partis-bcr 1.0.8__py3-none-any.whl → 1.0.8.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-1.0.8.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.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 +5 -5
  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 +8 -8
  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 +85 -101
  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 +394 -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 +393 -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 +414 -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 +413 -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 +376 -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 +375 -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 +453 -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-1.0.8.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  145. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  146. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  147. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  148. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/gctree-run.py +0 -0
  149. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  150. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/parse-output.py +0 -0
  151. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/partis-test.py +0 -0
  152. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/split-loci.py +0 -0
  153. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/WHEEL +0 -0
  154. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/entry_points.txt +0 -0
  155. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/licenses/COPYING +0 -0
  156. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/top_level.txt +0 -0
@@ -1,5 +1,5 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
3
  Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
@@ -9,15 +9,15 @@ Ignored unknown character X (seen 32 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
11
  Total branch-length 0.172 after 0.01 sec
12
- ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.01
12
+ ML-NNI round 1: LogLk = -1718.413 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
14
- GTR rates(ac ag at cg ct gt) 1.2927 1.2254 1.4006 0.7465 1.0327 1.0000
14
+ GTR rates(ac ag at cg ct gt) 1.2877 1.2172 1.4016 0.7474 1.0325 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.666 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.04
19
+ ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.05 (final)
22
- Optimize all lengths: LogLk = -1660.925 Time 0.05
23
- Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5
21
+ ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
22
+ Optimize all lengths: LogLk = -1661.140 Time 0.08
23
+ Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
@@ -1 +1 @@
1
- (c0fcfe005f_contig_igh+igk:0.004295104,d1ee7f9ce6_contig_igh+igk:0.001427179,(665985d2d1_contig_igh+igk:0.004608641,(c2cc9da0c3_contig_igh+igk:0.029272677,(XnaiveX:0.002631431,(6cf028b770_contig_igh+igk:0.019426490,(4f03967793_contig_igh+igk:0.018933964,6577576bb8_contig_igh+igk:0.011347766)0.805:0.002739671)0.994:0.013039128)0.804:0.003357001)0.973:0.010298361)0.732:0.001145451);
1
+ (c0fcfe005f_contig_igh+igk:0.00430,d1ee7f9ce6_contig_igh+igk:0.00142,(665985d2d1_contig_igh+igk:0.00459,(c2cc9da0c3_contig_igh+igk:0.02928,(XnaiveX:0.00263,(6cf028b770_contig_igh+igk:0.01943,(4f03967793_contig_igh+igk:0.01894,6577576bb8_contig_igh+igk:0.01135)0.827:0.00273)0.993:0.01304)0.832:0.00336)0.974:0.01031)0.800:0.00114);
@@ -1,5 +1,5 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
3
  Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
@@ -11,13 +11,13 @@ Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
11
  Total branch-length 0.116 after 0.01 sec
12
12
  ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
14
- GTR rates(ac ag at cg ct gt) 0.7182 0.4393 0.9759 0.8068 0.8119 1.0000
14
+ GTR rates(ac ag at cg ct gt) 0.7186 0.4400 0.9760 0.8085 0.8107 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.652 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04
19
+ ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
21
  ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.06 (final)
22
- Optimize all lengths: LogLk = -1478.012 Time 0.06
22
+ Optimize all lengths: LogLk = -1478.012 Time 0.07
23
23
  Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
@@ -1 +1 @@
1
- (453132f3ab_contig_igh+igk:0.019408269,f3509e0ef3_contig_igh+igk:0.013413701,(XnaiveX:0.000000005,(f094dfd68a_contig_igh+igk:0.013255979,(3a07b6f0a9_contig_igh+igk:0.007344406,7334912e1e_contig_igh+igk:0.013294093)0.736:0.001451666)0.885:0.005862794)0.385:0.002794533);
1
+ (XnaiveX:0.00055,(f094dfd68a_contig_igh+igk:0.01324,(3a07b6f0a9_contig_igh+igk:0.00734,7334912e1e_contig_igh+igk:0.01329)0.742:0.00148)0.878:0.00576,(453132f3ab_contig_igh+igk:0.01929,f3509e0ef3_contig_igh+igk:0.01351)0.353:0.00274);
@@ -1,5 +1,5 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
3
  Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
@@ -9,15 +9,15 @@ Ignored unknown character X (seen 132 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 10 rounds ME-NNIs, 2 rounds ME-SPRs, 5 rounds ML-NNIs
11
11
  Total branch-length 0.072 after 0.00 sec
12
- ML-NNI round 1: LogLk = -1300.628 NNIs 1 max delta 1.15 Time 0.01
12
+ ML-NNI round 1: LogLk = -1300.914 NNIs 1 max delta 0.86 Time 0.01
13
13
  GTR Frequencies: 0.2567 0.2538 0.2729 0.2166
14
- GTR rates(ac ag at cg ct gt) 0.8073 1.2192 0.7088 1.1279 0.4727 1.0000
14
+ GTR rates(ac ag at cg ct gt) 0.8119 1.2276 0.7151 1.1364 0.4746 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.641 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03
19
+ ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.05
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
22
- Optimize all lengths: LogLk = -1274.638 Time 0.04
23
- Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3
21
+ ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.06 (final)
22
+ Optimize all lengths: LogLk = -1274.921 Time 0.06
23
+ Total time: 0.07 seconds Unique: 6/6 Bad splits: 0/3
@@ -1 +1 @@
1
- (c0fcfe005f-igh:0.008166070,d1ee7f9ce6-igh:0.002713639,(665985d2d1-igh:0.010894197,(c2cc9da0c3-igh:0.058751821,(XnaiveX:0.005553003,(6cf028b770-igh:0.037840124,(4f03967793-igh:0.033801661,6577576bb8-igh:0.021886898)0.768:0.004537196)0.994:0.025260536)0.732:0.003647169)0.965:0.021970589)0.870:0.000000005);
1
+ (c0fcfe005f-igh:0.00816,d1ee7f9ce6-igh:0.00271,(665985d2d1-igh:0.01049,(c2cc9da0c3-igh:0.05841,(XnaiveX:0.00550,(6cf028b770-igh:0.03785,(4f03967793-igh:0.03380,6577576bb8-igh:0.02188)0.794:0.00453)0.995:0.02527)0.741:0.00404)0.967:0.02158)0.870:0.00054);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -11,13 +11,13 @@ Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
11
  Total branch-length 0.217 after 0.00 sec
12
12
  ML-NNI round 1: LogLk = -1009.286 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2219 0.2395 0.3219 0.2167
14
- GTR rates(ac ag at cg ct gt) 0.9477 0.4171 1.2893 0.8129 0.9896 1.0000
14
+ GTR rates(ac ag at cg ct gt) 0.9485 0.4177 1.2903 0.8145 0.9882 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.678 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.03
19
+ ML-NNI round 2: LogLk = -968.466 NNIs 0 max delta 0.00 Time 0.03
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.03 (final)
22
- Optimize all lengths: LogLk = -968.417 Time 0.03
23
- Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
21
+ ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.04 (final)
22
+ Optimize all lengths: LogLk = -968.442 Time 0.04
23
+ Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5
@@ -1 +1 @@
1
- (f094dfd68a-igh:0.022874542,(3a07b6f0a9-igh:0.014363564,7334912e1e-igh:0.026057703)0.752:0.002901869,(453132f3ab-igh:0.037592312,(XnaiveX:0.000000005,(f3509e0ef3-igh:0.008547223,b997fa9304-igh:0.000000005)0.999:0.025882769)0.660:0.003658265)0.676:0.008038400);
1
+ (XnaiveX:0.00053,(f3509e0ef3-igh:0.00839,b997fa9304-igh:0.00053)0.996:0.02555,(453132f3ab-igh:0.03734,(f094dfd68a-igh:0.02262,(3a07b6f0a9-igh:0.01440,7334912e1e-igh:0.02607)0.756:0.00314)0.692:0.00806)0.619:0.00365);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -9,15 +9,15 @@ Ignored unknown character X (seen 21 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 11 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
