17 1080.671 1082.410 1147.201
139
+ 575 TIM+G4 523.336 17 1080.672 1082.410 1147.201
140
+ 595 TIM+F 519.818 19 1077.635 1079.806 1151.992
141
+ 596 TIM+F+I 519.818 20 1079.636 1082.042 1157.906
142
+ 597 TIM+F+G4 519.818 20 1079.635 1082.042 1157.905
143
+ 617 TIM2e 523.390 16 1078.780 1080.321 1141.396
144
+ 618 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
145
+ 619 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
146
+ 639 TIM2e 523.390 16 1078.780 1080.321 1141.396
147
+ 640 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
148
+ 641 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
149
+ 661 TIM2 523.390 16 1078.780 1080.321 1141.396
150
+ 662 TIM2+I 523.390 17 1080.780 1082.518 1147.309
151
+ 663 TIM2+G4 523.390 17 1080.780 1082.518 1147.309
152
+ 683 TIM2+F 519.933 19 1077.866 1080.037 1152.222
153
+ 684 TIM2+F+I 519.933 20 1079.866 1082.273 1158.136
154
+ 685 TIM2+F+G4 519.933 20 1079.866 1082.273 1158.136
155
+ 705 TIM3e 523.262 16 1078.523 1080.064 1141.139
156
+ 706 TIM3e+I 523.262 17 1080.523 1082.262 1147.053
157
+ 707 TIM3e+G4 523.262 17 1080.523 1082.262 1147.053
158
+ 727 TIM3e 523.262 16 1078.523 1080.064 1141.139
159
+ 728 TIM3e+I 523.262 17 1080.523 1082.262 1147.053
160
+ 729 TIM3e+G4 523.262 17 1080.523 1082.262 1147.053
161
+ 749 TIM3 523.262 16 1078.523 1080.064 1141.139
162
+ 750 TIM3+I 523.262 17 1080.523 1082.262 1147.053
163
+ 751 TIM3+G4 523.262 17 1080.523 1082.262 1147.053
164
+ 771 TIM3+F 519.670 19 1077.339 1079.511 1151.696
165
+ 772 TIM3+F+I 519.669 20 1079.339 1081.746 1157.609
166
+ 773 TIM3+F+G4 519.669 20 1079.339 1081.746 1157.609
167
+ 793 TVMe 523.261 17 1080.522 1082.261 1147.052
168
+ 794 TVMe+I 523.261 18 1082.522 1084.471 1152.965
169
+ 795 TVMe+G4 523.261 18 1082.522 1084.471 1152.965
170
+ 815 TVMe 523.261 17 1080.522 1082.261 1147.052
171
+ 816 TVMe+I 523.261 18 1082.522 1084.471 1152.965
172
+ 817 TVMe+G4 523.261 18 1082.522 1084.471 1152.965
173
+ 837 TVM 523.261 17 1080.522 1082.261 1147.052
174
+ 838 TVM+I 523.261 18 1082.522 1084.471 1152.965
175
+ 839 TVM+G4 523.261 18 1082.522 1084.471 1152.965
176
+ 859 TVM+F 519.650 20 1079.300 1081.707 1157.570
177
+ 860 TVM+F+I 519.650 21 1081.300 1083.955 1163.483
178
+ 861 TVM+F+G4 519.650 21 1081.300 1083.955 1163.483
179
+ 881 SYM 522.627 18 1081.254 1083.203 1151.697
180
+ 882 SYM+I 522.627 19 1083.254 1085.425 1157.611
181
+ 883 SYM+G4 522.627 19 1083.254 1085.425 1157.611
182
+ 903 SYM 522.627 18 1081.254 1083.203 1151.697
183
+ 904 SYM+I 522.627 19 1083.254 1085.425 1157.611
184
+ 905 SYM+G4 522.627 19 1083.254 1085.425 1157.611
185
+ 925 GTR 522.627 18 1081.254 1083.203 1151.697
186
+ 926 GTR+I 522.627 19 1083.254 1085.425 1157.611
187
+ 927 GTR+G4 522.627 19 1083.254 1085.425 1157.611
188
+ 947 GTR+F 519.077 21 1080.154 1082.810 1162.338
189
+ 948 GTR+F+I 519.077 22 1082.154 1085.071 1168.251
190
+ 949 GTR+F+G4 519.077 22 1082.154 1085.071 1168.251
191
+ Akaike Information Criterion: F81+F
192
+ Corrected Akaike Information Criterion: F81+F
193
+ Bayesian Information Criterion: F81
194
+ Best-fit model: F81 chosen according to BIC
195
+
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+ All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz
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+ CPU time for ModelFinder: 0.115 seconds (0h:0m:0s)
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+ Wall-clock time for ModelFinder: 0.130 seconds (0h:0m:0s)
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+
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+ NOTE: 0 MB RAM (0 GB) is required!