11
11
  Total branch-length 0.133 after 0.00 sec
12
- ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.01
12
+ ML-NNI round 1: LogLk = -824.239 NNIs 0 max delta 0.00 Time 0.01
13
13
  GTR Frequencies: 0.2278 0.2456 0.3207 0.2059
14
- GTR rates(ac ag at cg ct gt) 1.1354 1.3036 0.8502 1.1285 0.5919 1.0000
14
+ GTR rates(ac ag at cg ct gt) 1.1229 1.2867 0.8408 1.1118 0.5795 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.658 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -794.353 NNIs 0 max delta 0.00 Time 0.02
19
+ ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.03
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.03 (final)
22
- Optimize all lengths: LogLk = -794.321 Time 0.03
23
- Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4
21
+ ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.04 (final)
22
+ Optimize all lengths: LogLk = -794.513 Time 0.04
23
+ Total time: 0.05 seconds Unique: 7/7 Bad splits: 0/4
@@ -1 +1 @@
1
- [{"unique_ids": ["4f03967793-igh", "6577576bb8-igh", "665985d2d1-igh", "6cf028b770-igh", "c0fcfe005f-igh", "c2cc9da0c3-igh", "d1ee7f9ce6-igh"], "lb": {"tree": "[&R] (((6cf028b770-igh:0.037840124,(4f03967793-igh:0.033801661,6577576bb8-igh:0.021886898)bop:0.004537196)dkn:0.025260536,(c2cc9da0c3-igh:0.058751821,(665985d2d1-igh:0.010894197,(c0fcfe005f-igh:0.00816607,d1ee7f9ce6-igh:0.002713639)bnw:5e-09)psx:0.021970589)ikm:0.003647169)amz:0.005553003)XnaiveX;\n", "cons-dist-aa": {"4f03967793-igh": -12, "6577576bb8-igh": -13, "665985d2d1-igh": -6, "6cf028b770-igh": -14, "c0fcfe005f-igh": -6, "c2cc9da0c3-igh": -17, "d1ee7f9ce6-igh": -6}, "lbi": {"6cf028b770-igh": 9.544073997308833e-08, "4f03967793-igh": 4.5174042008864267e-07, "6577576bb8-igh": 4.4376977150953884e-05, "bop": 0.3751553446495842, "dkn": 0.3751974008849098, "c2cc9da0c3-igh": 3.227881450845884e-11, "665985d2d1-igh": 0.0041778869292159225, "c0fcfe005f-igh": 0.012151396154447242, "d1ee7f9ce6-igh": 0.11788609642688522, "bnw": 0.4469674813093698, "psx": 0.4469676075580396, "ikm": 0.38754606279855686, "amz": 0.38751060755795147, "XnaiveX": 0.19789095002428203}, "lbr": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.7028955585745085, "dkn": 2.1741264865017382, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 0.8085450845899526, "psx": 2.5893409741031848, "ikm": 1.6059365687200922, "amz": 2.245738221970469, "XnaiveX": 0.0}, "lbf": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.9901500384351718, "dkn": 2.1638193256710423, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 1.5973794385579372, "psx": 2.5775541855965582, "ikm": 1.990705744401615, "amz": 2.2349132532526115, "XnaiveX": 1.1413508491731865}, "aa-tree": "[&R] (((6cf028b770-igh:0.037840124,(4f03967793-igh:0.033801661,6577576bb8-igh:0.021886898)bop:0.004537196)dkn:0.025260536,(c2cc9da0c3-igh:0.058751821,(665985d2d1-igh:0.010894197,(c0fcfe005f-igh:0.00816607,d1ee7f9ce6-igh:0.002713639)bnw:5e-09)psx:0.021970589)ikm:0.003647169)amz:0.005553003)XnaiveX;\n", "aa-lbi": {"6cf028b770-igh": 9.544073997308833e-08, "4f03967793-igh": 4.5174042008864267e-07, "6577576bb8-igh": 4.4376977150953884e-05, "bop": 0.3751553446495842, "dkn": 0.3751974008849098, "c2cc9da0c3-igh": 3.227881450845884e-11, "665985d2d1-igh": 0.0041778869292159225, "c0fcfe005f-igh": 0.012151396154447242, "d1ee7f9ce6-igh": 0.11788609642688522, "bnw": 0.4469674813093698, "psx": 0.4469676075580396, "ikm": 0.38754606279855686, "amz": 0.38751060755795147, "XnaiveX": 0.19789095002428203}, "aa-lbr": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.7028955585745085, "dkn": 2.1741264865017382, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 0.8085450845899526, "psx": 2.5893409741031848, "ikm": 1.6059365687200922, "amz": 2.245738221970469, "XnaiveX": 0.0}, "aa-lbf": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.9901500384351718, "dkn": 2.1638193256710423, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 1.5973794385579372, "psx": 2.5775541855965582, "ikm": 1.990705744401615, "amz": 2.2349132532526115, "XnaiveX": 1.1413508491731865}}}, {"unique_ids": ["3a07b6f0a9-igh", "453132f3ab-igh", "7334912e1e-igh", "f094dfd68a-igh", "f3509e0ef3-igh", "b997fa9304-igh"], "lb": {"tree": "[&R] (((f3509e0ef3-igh:0.008547223)b997fa9304-igh:0.025882769,(453132f3ab-igh:0.037592312,(f094dfd68a-igh:0.022874542,(3a07b6f0a9-igh:0.014363564,7334912e1e-igh:0.026057703)flx:0.002901869)eov:0.0080384)npq:0.003658265)ily:5e-09)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9-igh": -6, "453132f3ab-igh": -10, "7334912e1e-igh": -11, "f094dfd68a-igh": -7, "f3509e0ef3-igh": -9, "b997fa9304-igh": -8}, "lbi": {"f3509e0ef3-igh": 5.798371440346434e-07, "b997fa9304-igh": 0.16510948286548932, "453132f3ab-igh": 1.8521095975870042e-07, "f094dfd68a-igh": 4.748968936888683e-05, "3a07b6f0a9-igh": 0.0011034327206784398, "7334912e1e-igh": 1.4024987747500558e-05, "flx": 0.40555430832563155, "eov": 0.4132042841861135, "npq": 0.3998729820663575, "ily": 0.39131901197625396, "XnaiveX": 0.3913186032878036}, "lbr": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 0.9586721553286679, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "flx": 1.4671574213406489, "eov": 2.199268273638714, "npq": 1.646112976271383, "ily": 2.2726359094624318, "XnaiveX": 0.0}, "lbf": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 1.4544390913484173, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "flx": 3.0267911096873847, "eov": 3.545217334883834, "npq": 3.13517715501326, "ily": 3.4474670332268644, "XnaiveX": 3.4474634329378278}, "aa-tree": "[&R] (((f3509e0ef3-igh:0.016260162601626018)b997fa9304-igh:0.025882769,(453132f3ab-igh:0.037592312,(f094dfd68a-igh:0.022874542,(3a07b6f0a9-igh:0.014363564,7334912e1e-igh:0.026057703)flx:0.002901869)eov:0.0080384)npq:0.003658265)ily:5e-09)XnaiveX;\n", "aa-lbi": {"f3509e0ef3-igh": 3.264921480756916e-08, "b997fa9304-igh": 0.17181264242960936, "453132f3ab-igh": 1.8521104911865375e-07, "f094dfd68a-igh": 4.748969044842081e-05, "3a07b6f0a9-igh": 0.0011034327294254366, "7334912e1e-igh": 1.4024987859061223e-05, "flx": 0.40555431018189114, "eov": 0.41320428966532197, "npq": 0.39987309193482146, "ily": 0.39131944198980106, "XnaiveX": 0.3913190333005487}, "aa-lbr": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 0.9975959013096771, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "flx": 1.4671574097109037, "eov": 2.1992682077832413, "npq": 1.6461121397240472, "ily": 2.2726384067719807, "XnaiveX": 0.0}, "aa-lbf": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 1.4502001432526774, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "flx": 2.900215785334542, "eov": 3.3969622958664276, "npq": 3.0040693081488588, "ily": 3.3033033776359204, "XnaiveX": 3.3032999278981596}}}]
1
+ [{"unique_ids": ["4f03967793-igh", "6577576bb8-igh", "665985d2d1-igh", "6cf028b770-igh", "c0fcfe005f-igh", "c2cc9da0c3-igh", "d1ee7f9ce6-igh"], "lb": {"tree": "[&R] (((6cf028b770-igh:0.03785,(4f03967793-igh:0.0338,6577576bb8-igh:0.02188)bop:0.00453)dkn:0.02527,(c2cc9da0c3-igh:0.05841,(665985d2d1-igh:0.01049,(c0fcfe005f-igh:0.00816,d1ee7f9ce6-igh:0.00271)bnw:0.00054)psx:0.02158)ikm:0.00404)amz:0.0055)XnaiveX;\n", "cons-dist-aa": {"4f03967793-igh": -12, "6577576bb8-igh": -13, "665985d2d1-igh": -6, "6cf028b770-igh": -14, "c0fcfe005f-igh": -6, "c2cc9da0c3-igh": -17, "d1ee7f9ce6-igh": -6}, "lbi": {"6cf028b770-igh": 9.511748955499152e-08, "4f03967793-igh": 4.5221522414241074e-07, "6577576bb8-igh": 4.4513297687752614e-05, "bop": 0.37523863402438323, "dkn": 0.37528041821359037, "c2cc9da0c3-igh": 3.58010208213129e-11, "665985d2d1-igh": 0.004534615721231545, "c0fcfe005f-igh": 0.0107820150912103, "d1ee7f9ce6-igh": 0.10668041266848334, "bnw": 0.4146035123061748, "psx": 0.4268524604937113, "ikm": 0.381602463664958, "amz": 0.3815618069341187, "XnaiveX": 0.19769760046034998}, "lbr": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.7021945713687432, "dkn": 2.1746149313912713, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 0.8922803171084732, "psx": 2.472680142236951, "ikm": 1.6516658645723779, "amz": 2.211263604986764, "XnaiveX": 0.0}, "lbf": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.9921562005747742, "dkn": 2.1664827734658427, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 1.5983983372798543, "psx": 2.463990996610526, "ikm": 1.9927389233040789, "amz": 2.202823521908247, "XnaiveX": 1.1413854781581723}, "aa-tree": "[&R] (((6cf028b770-igh:0.03785,(4f03967793-igh:0.0338,6577576bb8-igh:0.02188)bop:0.00453)dkn:0.02527,(c2cc9da0c3-igh:0.05841,(665985d2d1-igh:0.01049,(c0fcfe005f-igh:0.00816,d1ee7f9ce6-igh:0.00271)bnw:0.00054)psx:0.02158)ikm:0.00404)amz:0.0055)XnaiveX;\n", "aa-lbi": {"6cf028b770-igh": 9.511748955499152e-08, "4f03967793-igh": 4.5221522414241074e-07, "6577576bb8-igh": 4.4513297687752614e-05, "bop": 0.37523863402438323, "dkn": 0.37528041821359037, "c2cc9da0c3-igh": 3.58010208213129e-11, "665985d2d1-igh": 0.004534615721231545, "c0fcfe005f-igh": 0.0107820150912103, "d1ee7f9ce6-igh": 0.10668041266848334, "bnw": 0.4146035123061748, "psx": 0.4268524604937113, "ikm": 0.381602463664958, "amz": 0.3815618069341187, "XnaiveX": 0.19769760046034998}, "aa-lbr": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.7021945713687432, "dkn": 2.1746149313912713, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 0.8922803171084732, "psx": 2.472680142236951, "ikm": 1.6516658645723779, "amz": 2.211263604986764, "XnaiveX": 0.0}, "aa-lbf": {"6cf028b770-igh": 0.0, "4f03967793-igh": 0.0, "6577576bb8-igh": 0.0, "bop": 1.9921562005747742, "dkn": 2.1664827734658427, "c2cc9da0c3-igh": 0.0, "665985d2d1-igh": 0.0, "c0fcfe005f-igh": 0.0, "d1ee7f9ce6-igh": 0.0, "bnw": 1.5983983372798543, "psx": 2.463990996610526, "ikm": 1.9927389233040789, "amz": 2.202823521908247, "XnaiveX": 1.1413854781581723}}}, {"unique_ids": ["3a07b6f0a9-igh", "453132f3ab-igh", "7334912e1e-igh", "f094dfd68a-igh", "f3509e0ef3-igh", "b997fa9304-igh"], "lb": {"tree": "[&R] (((f3509e0ef3-igh:0.00839)b997fa9304-igh:0.02555,(453132f3ab-igh:0.03734,(f094dfd68a-igh:0.02262,(3a07b6f0a9-igh:0.0144,7334912e1e-igh:0.02607)dst:0.00314)ily:0.00806)npq:0.00365)eov:0.00053)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9-igh": -6, "453132f3ab-igh": -10, "7334912e1e-igh": -11, "f094dfd68a-igh": -7, "f3509e0ef3-igh": -9, "b997fa9304-igh": -8}, "lbi": {"f3509e0ef3-igh": 6.963055994869483e-07, "b997fa9304-igh": 0.16468233171669636, "453132f3ab-igh": 2.0330935138632158e-07, "f094dfd68a-igh": 5.11339483547137e-05, "3a07b6f0a9-igh": 0.001063930853243648, "7334912e1e-igh": 1.3644783268180135e-05, "dst": 0.40027178933291196, "ily": 0.40818992544654376, "npq": 0.3996728945144763, "eov": 0.39137904461038847, "XnaiveX": 0.3520608156101012}, "lbr": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 0.956170633277273, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "dst": 1.501137194470207, "ily": 2.1732480084290104, "npq": 1.6435223941772872, "eov": 2.272957895053925, "XnaiveX": 0.0}, "lbf": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 1.4520288750560206, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "dst": 3.0297450552572824, "ily": 3.505050491923972, "npq": 3.1351712477773033, "eov": 3.4512380478767137, "XnaiveX": 3.104542163683332}, "aa-tree": "[&R] (((f3509e0ef3-igh:0.016260162601626018)b997fa9304-igh:0.02555,(453132f3ab-igh:0.03734,(f094dfd68a-igh:0.02262,(3a07b6f0a9-igh:0.0144,7334912e1e-igh:0.02607)dst:0.00314)ily:0.00806)npq:0.00365)eov:0.00053)XnaiveX;\n", "aa-lbi": {"f3509e0ef3-igh": 3.697411203508079e-08, "b997fa9304-igh": 0.171814504471641, "453132f3ab-igh": 2.033094700501e-07, "f094dfd68a-igh": 5.113394977753697e-05, "3a07b6f0a9-igh": 0.0010639308627075302, "7334912e1e-igh": 1.3644783389963712e-05, "dst": 0.40027179136878854, "ily": 0.40818993201413073, "npq": 0.3996730272722848, "eov": 0.39137956261102974, "XnaiveX": 0.35206124069396677}, "aa-lbr": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 0.9975851149595742, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "dst": 1.5011371811178982, "ily": 2.17324793039205, "npq": 1.643521385574832, "eov": 2.272960903325226, "XnaiveX": 0.0}, "aa-lbf": {"f3509e0ef3-igh": 0.0, "b997fa9304-igh": 1.4502742849375192, "453132f3ab-igh": 0.0, "f094dfd68a-igh": 0.0, "3a07b6f0a9-igh": 0.0, "7334912e1e-igh": 0.0, "dst": 2.9004569228271255, "ily": 3.355479678568599, "npq": 3.0013842696385002, "eov": 3.3039679425916275, "XnaiveX": 2.9720658070832493}}}]
@@ -1 +1 @@
1
- ((XnaiveX:0.0,3a07b6f0a9-igk:0.0,7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0):0.000000005,453132f3ab-igk:0.003169296,f094dfd68a-igk:0.003168437);
1
+ ((XnaiveX:0.0,3a07b6f0a9-igk:0.0,7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0):0.00055,453132f3ab-igk:0.00317,f094dfd68a-igk:0.00317);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -9,15 +9,15 @@ Ignored unknown character X (seen 45 times)
9
9
  Initial topology in 0.00 seconds
10
10
  Refining topology: 6 rounds ME-NNIs, 2 rounds ME-SPRs, 3 rounds ML-NNIs
11
11
  Total branch-length 0.006 after 0.00 sec
12
- ML-NNI round 1: LogLk = -462.130 NNIs 0 max delta 0.00 Time 0.00
12
+ ML-NNI round 1: LogLk = -462.305 NNIs 0 max delta 0.00 Time 0.00
13
13
  GTR Frequencies: 0.2897 0.2649 0.2175 0.2278
14
- GTR rates(ac ag at cg ct gt) 1.0000 1.0000 74.6330 1.0000 85.7951 1.0000
14
+ GTR rates(ac ag at cg ct gt) 1.0000 1.0003 75.0571 1.0010 86.3332 1.0000
15
15
  Switched to using 20 rate categories (CAT approximation)
16
16
  Rate categories were divided by 0.624 so that average rate = 1.0
17
17
  CAT-based log-likelihoods may not be comparable across runs
18
18
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
19
- ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00
19
+ ML-NNI round 2: LogLk = -457.317 NNIs 0 max delta 0.00 Time 0.00
20
20
  Turning off heuristics for final round of ML NNIs (converged)
21
- ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00 (final)
22
- Optimize all lengths: LogLk = -457.145 Time 0.00
21
+ ML-NNI round 3: LogLk = -457.317 NNIs 0 max delta 0.00 Time 0.00 (final)
22
+ Optimize all lengths: LogLk = -457.317 Time 0.00
23
23
  Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0
@@ -1 +1 @@
1
- ((XnaiveX:0.0,6577576bb8-igk:0.0,665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0):0.001578281,4f03967793-igk:0.001578281);
1
+ ((XnaiveX:0.0,6577576bb8-igk:0.0,665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0):0.00158,4f03967793-igk:0.00158);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -12,7 +12,7 @@ Total branch-length 0.003 after 0.00 sec
12
12
  ML-NNI round 1: LogLk = -458.427 NNIs 0 max delta 0.00 Time 0.00
13
13
  Turning off heuristics for final round of ML NNIs
14
14
  GTR Frequencies: 0.2813 0.2584 0.2294 0.2309
15
- GTR rates(ac ag at cg ct gt) 1.0000 398.8171 1.0000 1.0000 1.0000 1.0000
15
+ GTR rates(ac ag at cg ct gt) 0.9987 398.2894 1.0043 1.0033 0.9993 1.0000
16
16
  Switched to using 20 rate categories (CAT approximation)
17
17
  Rate categories were divided by 0.624 so that average rate = 1.0
18
18
  CAT-based log-likelihoods may not be comparable across runs
@@ -1 +1 @@
1
- [{"unique_ids": ["3a07b6f0a9-igk", "453132f3ab-igk", "7334912e1e-igk", "f094dfd68a-igk", "f3509e0ef3-igk", "4219142930-igk", "9c1dc5e656-igk"], "lb": {"tree": "[&R] ((7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0,(453132f3ab-igk:0.003169296,f094dfd68a-igk:0.003168437)bnw:5e-09)3a07b6f0a9-igk:0.0)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9-igk": 0, "453132f3ab-igk": 0, "7334912e1e-igk": 0, "f094dfd68a-igk": 0, "f3509e0ef3-igk": 0, "4219142930-igk": 0, "9c1dc5e656-igk": 0}, "lbi": {"7334912e1e-igk": 0.22798933249280592, "f3509e0ef3-igk": 0.22798933249280592, "4219142930-igk": 0.22798933249280592, "9c1dc5e656-igk": 0.22798933249280592, "453132f3ab-igk": 0.03917304571780813, "f094dfd68a-igk": 0.03919032922517414, "bnw": 0.22798942398669525, "3a07b6f0a9-igk": 0.22798933249280592, "XnaiveX": 0.22798933249280592}, "lbr": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 1.3126059074466612, "3a07b6f0a9-igk": 1.3126053808830704, "XnaiveX": 0.0}, "lbf": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 10.815474878813825, "3a07b6f0a9-igk": 10.815470539262009, "XnaiveX": 10.815470539262009}, "aa-tree": "[&R] ((7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0,(453132f3ab-igk:0.003169296,f094dfd68a-igk:0.003168437)bnw:5e-09)3a07b6f0a9-igk:0.0)XnaiveX;\n", "aa-lbi": {"7334912e1e-igk": 0.22798933249280592, "f3509e0ef3-igk": 0.22798933249280592, "4219142930-igk": 0.22798933249280592, "9c1dc5e656-igk": 0.22798933249280592, "453132f3ab-igk": 0.03917304571780813, "f094dfd68a-igk": 0.03919032922517414, "bnw": 0.22798942398669525, "3a07b6f0a9-igk": 0.22798933249280592, "XnaiveX": 