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+ Estimate model parameters (epsilon = 0.100)
202
+ 1. Initial log-likelihood: -521.218
203
+ Optimal log-likelihood: -521.218
204
+ Rate parameters: A-C: 1.00000 A-G: 1.00000 A-T: 1.00000 C-G: 1.00000 C-T: 1.00000 G-T: 1.00000
205
+ Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
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+ Parameters optimization took 1 rounds (0.000 sec)
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+ Wrote distance file to...
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+ Computing ML distances based on estimated model parameters...
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+ Calculating distance matrix: done in 0.000120125 secs using 99.06% CPU
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+ Computing ML distances took 0.000137 sec (of wall-clock time) 0.000140 sec (of CPU time)
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+ Setting up auxiliary I and S matrices: done in 2.6339e-05 secs using 83.53% CPU
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+ Constructing RapidNJ tree: done in 4.2149e-05 secs using 85.41% CPU
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+ Computing RapidNJ tree took 0.000090 sec (of wall-clock time) 0.000078 sec (of CPU time)
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+ Log-likelihood of RapidNJ tree: -521.220
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+ --------------------------------------------------------------------
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+ | INITIALIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Generating 98 parsimony trees... 0.011 second
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+ Computing log-likelihood of 98 initial trees ... 0.011 seconds
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+ Current best score: -521.218
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+
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+ Do NNI search on 20 best initial trees
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+ Optimizing NNI: done in 0.000176579 secs using 87.78% CPU
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+ Estimate model parameters (epsilon = 0.100)
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+ BETTER TREE FOUND at iteration 1: -521.218
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+ Optimizing NNI: done in 0.000170098 secs using 87.6% CPU
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+ Optimizing NNI: done in 0.000167813 secs using 98.92% CPU
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+ Optimizing NNI: done in 0.000166631 secs using 99.02% CPU
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+ Optimizing NNI: done in 0.000167212 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000232724 secs using 99.26% CPU
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+ Optimizing NNI: done in 0.000207367 secs using 99.34% CPU
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+ Optimizing NNI: done in 0.000205183 secs using 99.42% CPU
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+ Optimizing NNI: done in 0.000206876 secs using 99.09% CPU
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+ Optimizing NNI: done in 0.000213028 secs using 99.52% CPU
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+ Iteration 10 / LogL: -521.218 / Time: 0h:0m:0s
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+ Optimizing NNI: done in 0.000216985 secs using 99.55% CPU
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+ Optimizing NNI: done in 0.000209201 secs using 99.43% CPU
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+ Optimizing NNI: done in 0.000229157 secs using 99.5% CPU
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+ Optimizing NNI: done in 0.000203209 secs using 99.41% CPU
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+ Optimizing NNI: done in 0.000207107 secs using 99.47% CPU
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+ Optimizing NNI: done in 0.000224719 secs using 99.68% CPU
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+ Optimizing NNI: done in 0.000207397 secs using 99.33% CPU
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+ Optimizing NNI: done in 0.000207266 secs using 99.87% CPU
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+ Optimizing NNI: done in 0.000211395 secs using 98.39% CPU
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+ Optimizing NNI: done in 0.000209511 secs using 99.76% CPU
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+ Iteration 20 / LogL: -521.218 / Time: 0h:0m:0s
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+ Finish initializing candidate tree set (20)
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+ Current best tree score: -521.218 / CPU time: 0.028
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+ Number of iterations: 20
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+ --------------------------------------------------------------------
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+ | OPTIMIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Optimizing NNI: done in 0.000168214 secs using 98.68% CPU