0.22798933249280592}, "aa-lbr": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 1.3126059074466612, "3a07b6f0a9-igk": 1.3126053808830704, "XnaiveX": 0.0}, "aa-lbf": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 10.815474878813825, "3a07b6f0a9-igk": 10.815470539262009, "XnaiveX": 10.815470539262009}}}, {"unique_ids": ["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "d1ee7f9ce6-igk"], "lb": {"tree": "[&R] ((665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0,(4f03967793-igk:0.001578281)eov:0.001578281)6577576bb8-igk:0.0)XnaiveX;\n", "cons-dist-aa": {"4f03967793-igk": -1, "6577576bb8-igk": 0, "665985d2d1-igk": 0, "6cf028b770-igk": 0, "c0fcfe005f-igk": 0, "c2cc9da0c3-igk": 0, "d1ee7f9ce6-igk": 0}, "lbi": {"665985d2d1-igk": 0.11412635831690991, "6cf028b770-igk": 0.11412635831690991, "c0fcfe005f-igk": 0.11412635831690991, "c2cc9da0c3-igk": 0.11412635831690991, "d1ee7f9ce6-igk": 0.11412635831690991, "4f03967793-igk": -2.6920443294540715e-06, "eov": 0.07201692190755538, "6577576bb8-igk": 0.11412635831690991, "XnaiveX": 0.11412635831690991}, "lbr": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 0.4152871425303524, "6577576bb8-igk": 0.6581278609437264, "XnaiveX": 0.0}, "lbf": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 3.7502704959547453, "6577576bb8-igk": 5.943143218366439, "XnaiveX": 5.943143218366439}, "aa-tree": "[&R] ((665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0,(4f03967793-igk:0.001578281)eov:0.001578281)6577576bb8-igk:0.0)XnaiveX;\n", "aa-lbi": {"665985d2d1-igk": 0.11412635831690991, "6cf028b770-igk": 0.11412635831690991, "c0fcfe005f-igk": 0.11412635831690991, "c2cc9da0c3-igk": 0.11412635831690991, "d1ee7f9ce6-igk": 0.11412635831690991, "4f03967793-igk": -2.6920443294540715e-06, "eov": 0.07201692190755538, "6577576bb8-igk": 0.11412635831690991, "XnaiveX": 0.11412635831690991}, "aa-lbr": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 0.4152871425303524, "6577576bb8-igk": 0.6581278609437264, "XnaiveX": 0.0}, "aa-lbf": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 3.7502704959547453, "6577576bb8-igk": 5.943143218366439, "XnaiveX": 5.943143218366439}}}]
1
+ [{"unique_ids": ["3a07b6f0a9-igk", "453132f3ab-igk", "7334912e1e-igk", "f094dfd68a-igk", "f3509e0ef3-igk", "4219142930-igk", "9c1dc5e656-igk"], "lb": {"tree": "[&R] ((7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0,(453132f3ab-igk:0.00317,f094dfd68a-igk:0.00317)bnw:0.00055)3a07b6f0a9-igk:0.0)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9-igk": 0, "453132f3ab-igk": 0, "7334912e1e-igk": 0, "f094dfd68a-igk": 0, "f3509e0ef3-igk": 0, "4219142930-igk": 0, "9c1dc5e656-igk": 0}, "lbi": {"7334912e1e-igk": 0.21884197400500868, "f3509e0ef3-igk": 0.21884197400500868, "4219142930-igk": 0.21884197400500868, "9c1dc5e656-igk": 0.21884197400500868, "453132f3ab-igk": 0.03917501624827415, "f094dfd68a-igk": 0.03917501624827415, "bnw": 0.22803636599836072, "3a07b6f0a9-igk": 0.21884197400500868, "XnaiveX": 0.21884197400500868}, "lbr": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 1.3128583920077594, "3a07b6f0a9-igk": 1.2599430193050778, "XnaiveX": 0.0}, "lbf": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 10.65424712256813, "3a07b6f0a9-igk": 10.224744159238824, "XnaiveX": 10.224744159238824}, "aa-tree": "[&R] ((7334912e1e-igk:0.0,f3509e0ef3-igk:0.0,4219142930-igk:0.0,9c1dc5e656-igk:0.0,(453132f3ab-igk:0.00317,f094dfd68a-igk:0.00317)bnw:0.00055)3a07b6f0a9-igk:0.0)XnaiveX;\n", "aa-lbi": {"7334912e1e-igk": 0.21884197400500868, "f3509e0ef3-igk": 0.21884197400500868, "4219142930-igk": 0.21884197400500868, "9c1dc5e656-igk": 0.21884197400500868, "453132f3ab-igk": 0.03917501624827415, "f094dfd68a-igk": 0.03917501624827415, "bnw": 0.22803636599836072, "3a07b6f0a9-igk": 0.21884197400500868, "XnaiveX": 0.21884197400500868}, "aa-lbr": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 1.3128583920077594, "3a07b6f0a9-igk": 1.2599430193050778, "XnaiveX": 0.0}, "aa-lbf": {"7334912e1e-igk": 0.0, "f3509e0ef3-igk": 0.0, "4219142930-igk": 0.0, "9c1dc5e656-igk": 0.0, "453132f3ab-igk": 0.0, "f094dfd68a-igk": 0.0, "bnw": 10.65424712256813, "3a07b6f0a9-igk": 10.224744159238824, "XnaiveX": 10.224744159238824}}}, {"unique_ids": ["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "d1ee7f9ce6-igk"], "lb": {"tree": "[&R] ((665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0,(4f03967793-igk:0.00158)eov:0.00158)6577576bb8-igk:0.0)XnaiveX;\n", "cons-dist-aa": {"4f03967793-igk": -1, "6577576bb8-igk": 0, "665985d2d1-igk": 0, "6cf028b770-igk": 0, "c0fcfe005f-igk": 0, "c2cc9da0c3-igk": 0, "d1ee7f9ce6-igk": 0}, "lbi": {"665985d2d1-igk": 0.11419563036250076, "6cf028b770-igk": 0.11419563036250076, "c0fcfe005f-igk": 0.11419563036250076, "c2cc9da0c3-igk": 0.11419563036250076, "d1ee7f9ce6-igk": 0.11419563036250076, "4f03967793-igk": -2.6888993834587037e-06, "eov": 0.07207617674302148, "6577576bb8-igk": 0.11419563036250076, "XnaiveX": 0.11419563036250076}, "lbr": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 0.4156287930237286, "6577576bb8-igk": 0.6585273016931852, "XnaiveX": 0.0}, "lbf": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 3.752959672872926, "6577576bb8-igk": 5.946122630570881, "XnaiveX": 5.946122630570881}, "aa-tree": "[&R] ((665985d2d1-igk:0.0,6cf028b770-igk:0.0,c0fcfe005f-igk:0.0,c2cc9da0c3-igk:0.0,d1ee7f9ce6-igk:0.0,(4f03967793-igk:0.00158)eov:0.00158)6577576bb8-igk:0.0)XnaiveX;\n", "aa-lbi": {"665985d2d1-igk": 0.11419563036250076, "6cf028b770-igk": 0.11419563036250076, "c0fcfe005f-igk": 0.11419563036250076, "c2cc9da0c3-igk": 0.11419563036250076, "d1ee7f9ce6-igk": 0.11419563036250076, "4f03967793-igk": -2.6888993834587037e-06, "eov": 0.07207617674302148, "6577576bb8-igk": 0.11419563036250076, "XnaiveX": 0.11419563036250076}, "aa-lbr": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 0.4156287930237286, "6577576bb8-igk": 0.6585273016931852, "XnaiveX": 0.0}, "aa-lbf": {"665985d2d1-igk": 0.0, "6cf028b770-igk": 0.0, "c0fcfe005f-igk": 0.0, "c2cc9da0c3-igk": 0.0, "d1ee7f9ce6-igk": 0.0, "4f03967793-igk": 0.0, "eov": 3.752959672872926, "6577576bb8-igk": 5.946122630570881, "XnaiveX": 5.946122630570881}}}]
@@ -1 +1 @@
1
- (b1e56e40a1-igh:0.016590950,(8d79fca804-igh:0.000000005,a3baa83300-igh:0.008244148)0.836:0.002747853,(b02ee7754a-igh:0.008224289,(a2238f4e9a-igh:0.063608985,(XnaiveX:0.022214108,(0eb272ee70-igh:0.064814496,(aa25e6c0ce-igh:0.012924769,9ed10b6475-igh:0.023970600)0.979:0.031919049)0.872:0.012478052)0.957:0.020824638)0.965:0.020078938)0.874:0.000000005);
1
+ (b1e56e40a1-igh:0.01659,(8d79fca804-igh:0.00055,a3baa83300-igh:0.00825)0.827:0.00274,(b02ee7754a-igh:0.00799,(a2238f4e9a-igh:0.06353,(XnaiveX:0.02221,(0eb272ee70-igh:0.06480,(aa25e6c0ce-igh:0.01292,9ed10b6475-igh:0.02397)0.979:0.03193)0.872:0.01250)0.959:0.02093)0.963:0.02002)0.966:0.00054);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -8,15 +8,15 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Initial topology in 0.00 seconds
9
9
  Refining topology: 13 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
10
10
  Total branch-length 0.284 after 0.00 sec
11
- ML-NNI round 1: LogLk = -1122.563 NNIs 0 max delta 0.00 Time 0.01
11
+ ML-NNI round 1: LogLk = -1122.853 NNIs 0 max delta 0.00 Time 0.01
12
12
  GTR Frequencies: 0.2140 0.2925 0.2783 0.2152
13
- GTR rates(ac ag at cg ct gt) 1.3956 1.1142 1.5463 0.9911 1.2525 1.0000
13
+ GTR rates(ac ag at cg ct gt) 1.3942 1.1072 1.5470 0.9944 1.2518 1.0000
14
14
  Switched to using 20 rate categories (CAT approximation)
15
15
  Rate categories were divided by 0.695 so that average rate = 1.0
16
16
  CAT-based log-likelihoods may not be comparable across runs
17
17
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
18
- ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.03
18
+ ML-NNI round 2: LogLk = -1077.992 NNIs 0 max delta 0.00 Time 0.03
19
19
  Turning off heuristics for final round of ML NNIs (converged)
20
- ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.04 (final)
21
- Optimize all lengths: LogLk = -1077.702 Time 0.04
22
- Total time: 0.06 seconds Unique: 9/9 Bad splits: 0/6
20
+ ML-NNI round 3: LogLk = -1077.990 NNIs 0 max delta 0.00 Time 0.04 (final)
21
+ Optimize all lengths: LogLk = -1077.990 Time 0.04
22
+ Total time: 0.05 seconds Unique: 9/9 Bad splits: 0/6
@@ -1 +1 @@
1
- [{"unique_ids": ["0eb272ee70-igh", "8d79fca804-igh", "a2238f4e9a-igh", "a3baa83300-igh", "aa25e6c0ce-igh", "b02ee7754a-igh", "b1e56e40a1-igh", "9ed10b6475-igh"], "lb": {"tree": "[&R] (((0eb272ee70-igh:0.064814496,(aa25e6c0ce-igh:0.012924769,9ed10b6475-igh:0.0239706)bev:0.031919049)bop:0.012478052,(a2238f4e9a-igh:0.063608985,(b02ee7754a-igh:0.008224289,(b1e56e40a1-igh:0.01659095,(a3baa83300-igh:0.008244148)8d79fca804-igh:0.002747853)bnw:5e-09)ikm:0.020078938)amz:0.020824638)dkn:0.022214108)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70-igh": -23, "8d79fca804-igh": -2, "a2238f4e9a-igh": -15, "a3baa83300-igh": -4, "aa25e6c0ce-igh": -20, "b02ee7754a-igh": -2, "b1e56e40a1-igh": -6, "9ed10b6475-igh": -24}, "lbi": {"0eb272ee70-igh": 4.5316716576647904e-12, "aa25e6c0ce-igh": 0.0013352299546976333, "9ed10b6475-igh": 2.0821067033519956e-05, "bev": 0.34313966875624674, "bop": 0.34607626810637676, "a2238f4e9a-igh": 7.075516226115921e-12, "b02ee7754a-igh": 0.015502118677622983, "b1e56e40a1-igh": 0.0006524347977552615, "a3baa83300-igh": 0.0053945888341898045, "8d79fca804-igh": 0.28421114916766016, "bnw": 0.5059150747053043, "ikm": 0.5059150660004846, "amz": 0.34473963827016346, "dkn": 0.3461431542621581, "XnaiveX": 0.17228067066273706}, "lbr": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.9921131370556442, "bop": 1.981824244382238, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.5633627219247476, "bnw": 1.0137500125996186, "ikm": 2.935068735531811, "amz": 2.000216617988823, "dkn": 2.0095687286034396, "XnaiveX": 0.0}, "lbf": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.58043771093299, "bop": 1.5866897383800882, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.7575958489288585, "bnw": 1.572414108210542, "ikm": 2.329740574124737, "amz": 1.5874934825934957, "dkn": 1.5942761714437599, "XnaiveX": 0.7935313192533607}, "aa-tree": "[&R] (((0eb272ee70-igh:0.064814496,(aa25e6c0ce-igh:0.012924769,9ed10b6475-igh:0.0239706)bev:0.031919049)bop:0.012478052,(a2238f4e9a-igh:0.063608985,(b02ee7754a-igh:0.008224289,(b1e56e40a1-igh:0.01659095,(a3baa83300-igh:0.016)8d79fca804-igh:0.002747853)bnw:5e-09)ikm:0.020078938)amz:0.020824638)dkn:0.022214108)XnaiveX;\n", "aa-lbi": {"0eb272ee70-igh": 4.5316716576647904e-12, "aa25e6c0ce-igh": 0.0013352299546976333, "9ed10b6475-igh": 2.0821067033519956e-05, "bev": 0.34313966875624674, "bop": 0.3460762681113898, "a2238f4e9a-igh": 7.075572400846092e-12, "b02ee7754a-igh": 0.015620712097964043, "b1e56e40a1-igh": 0.0006575378475057576, "a3baa83300-igh": 0.00029205767807145345, "8d79fca804-igh": 0.2915521339511227, "bnw": 0.5085275032675214, "ikm": 0.5085274896513406, "amz": 0.3447410131316421, "dkn": 0.34614315480880314, "XnaiveX": 0.17228067066286593}, "aa-lbr": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.9921131370556437, "bop": 1.9818242443250833, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.588505464528171, "bnw": 1.0215074123164622, "ikm": 2.95022744138257, "amz": 2.0002245966832026, "dkn": 2.009568731777042, "XnaiveX": 0.0}, "aa-lbf": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.5447003644470472, "bop": 1.550811019115218, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.7735116254517654, "bnw": 1.548618512698541, "ikm": 2.2888200561494085, "amz": 1.5516027780029504, "dkn": 1.558225907868134, "XnaiveX": 0.7755877435549889}}}]
1
+ [{"unique_ids": ["0eb272ee70-igh", "8d79fca804-igh", "a2238f4e9a-igh", "a3baa83300-igh", "aa25e6c0ce-igh", "b02ee7754a-igh", "b1e56e40a1-igh", "9ed10b6475-igh"], "lb": {"tree": "[&R] (((0eb272ee70-igh:0.0648,(aa25e6c0ce-igh:0.01292,9ed10b6475-igh:0.02397)bev:0.03193)bop:0.0125,(a2238f4e9a-igh:0.06353,(b02ee7754a-igh:0.00799,(b1e56e40a1-igh:0.01659,(a3baa83300-igh:0.00825)8d79fca804-igh:0.00274)bnw:0.00054)ikm:0.02002)amz:0.02093)dkn:0.02221)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70-igh": -23, "8d79fca804-igh": -2, "a2238f4e9a-igh": -15, "a3baa83300-igh": -4, "aa25e6c0ce-igh": -20, "b02ee7754a-igh": -2, "b1e56e40a1-igh": -6, "9ed10b6475-igh": -24}, "lbi": {"0eb272ee70-igh": 4.55605149055922e-12, "aa25e6c0ce-igh": 0.0013376262907693651, "9ed10b6475-igh": 2.0825472216565778e-05, "bev": 0.3431372628758717, "bop": 0.3460632522552838, "a2238f4e9a-igh": 7.288137579815034e-12, "b02ee7754a-igh": 0.015388797031642124, "b1e56e40a1-igh": 0.000592445481709546, "a3baa83300-igh": 0.00490413240938843, "8d79fca804-igh": 0.27358301063407214, "bnw": 0.4750960211652892, "ikm": 0.47411365627178476, "amz": 0.3447237701393863, "dkn": 0.3461275042019516, "XnaiveX": 0.17228073035303182}, "lbr": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.9920992470596912, "bop": 1.981972576122494, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.584740560439218, "bnw": 1.11585321153692, "ikm": 2.7504954317319457, "amz": 2.000171356430019, "dkn": 2.009477870662734, "XnaiveX": 0.0}, "lbf": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.579111872506186, "bop": 1.5853697302406584, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.7570440981721852, "bnw": 1.5710958761683216, "ikm": 2.181443085030044, "amz": 1.5861121774503886, "dkn": 1.5928778504202934, "XnaiveX": 0.7928714447139841}, "aa-tree": "[&R] (((0eb272ee70-igh:0.0648,(aa25e6c0ce-igh:0.01292,9ed10b6475-igh:0.02397)bev:0.03193)bop:0.0125,(a2238f4e9a-igh:0.06353,(b02ee7754a-igh:0.00799,(b1e56e40a1-igh:0.01659,(a3baa83300-igh:0.016)8d79fca804-igh:0.00274)bnw:0.00054)ikm:0.02002)amz:0.02093)dkn:0.02221)XnaiveX;\n", "aa-lbi": {"0eb272ee70-igh": 4.55605149055922e-12, "aa25e6c0ce-igh": 0.0013376262907693651, "9ed10b6475-igh": 2.0825472216565778e-05, "bev": 0.3431372628758717, "bop": 0.3460632522592743, "a2238f4e9a-igh": 7.28816566718012e-12, "b02ee7754a-igh": 0.01549457918658551, "b1e56e40a1-igh": 0.0005975535527071124, "a3baa83300-igh": 0.00026608970200979817, "8d79fca804-igh": 0.2809069368932764, "bnw": 0.47771008636758067, "ikm": 0.47624737546760826, "amz": 0.34472491823184936, "dkn": 0.34612750464070274, "XnaiveX": 0.1722807303531354}, "aa-lbr": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.992099247059691, "bop": 1.9819725760769904, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.6107740487569222, "bnw": 1.12439732791279, "ikm": 2.7628762875465096, "amz": 2.000178019226232, "dkn": 2.0094778732099474, "XnaiveX": 0.0}, "aa-lbf": {"0eb272ee70-igh": 0.0, "aa25e6c0ce-igh": 0.0, "9ed10b6475-igh": 0.0, "bev": 1.5434598530385832, "bop": 1.5495764254913353, "a2238f4e9a-igh": 0.0, "b02ee7754a-igh": 0.0, "b1e56e40a1-igh": 0.0, "a3baa83300-igh": 0.0, "8d79fca804-igh": 0.7728958460501232, "bnw": 1.5473831542982228, "ikm": 2.1417897526338123, "amz": 1.5503072745083557, "dkn": 1.5569150348623815, "XnaiveX": 0.7749705798837738}}}]
@@ -1 +1 @@
1
- ((b02ee7754a-igl:0.0,b1e56e40a1-igl:0.0):0.000000005,(d5ddf0c2ec-igl:0.003119820,(0eb272ee70-igl:0.015741693,(a2238f4e9a-igl:0.006269137,(XnaiveX:0.012708671,aa25e6c0ce-igl:0.019059075)0.754:0.003066989)0.845:0.000000005)0.931:0.009385895)0.914:0.000000005,(8d79fca804-igl:0.006254364,a3baa83300-igl:0.003117766)0.898:0.000000005);
1
+ ((d5ddf0c2ec-igl:0.00311,(0eb272ee70-igl:0.01564,(a2238f4e9a-igl:0.00626,(XnaiveX:0.01271,aa25e6c0ce-igl:0.01905)0.764:0.00306)0.894:0.00054)0.922:0.00920)0.638:0.00055,(b02ee7754a-igl:0.0,b1e56e40a1-igl:0.0):0.00055,(a3baa83300-igl:0.00313,8d79fca804-igl:0.00626)0.404:0.00055);
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -8,15 +8,15 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
8
8
  Initial topology in 0.00 seconds
9
9
  Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
10
10
  Total branch-length 0.074 after 0.00 sec
11
- ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.01
11
+ ML-NNI round 1: LogLk = -630.804 NNIs 0 max delta 0.00 Time 0.00
12
12
  GTR Frequencies: 0.2044 0.3132 0.2728 0.2096
13
- GTR rates(ac ag at cg ct gt) 0.8954 1.2357 1.0576 0.3959 0.3435 1.0000
13
+ GTR rates(ac ag at cg ct gt) 0.9124 1.2525 1.1000 0.4025 0.3491 1.0000
14
14
  Switched to using 20 rate categories (CAT approximation)
15
15
  Rate categories were divided by 0.641 so that average rate = 1.0
16
16
  CAT-based log-likelihoods may not be comparable across runs
17
17
  Use -gamma for approximate but comparable Gamma(20) log-likelihoods
18
- ML-NNI round 2: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02
18
+ ML-NNI round 2: LogLk = -613.867 NNIs 0 max delta 0.00 Time 0.02
19
19
  Turning off heuristics for final round of ML NNIs (converged)
20
- ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02 (final)
21