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+ Optimizing NNI: done in 0.000213499 secs using 99.3% CPU
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+ Optimizing NNI: done in 0.000159698 secs using 99.56% CPU
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+ Optimizing NNI: done in 0.000161611 secs using 94.05% CPU
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+ Optimizing NNI: done in 0.000206766 secs
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+ Optimizing NNI: done in 0.00019866 secs
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+ Optimizing NNI: done in 0.000157874 secs using 87.41% CPU
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+ Optimizing NNI: done in 0.000156201 secs using 87.71% CPU
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+ Optimizing NNI: done in 0.000161001 secs using 87.58% CPU
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+ Optimizing NNI: done in 0.000204602 secs using 99.22% CPU
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+ Iteration 30 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000162954 secs using 99.41% CPU
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+ Optimizing NNI: done in 0.00023065 secs using 99.72% CPU
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+ Optimizing NNI: done in 0.000158155 secs using 99.27% CPU
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+ Optimizing NNI: done in 0.000166801 secs using 99.52% CPU
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+ Optimizing NNI: done in 0.000201646 secs using 99.18% CPU
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+ Optimizing NNI: done in 0.000162884 secs using 98.84% CPU
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+ Optimizing NNI: done in 0.000215662 secs
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+ Optimizing NNI: done in 0.00016091 secs
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+ Optimizing NNI: done in 0.000159578 secs
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+ Optimizing NNI: done in 0.000205554 secs using 99.73% CPU
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+ Iteration 40 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000165779 secs using 94.7% CPU
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+ Optimizing NNI: done in 0.000173223 secs using 99.29% CPU
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+ Optimizing NNI: done in 0.000173473 secs using 99.15% CPU
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+ Optimizing NNI: done in 0.00019865 secs using 99.17% CPU
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+ Optimizing NNI: done in 0.00016043 secs using 99.11% CPU
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+ Optimizing NNI: done in 0.00016045 secs using 99.1% CPU
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+ Optimizing NNI: done in 0.000158255 secs using 90.36% CPU
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+ Optimizing NNI: done in 0.000158806 secs using 98.86% CPU
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+ Optimizing NNI: done in 0.000162052 secs using 99.35% CPU
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+ Optimizing NNI: done in 0.000224349 secs
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+ Iteration 50 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000158576 secs
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+ Optimizing NNI: done in 0.000208389 secs using 1.919% CPU
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+ Optimizing NNI: done in 0.000201456 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000172602 secs using 99.07% CPU
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+ Optimizing NNI: done in 0.000215653 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000202558 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000161871 secs using 99.46% CPU
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+ Optimizing NNI: done in 0.000160139 secs using 99.91% CPU
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+ Optimizing NNI: done in 0.000159538 secs using 99.04% CPU
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+ Optimizing NNI: done in 0.000195735 secs using 99.11% CPU
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+ Iteration 60 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000199342 secs using 99.33% CPU
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+ Optimizing NNI: done in 0.000159248 secs using 99.22% CPU
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+ Optimizing NNI: done in 0.000162874 secs using 98.85% CPU
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+ Optimizing NNI: done in 0.00016084 secs using 99.48% CPU
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+ Optimizing NNI: done in 0.000160851 secs using 95.12% CPU
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+ Optimizing NNI: done in 0.000220902 secs using 99.59% CPU
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+ Optimizing NNI: done in 0.000159017 secs using 99.36% CPU