- Optimize all lengths: LogLk = -613.260 Time 0.03
22
- Total time: 0.03 seconds Unique: 8/9 Bad splits: 0/5
20
+ ML-NNI round 3: LogLk = -613.867 NNIs 0 max delta 0.00 Time 0.03 (final)
21
+ Optimize all lengths: LogLk = -613.867 Time 0.03
22
+ Total time: 0.04 seconds Unique: 8/9 Bad splits: 0/5
@@ -1,6 +1,6 @@
1
- run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
2
- FastTree Version 2.2.0 Double precision
3
- Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
1
+ run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
2
+ FastTree Version 2.1.10 SSE3
3
+ Alignment: /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
4
4
  Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
5
5
  Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
6
6
  TopHits: 1.00*sqrtN close=default refresh=0.80
@@ -1 +1 @@
1
- [{"unique_ids": ["0eb272ee70-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl"], "lb": {"tree": "[&R] ((aa25e6c0ce-igl:0.019059075,(a2238f4e9a-igl:0.006269137,(0eb272ee70-igl:0.015741693,(d5ddf0c2ec-igl:0.00311982,b1e56e40a1-igl:0.0,(8d79fca804-igl:0.006254364,a3baa83300-igl:0.003117766)bev:5e-09)b02ee7754a-igl:0.009385895)amz:5e-09)dkn:0.003066989)bop:0.012708671)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70-igl": -6, "8d79fca804-igl": -1, "a2238f4e9a-igl": -3, "a3baa83300-igl": 0, "aa25e6c0ce-igl": -5, "b02ee7754a-igl": 0, "b1e56e40a1-igl": 0, "d5ddf0c2ec-igl": 0}, "lbi": {"aa25e6c0ce-igl": 0.0005057256913561012, "a2238f4e9a-igl": 0.0515422644807014, "0eb272ee70-igl": 0.0020714327110495975, "d5ddf0c2ec-igl": 0.09944955598081857, "b1e56e40a1-igl": 0.3945626546685017, "8d79fca804-igl": 0.029975631619455063, "a3baa83300-igl": 0.09953265165405471, "bev": 0.3945625904255435, "b02ee7754a-igl": 0.3945626546685017, "amz": 0.5709103920923194, "dkn": 0.5709104471555443, "bop": 0.46782548068832935, "XnaiveX": 0.17821532767895326}, "lbr": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "8d79fca804-igl": 0.0, "a3baa83300-igl": 0.0, "bev": 0.8732584949693735, "b02ee7754a-igl": 1.9785131506399307, "amz": 0.9152281750682184, "dkn": 2.1514261276362343, "bop": 2.688501873778682, "XnaiveX": 0.0}, "lbf": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "8d79fca804-igl": 0.0, "a3baa83300-igl": 0.0, "bev": 4.196881501471522, "b02ee7754a-igl": 5.98027378675946, "amz": 5.636563742546634, "dkn": 8.052391890048282, "bop": 7.407637911469453, "XnaiveX": 2.8220199051324086}, "aa-tree": "[&R] ((aa25e6c0ce-igl:0.019059075,(a2238f4e9a-igl:0.006269137,(0eb272ee70-igl:0.015741693,(d5ddf0c2ec-igl:0.0,b1e56e40a1-igl:0.0,(8d79fca804-igl:0.006254364,a3baa83300-igl:0.003117766)bev:5e-09)b02ee7754a-igl:0.009385895)amz:5e-09)dkn:0.003066989)bop:0.012708671)XnaiveX;\n", "aa-lbi": {"aa25e6c0ce-igl": 0.0005027008400729759, "a2238f4e9a-igl": 0.05093856559158804, "0eb272ee70-igl": 0.0020459182979604374, "d5ddf0c2ec-igl": 0.2819332724841785, "b1e56e40a1-igl": 0.2819332724841785, "8d79fca804-igl": 0.016030319839114505, "a3baa83300-igl": 0.05977639969632516, "bev": 0.28193339633213166, "b02ee7754a-igl": 0.2819332724841785, "amz": 0.5660104974922846, "dkn": 0.5660105607383265, "bop": 0.46606631844311847, "XnaiveX": 0.17819010113267814}, "aa-lbr": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "8d79fca804-igl": 0.0, "a3baa83300-igl": 0.0, "bev": 1.388496039604725, "b02ee7754a-igl": 1.388495038068322, "amz": 0.9026302951379177, "dkn": 2.130696890647008, "bop": 2.678392313606184, "XnaiveX": 0.0}, "aa-lbf": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "8d79fca804-igl": 0.0, "a3baa83300-igl": 0.0, "bev": 4.3209392367459225, "b02ee7754a-igl": 4.320936758152764, "amz": 5.723298524448994, "dkn": 8.210537486990974, "bop": 7.597925732499542, "XnaiveX": 2.9050261644816384}}}, {"unique_ids": ["14195e4958-igl", "21cea6e4d0-igl", "57537e5f22-igl", "20909c3943-igl", "8807c8ff04-igl", "971ac047ee-igl"], "lb": {"tree": "[&R] ((21cea6e4d0-igl:0.0,57537e5f22-igl:0.0,20909c3943-igl:0.0,8807c8ff04-igl:0.0,971ac047ee-igl:0.0)14195e4958-igl:0.0)XnaiveX;\n", "cons-dist-aa": {"14195e4958-igl": 0, "21cea6e4d0-igl": 0, "57537e5f22-igl": 0, "20909c3943-igl": 0, "8807c8ff04-igl": 0, "971ac047ee-igl": 0}, "lbi": {"21cea6e4d0-igl": -7.900036500751009e-06, "57537e5f22-igl": -7.900036500751009e-06, "20909c3943-igl": -7.900036500751009e-06, "8807c8ff04-igl": -7.900036500751009e-06, "971ac047ee-igl": -7.900036500751009e-06, "14195e4958-igl": -7.900036500751009e-06, "XnaiveX": -7.900036500751009e-06}, "lbr": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "lbf": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "aa-tree": "[&R] ((21cea6e4d0-igl:0.0,57537e5f22-igl:0.0,20909c3943-igl:0.0,8807c8ff04-igl:0.0,971ac047ee-igl:0.0)14195e4958-igl:0.0)XnaiveX;\n", "aa-lbi": {"21cea6e4d0-igl": -7.900036500751009e-06, "57537e5f22-igl": -7.900036500751009e-06, "20909c3943-igl": -7.900036500751009e-06, "8807c8ff04-igl": -7.900036500751009e-06, "971ac047ee-igl": -7.900036500751009e-06, "14195e4958-igl": -7.900036500751009e-06, "XnaiveX": -7.900036500751009e-06}, "aa-lbr": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "aa-lbf": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}}}]
1
+ [{"unique_ids": ["0eb272ee70-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl"], "lb": {"tree": "[&R] ((aa25e6c0ce-igl:0.01905,(a2238f4e9a-igl:0.00626,(0eb272ee70-igl:0.01564,(d5ddf0c2ec-igl:0.00311,b1e56e40a1-igl:0.0,(a3baa83300-igl:0.00313,8d79fca804-igl:0.00626)bev:0.00055)b02ee7754a-igl:0.0092)ikm:0.00054)amz:0.00306)dkn:0.01271)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70-igl": -6, "8d79fca804-igl": -1, "a2238f4e9a-igl": -3, "a3baa83300-igl": 0, "aa25e6c0ce-igl": -5, "b02ee7754a-igl": 0, "b1e56e40a1-igl": 0, "d5ddf0c2ec-igl": 0}, "lbi": {"aa25e6c0ce-igl": 0.0004889789283955255, "a2238f4e9a-igl": 0.04798919649343048, "0eb272ee70-igl": 0.0019515336339243183, "d5ddf0c2ec-igl": 0.09425725563991695, "b1e56e40a1-igl": 0.37876616443784406, "a3baa83300-igl": 0.09127818066336646, "8d79fca804-igl": 0.027186076784943836, "bev": 0.3724870027898161, "b02ee7754a-igl": 0.37876616443784406, "ikm": 0.5353373247955409, "amz": 0.5408198009650945, "dkn": 0.45722450928460584, "XnaiveX": 0.17806150642077095}, "lbr": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "a3baa83300-igl": 0.0, "8d79fca804-igl": 0.0, "bev": 0.9437636055727878, "b02ee7754a-igl": 1.904266245167442, "ikm": 1.0064016113372598, "amz": 2.0222666194782715, "dkn": 2.6275801706052597, "XnaiveX": 0.0}, "lbf": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "a3baa83300-igl": 0.0, "8d79fca804-igl": 0.0, "bev": 4.171294440097729, "b02ee7754a-igl": 5.697755826243999, "ikm": 5.593397638353364, "amz": 7.519199247151807, "dkn": 7.187750362062951, "XnaiveX": 2.79932089762993}, "aa-tree": "[&R] ((aa25e6c0ce-igl:0.01905,(a2238f4e9a-igl:0.00626,(0eb272ee70-igl:0.01564,(d5ddf0c2ec-igl:0.0,b1e56e40a1-igl:0.0,(a3baa83300-igl:0.00313,8d79fca804-igl:0.00626)bev:0.00055)b02ee7754a-igl:0.0092)ikm:0.00054)amz:0.00306)dkn:0.01271)XnaiveX;\n", "aa-lbi": {"aa25e6c0ce-igl": 0.0004862818586533332, "a2238f4e9a-igl": 0.04745216007903477, "0eb272ee70-igl": 0.001923497171204135, "d5ddf0c2ec-igl": 0.2663384334481198, "b1e56e40a1-igl": 0.2663384334481198, "a3baa83300-igl": 0.058387458265412355, "8d79fca804-igl": 0.01562353607120707, "bev": 0.2789262840306545, "b02ee7754a-igl": 0.2663384334481198, "ikm": 0.5301328925158098, "amz": 0.5364742583914792, "dkn": 0.4556607220024515, "XnaiveX": 0.17803909152106903}, "aa-lbr": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "a3baa83300-igl": 0.0, "8d79fca804-igl": 0.0, "bev": 1.4144585421877462, "b02ee7754a-igl": 1.3135748337035875, "ikm": 0.9916807790196259, "amz": 2.003893867836341, "dkn": 2.6185933920040267, "XnaiveX": 0.0}, "aa-lbf": {"aa25e6c0ce-igl": 0.0, "a2238f4e9a-igl": 0.0, "0eb272ee70-igl": 0.0, "d5ddf0c2ec-igl": 0.0, "b1e56e40a1-igl": 0.0, "a3baa83300-igl": 0.0, "8d79fca804-igl": 0.0, "bev": 4.293287209505209, "b02ee7754a-igl": 4.045293904317348, "ikm": 5.672772447471864, "amz": 7.668792592979826, "dkn": 7.372659436318552, "XnaiveX": 2.8808265510142634}}}, {"unique_ids": ["14195e4958-igl", "21cea6e4d0-igl", "57537e5f22-igl", "20909c3943-igl", "8807c8ff04-igl", "971ac047ee-igl"], "lb": {"tree": "[&R] ((21cea6e4d0-igl:0.0,57537e5f22-igl:0.0,20909c3943-igl:0.0,8807c8ff04-igl:0.0,971ac047ee-igl:0.0)14195e4958-igl:0.0)XnaiveX;\n", "cons-dist-aa": {"14195e4958-igl": 0, "21cea6e4d0-igl": 0, "57537e5f22-igl": 0, "20909c3943-igl": 0, "8807c8ff04-igl": 0, "971ac047ee-igl": 0}, "lbi": {"21cea6e4d0-igl": -7.900036500751009e-06, "57537e5f22-igl": -7.900036500751009e-06, "20909c3943-igl": -7.900036500751009e-06, "8807c8ff04-igl": -7.900036500751009e-06, "971ac047ee-igl": -7.900036500751009e-06, "14195e4958-igl": -7.900036500751009e-06, "XnaiveX": -7.900036500751009e-06}, "lbr": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "lbf": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "aa-tree": "[&R] ((21cea6e4d0-igl:0.0,57537e5f22-igl:0.0,20909c3943-igl:0.0,8807c8ff04-igl:0.0,971ac047ee-igl:0.0)14195e4958-igl:0.0)XnaiveX;\n", "aa-lbi": {"21cea6e4d0-igl": -7.900036500751009e-06, "57537e5f22-igl": -7.900036500751009e-06, "20909c3943-igl": -7.900036500751009e-06, "8807c8ff04-igl": -7.900036500751009e-06, "971ac047ee-igl": -7.900036500751009e-06, "14195e4958-igl": -7.900036500751009e-06, "XnaiveX": -7.900036500751009e-06}, "aa-lbr": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}, "aa-lbf": {"21cea6e4d0-igl": 0.0, "57537e5f22-igl": 0.0, "20909c3943-igl": 0.0, "8807c8ff04-igl": 0.0, "971ac047ee-igl": 0.0, "14195e4958-igl": 0.0, "XnaiveX": 0.0}}}]