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+ Optimizing NNI: done in 0.000216203 secs using 99.44% CPU
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+ Optimizing NNI: done in 0.000159418 secs using 99.11% CPU
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+ Optimizing NNI: done in 0.000161371 secs using 99.15% CPU
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+ Iteration 70 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000216534 secs using 99.29% CPU
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+ Optimizing NNI: done in 0.000156823 secs using 98.84% CPU
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+ Optimizing NNI: done in 0.000178843 secs using 99.53% CPU
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+ Optimizing NNI: done in 0.000159228 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000219189 secs using 99.46% CPU
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+ Optimizing NNI: done in 0.00020399 secs using 99.51% CPU
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+ Optimizing NNI: done in 0.000158136 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000184735 secs using 99.06% CPU
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+ Optimizing NNI: done in 0.00016096 secs using 99.4% CPU
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+ Optimizing NNI: done in 0.000201536 secs using 99.73% CPU
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+ Iteration 80 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000161391 secs using 99.14% CPU
320
+ Optimizing NNI: done in 0.000204912 secs using 99.55% CPU
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+ Optimizing NNI: done in 0.000215503 secs using 98.84% CPU
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+ Optimizing NNI: done in 0.000220651 secs using 99.25% CPU
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+ Optimizing NNI: done in 0.000157144 secs using 98.64% CPU
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+ Optimizing NNI: done in 0.000200384 secs using 99.31% CPU
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+ Optimizing NNI: done in 0.000157945 secs using 99.4% CPU
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+ Optimizing NNI: done in 0.000183652 secs using 99.64% CPU
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+ Optimizing NNI: done in 0.000158606 secs using 98.99% CPU
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+ Optimizing NNI: done in 0.000159457 secs using 99.71% CPU
329
+ Iteration 90 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000205012 secs using 99.51% CPU
331
+ Optimizing NNI: done in 0.000208129 secs using 99.46% CPU
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+ Optimizing NNI: done in 0.000157514 secs using 90.79% CPU
333
+ Optimizing NNI: done in 0.000163976 secs
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+ Optimizing NNI: done in 0.000177841 secs
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+ Optimizing NNI: done in 0.000174806 secs using 99.54% CPU
336
+ Optimizing NNI: done in 0.000206035 secs using 99.5% CPU
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+ Optimizing NNI: done in 0.000157975 secs using 99.38% CPU
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+ Optimizing NNI: done in 0.000208429 secs using 99.31% CPU
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+ Optimizing NNI: done in 0.00019822 secs using 99.38% CPU
340
+ Iteration 100 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000180217 secs using 98.77% CPU
342
+ Optimizing NNI: done in 0.000156411 secs using 99.1% CPU
343
+ TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
344
+
345
+ --------------------------------------------------------------------
346
+ | FINALIZING TREE SEARCH |
347
+ --------------------------------------------------------------------
348
+ Performs final model parameters optimization
349
+ Estimate model parameters (epsilon = 0.010)
350
+ 1. Initial log-likelihood: -521.218
351
+ Optimal log-likelihood: -521.218
352
+ Rate parameters: A-C: 1.00000 A-G: 1.00000 A-T: 1.00000 C-G: 1.00000 C-T: 1.00000 G-T: 1.00000
353
+ Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
354
+ Parameters optimization took 1 rounds (0.000 sec)
355
+ BEST SCORE FOUND : -521.218
356
+ Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
357
+ Total tree length: 0.005
358
+
359
+ Total number of iterations: 102
360
+ CPU time used for tree search: 0.063 sec (0h:0m:0s)
361
+ Wall-clock time used for tree search: 0.060 sec (0h:0m:0s)
362
+ Total CPU time used: 0.191 sec (0h:0m:0s)
363
+ Total wall-clock time used: 0.205 sec (0h:0m:0s)
364
+
365
+ Analysis results written to:
366
+ IQ-TREE report: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree
367
+ Maximum-likelihood tree: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile
368
+ Likelihood distances: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist
369
+ Ancestral state: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
370
+ Screen log file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.log
371
+
372
+ Date and Time: Mon Aug 18 15:31:52 2025