@@ -1 +1 @@
1
- [{"unique_ids": ["0eb272ee70_contig_igh+igl", "8d79fca804_contig_igh+igl", "a2238f4e9a_contig_igh+igl", "a3baa83300_contig_igh+igl", "aa25e6c0ce_contig_igh+igl", "b02ee7754a_contig_igh+igl", "b1e56e40a1_contig_igh+igl"], "lb": {"tree": "[&R] ((('0eb272ee70_contig_igh+igl':0.042844768,'aa25e6c0ce_contig_igh+igl':0.033371995)amz:0.005332184,('a2238f4e9a_contig_igh+igl':0.036055485,('b02ee7754a_contig_igh+igl':0.00438213,('b1e56e40a1_contig_igh+igl':0.008795952,('8d79fca804_contig_igh+igl':0.002923944,'a3baa83300_contig_igh+igl':0.0058566)bop:0.001458648)dkn:5e-09)bnw:0.01519502)psx:0.011641835)ikm:0.018594844)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70_contig_igh+igl": -30, "8d79fca804_contig_igh+igl": -2, "a2238f4e9a_contig_igh+igl": -19, "a3baa83300_contig_igh+igl": -3, "aa25e6c0ce_contig_igh+igl": -26, "b02ee7754a_contig_igh+igl": -1, "b1e56e40a1_contig_igh+igl": -5}, "lbi": {"0eb272ee70_contig_igh+igl": 1.0148483035396578e-14, "aa25e6c0ce_contig_igh+igl": 8.787844460478334e-12, "amz": 0.38758247062008944, "a2238f4e9a_contig_igh+igl": 1.2657710302861883e-12, "b02ee7754a_contig_igh+igl": 0.019310368159540466, "b1e56e40a1_contig_igh+igl": 0.0008112377629780348, "8d79fca804_contig_igh+igl": 0.039787305283910654, "a3baa83300_contig_igh+igl": 0.0045837356800101274, "bop": 0.48883810102013436, "dkn": 0.6244669476183902, "bnw": 0.6244667111027574, "psx": 0.3833809658780795, "ikm": 0.3876284780228447, "XnaiveX": 0.19165386730185685}, "lbr": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.9565332818983527, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.1011908466607583, "dkn": 1.1766999205178217, "bnw": 3.2580798491935172, "psx": 1.9995420893337763, "ikm": 2.0224562358611142, "XnaiveX": 0.0}, "lbf": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.3973532129102806, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.300065082223556, "dkn": 1.6082950590077771, "bnw": 2.276388388698286, "psx": 1.3973838509605605, "ikm": 1.4130428594972546, "XnaiveX": 0.6986778308482073}, "aa-tree": "[&R] ((('0eb272ee70_contig_igh+igl':0.042844768,'aa25e6c0ce_contig_igh+igl':0.033371995)amz:0.005332184,('a2238f4e9a_contig_igh+igl':0.036055485,('b02ee7754a_contig_igh+igl':0.00438213,('b1e56e40a1_contig_igh+igl':0.008795952,('8d79fca804_contig_igh+igl':0.002923944,'a3baa83300_contig_igh+igl':0.0058566)bop:0.001458648)dkn:5e-09)bnw:0.01519502)psx:0.011641835)ikm:0.018594844)XnaiveX;\n", "aa-lbi": {"0eb272ee70_contig_igh+igl": 1.0148483035396578e-14, "aa25e6c0ce_contig_igh+igl": 8.787844460478334e-12, "amz": 0.38758247062008944, "a2238f4e9a_contig_igh+igl": 1.2657710302861883e-12, "b02ee7754a_contig_igh+igl": 0.019310368159540466, "b1e56e40a1_contig_igh+igl": 0.0008112377629780348, "8d79fca804_contig_igh+igl": 0.039787305283910654, "a3baa83300_contig_igh+igl": 0.0045837356800101274, "bop": 0.48883810102013436, "dkn": 0.6244669476183902, "bnw": 0.6244667111027574, "psx": 0.3833809658780795, "ikm": 0.3876284780228447, "XnaiveX": 0.19165386730185685}, "aa-lbr": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.9565332818983527, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.1011908466607583, "dkn": 1.1766999205178217, "bnw": 3.2580798491935172, "psx": 1.9995420893337763, "ikm": 2.0224562358611142, "XnaiveX": 0.0}, "aa-lbf": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.3973532129102806, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.300065082223556, "dkn": 1.6082950590077771, "bnw": 2.276388388698286, "psx": 1.3973838509605605, "ikm": 1.4130428594972546, "XnaiveX": 0.6986778308482073}}}, {"unique_ids": ["4f03967793_contig_igh+igk", "6577576bb8_contig_igh+igk", "665985d2d1_contig_igh+igk", "6cf028b770_contig_igh+igk", "c0fcfe005f_contig_igh+igk", "c2cc9da0c3_contig_igh+igk", "d1ee7f9ce6_contig_igh+igk"], "lb": {"tree": "[&R] ((('6cf028b770_contig_igh+igk':0.01942649,('4f03967793_contig_igh+igk':0.018933964,'6577576bb8_contig_igh+igk':0.011347766)doq:0.002739671)dst:0.013039128,('c2cc9da0c3_contig_igh+igk':0.029272677,('665985d2d1_contig_igh+igk':0.004608641,('c0fcfe005f_contig_igh+igk':0.004295104,'d1ee7f9ce6_contig_igh+igk':0.001427179)eov:0.001145451)flx:0.010298361)npq:0.003357001)ily:0.002631431)XnaiveX;\n", "cons-dist-aa": {"4f03967793_contig_igh+igk": -13, "6577576bb8_contig_igh+igk": -13, "665985d2d1_contig_igh+igk": -6, "6cf028b770_contig_igh+igk": -14, "c0fcfe005f_contig_igh+igk": -6, "c2cc9da0c3_contig_igh+igk": -17, "d1ee7f9ce6_contig_igh+igk": -6}, "lbi": {"6cf028b770_contig_igh+igk": 1.593115428395929e-07, "4f03967793_contig_igh+igk": 2.2807104826283021e-07, "6577576bb8_contig_igh+igk": 5.75390763968465e-05, "doq": 0.4235396221721609, "dst": 0.423597327148736, "c2cc9da0c3_contig_igh+igk": 1.1640344935605553e-10, "665985d2d1_contig_igh+igk": 0.008698389290064869, "c0fcfe005f_contig_igh+igk": 0.009230342127102087, "d1ee7f9ce6_contig_igh+igk": 0.09637773660309717, "eov": 0.40104842073106556, "flx": 0.4417888593954387, "npq": 0.41396886186035514, "ily": 0.4138609506537257, "XnaiveX": 0.2299778914865619}, "lbr": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 1.7607671290063436, "dst": 2.1355037767784557, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.1296501261399032, "flx": 2.2255543295282134, "npq": 1.8413292171171576, "ily": 2.0866876273802295, "XnaiveX": 0.0}, "lbf": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 2.013451773740834, "dst": 2.1503165524785244, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.6140117606240767, "flx": 2.2421470272258266, "npq": 2.0143880965444656, "ily": 2.1009778475775955, "XnaiveX": 1.1675318218004627}, "aa-tree": "[&R] ((('6cf028b770_contig_igh+igk':0.01942649,('4f03967793_contig_igh+igk':0.018933964,'6577576bb8_contig_igh+igk':0.011347766)doq:0.002739671)dst:0.013039128,('c2cc9da0c3_contig_igh+igk':0.029272677,('665985d2d1_contig_igh+igk':0.004608641,('c0fcfe005f_contig_igh+igk':0.004295104,'d1ee7f9ce6_contig_igh+igk':0.001427179)eov:0.001145451)flx:0.010298361)npq:0.003357001)ily:0.002631431)XnaiveX;\n", "aa-lbi": {"6cf028b770_contig_igh+igk": 1.593115428395929e-07, "4f03967793_contig_igh+igk": 2.2807104826283021e-07, "6577576bb8_contig_igh+igk": 5.75390763968465e-05, "doq": 0.4235396221721609, "dst": 0.423597327148736, "c2cc9da0c3_contig_igh+igk": 1.1640344935605553e-10, "665985d2d1_contig_igh+igk": 0.008698389290064869, "c0fcfe005f_contig_igh+igk": 0.009230342127102087, "d1ee7f9ce6_contig_igh+igk": 0.09637773660309717, "eov": 0.40104842073106556, "flx": 0.4417888593954387, "npq": 0.41396886186035514, "ily": 0.4138609506537257, "XnaiveX": 0.2299778914865619}, "aa-lbr": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 1.7607671290063436, "dst": 2.1355037767784557, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.1296501261399032, "flx": 2.2255543295282134, "npq": 1.8413292171171576, "ily": 2.0866876273802295, "XnaiveX": 0.0}, "aa-lbf": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 2.013451773740834, "dst": 2.1503165524785244, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.6140117606240767, "flx": 2.2421470272258266, "npq": 2.0143880965444656, "ily": 2.1009778475775955, "XnaiveX": 1.1675318218004627}}}, {"unique_ids": ["3a07b6f0a9_contig_igh+igk", "453132f3ab_contig_igh+igk", "7334912e1e_contig_igh+igk", "f094dfd68a_contig_igh+igk", "f3509e0ef3_contig_igh+igk"], "lb": {"tree": "[&R] ((('f094dfd68a_contig_igh+igk':0.013255979,('3a07b6f0a9_contig_igh+igk':0.007344406,'7334912e1e_contig_igh+igk':0.013294093)dhq:0.001451666)uvx:0.005862794,('453132f3ab_contig_igh+igk':0.019408269,'f3509e0ef3_contig_igh+igk':0.013413701)fnv:0.002794533)eyz:5e-09)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9_contig_igh+igk": -5, "453132f3ab_contig_igh+igk": -11, "7334912e1e_contig_igh+igk": -10, "f094dfd68a_contig_igh+igk": -6, "f3509e0ef3_contig_igh+igk": -10}, "lbi": {"f094dfd68a_contig_igh+igk": 2.03602372186383e-05, "3a07b6f0a9_contig_igh+igk": 0.0013769126845595283, "7334912e1e_contig_igh+igk": 1.9603158309693478e-05, "dhq": 0.4514492546629606, "uvx": 0.45423834097844573, "453132f3ab_contig_igh+igk": 2.0926970087384947e-07, "f3509e0ef3_contig_igh+igk": 1.5120480114275379e-05, "fnv": 0.40990684786076964, "eyz": 0.4133173948131334, "XnaiveX": 0.4133166034434894}, "lbr": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "dhq": 1.4657917525550619, "uvx": 2.312771506309926, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "fnv": 1.7562282675225844, "eyz": 2.156631777595631, "XnaiveX": 0.0}, "lbf": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "dhq": 3.0756227447510978, "uvx": 3.6277540451842176, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "fnv": 3.083771608264235, "eyz": 3.325245733189763, "XnaiveX": 3.325239366799497}, "aa-tree": "[&R] ((('f094dfd68a_contig_igh+igk':0.013255979,('3a07b6f0a9_contig_igh+igk':0.007344406,'7334912e1e_contig_igh+igk':0.013294093)dhq:0.001451666)uvx:0.005862794,('453132f3ab_contig_igh+igk':0.019408269,'f3509e0ef3_contig_igh+igk':0.013413701)fnv:0.002794533)eyz:5e-09)XnaiveX;\n", "aa-lbi": {"f094dfd68a_contig_igh+igk": 2.03602372186383e-05, "3a07b6f0a9_contig_igh+igk": 0.0013769126845595283, "7334912e1e_contig_igh+igk": 1.9603158309693478e-05, "dhq": 0.4514492546629606, "uvx": 0.45423834097844573, "453132f3ab_contig_igh+igk": 2.0926970087384947e-07, "f3509e0ef3_contig_igh+igk": 1.5120480114275379e-05, "fnv": 0.40990684786076964, "eyz": 0.4133173948131334, "XnaiveX": 0.4133166034434894}, "aa-lbr": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "dhq": 1.4657917525550619, "uvx": 2.312771506309926, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "fnv": 1.7562282675225844, "eyz": 2.156631777595631, "XnaiveX": 0.0}, "aa-lbf": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "dhq": 3.0756227447510978, "uvx": 3.6277540451842176, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "fnv": 3.083771608264235, "eyz": 3.325245733189763, "XnaiveX": 3.325239366799497}}}]
1
+ [{"unique_ids": ["0eb272ee70_contig_igh+igl", "8d79fca804_contig_igh+igl", "a2238f4e9a_contig_igh+igl", "a3baa83300_contig_igh+igl", "aa25e6c0ce_contig_igh+igl", "b02ee7754a_contig_igh+igl", "b1e56e40a1_contig_igh+igl"], "lb": {"tree": "[&R] ((('0eb272ee70_contig_igh+igl':0.04284,'aa25e6c0ce_contig_igh+igl':0.03337)amz:0.00533,('a2238f4e9a_contig_igh+igl':0.03598,('b02ee7754a_contig_igh+igl':0.0042,('b1e56e40a1_contig_igh+igl':0.0088,('8d79fca804_contig_igh+igl':0.00292,'a3baa83300_contig_igh+igl':0.00586)bop:0.00144)dkn:0.00053)bnw:0.01515)psx:0.01172)ikm:0.01859)XnaiveX;\n", "cons-dist-aa": {"0eb272ee70_contig_igh+igl": -30, "8d79fca804_contig_igh+igl": -2, "a2238f4e9a_contig_igh+igl": -19, "a3baa83300_contig_igh+igl": -3, "aa25e6c0ce_contig_igh+igl": -26, "b02ee7754a_contig_igh+igl": -1, "b1e56e40a1_contig_igh+igl": -5}, "lbi": {"0eb272ee70_contig_igh+igl": 1.0178156962400661e-14, "aa25e6c0ce_contig_igh+igl": 8.800693270871102e-12, "amz": 0.3875890588075661, "a2238f4e9a_contig_igh+igl": 1.3358608458698337e-12, "b02ee7754a_contig_igh+igl": 0.01809935006069261, "b1e56e40a1_contig_igh+igl": 0.0007009953003826337, "8d79fca804_contig_igh+igl": 0.03751771597389149, "a3baa83300_contig_igh+igl": 0.004279582137972093, "bop": 0.46961287624277726, "dkn": 0.5666869692017146, "bnw": 0.5452076579280357, "psx": 0.38337704186757526, "ikm": 0.3876325670405587, "XnaiveX": 0.19165386847255772}, "lbr": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.9564674919890839, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.1702582818394058, "dkn": 1.3968148000913896, "bnw": 2.84455038221464, "psx": 1.9995624441517232, "ikm": 2.022477570360922, "XnaiveX": 0.0}, "lbf": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.3954278248831782, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.2980556637614074, "dkn": 1.6088458104319385, "bnw": 1.9847221859032906, "psx": 1.395453634107048, "ikm": 1.4111107383634243, "XnaiveX": 0.6977151394093476}, "aa-tree": "[&R] ((('0eb272ee70_contig_igh+igl':0.04284,'aa25e6c0ce_contig_igh+igl':0.03337)amz:0.00533,('a2238f4e9a_contig_igh+igl':0.03598,('b02ee7754a_contig_igh+igl':0.0042,('b1e56e40a1_contig_igh+igl':0.0088,('8d79fca804_contig_igh+igl':0.00292,'a3baa83300_contig_igh+igl':0.00586)bop:0.00144)dkn:0.00053)bnw:0.01515)psx:0.01172)ikm:0.01859)XnaiveX;\n", "aa-lbi": {"0eb272ee70_contig_igh+igl": 1.0178156962400661e-14, "aa25e6c0ce_contig_igh+igl": 8.800693270871102e-12, "amz": 0.3875890588075661, "a2238f4e9a_contig_igh+igl": 1.3358608458698337e-12, "b02ee7754a_contig_igh+igl": 0.01809935006069261, "b1e56e40a1_contig_igh+igl": 0.0007009953003826337, "8d79fca804_contig_igh+igl": 0.03751771597389149, "a3baa83300_contig_igh+igl": 0.004279582137972093, "bop": 0.46961287624277726, "dkn": 0.5666869692017146, "bnw": 0.5452076579280357, "psx": 0.38337704186757526, "ikm": 0.3876325670405587, "XnaiveX": 0.19165386847255772}, "aa-lbr": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.9564674919890839, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.1702582818394058, "dkn": 1.3968148000913896, "bnw": 2.84455038221464, "psx": 1.9995624441517232, "ikm": 2.022477570360922, "XnaiveX": 0.0}, "aa-lbf": {"0eb272ee70_contig_igh+igl": 0.0, "aa25e6c0ce_contig_igh+igl": 0.0, "amz": 1.3954278248831782, "a2238f4e9a_contig_igh+igl": 0.0, "b02ee7754a_contig_igh+igl": 0.0, "b1e56e40a1_contig_igh+igl": 0.0, "8d79fca804_contig_igh+igl": 0.0, "a3baa83300_contig_igh+igl": 0.0, "bop": 1.2980556637614074, "dkn": 1.6088458104319385, "bnw": 1.9847221859032906, "psx": 1.395453634107048, "ikm": 1.4111107383634243, "XnaiveX": 0.6977151394093476}}}, {"unique_ids": ["4f03967793_contig_igh+igk", "6577576bb8_contig_igh+igk", "665985d2d1_contig_igh+igk", "6cf028b770_contig_igh+igk", "c0fcfe005f_contig_igh+igk", "c2cc9da0c3_contig_igh+igk", "d1ee7f9ce6_contig_igh+igk"], "lb": {"tree": "[&R] ((('6cf028b770_contig_igh+igk':0.01943,('4f03967793_contig_igh+igk':0.01894,'6577576bb8_contig_igh+igk':0.01135)doq:0.00273)dst:0.01304,('c2cc9da0c3_contig_igh+igk':0.02928,('665985d2d1_contig_igh+igk':0.00459,('c0fcfe005f_contig_igh+igk':0.0043,'d1ee7f9ce6_contig_igh+igk':0.00142)eov:0.00114)flx:0.01031)npq:0.00336)ily:0.00263)XnaiveX;\n", "cons-dist-aa": {"4f03967793_contig_igh+igk": -13, "6577576bb8_contig_igh+igk": -13, "665985d2d1_contig_igh+igk": -6, "6cf028b770_contig_igh+igk": -14, "c0fcfe005f_contig_igh+igk": -6, "c2cc9da0c3_contig_igh+igk": -17, "d1ee7f9ce6_contig_igh+igk": -6}, "lbi": {"6cf028b770_contig_igh+igk": 1.590387216565321e-07, "4f03967793_contig_igh+igk": 2.2726179576187187e-07, "6577576bb8_contig_igh+igk": 5.749401503946767e-05, "doq": 0.423730155600042, "dst": 0.42378771362700035, "c2cc9da0c3_contig_igh+igk": 1.1576295368507477e-10, "665985d2d1_contig_igh+igk": 0.008819474476511727, "c0fcfe005f_contig_igh+igk": 0.009194049754989489, "d1ee7f9ce6_contig_igh+igk": 0.09699719743663368, "eov": 0.4010009955272404, "flx": 0.44175344158797664, "npq": 0.4139302316133695, "ily": 0.4138233482832746, "XnaiveX": 0.23000539938349435}, "lbr": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 1.7592800484341533, "dst": 2.1364638240684584, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.1272941502962917, "flx": 2.225392437032795, "npq": 1.8416442198661118, "ily": 2.086498058247843, "XnaiveX": 0.0}, "lbf": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 2.013494523777629, "dst": 2.1513283427006487, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.6123357113964245, "flx": 2.2420195367507216, "npq": 2.014424618766412, "ily": 2.1008311286083865, "XnaiveX": 1.1676960129739724}, "aa-tree": "[&R] ((('6cf028b770_contig_igh+igk':0.01943,('4f03967793_contig_igh+igk':0.01894,'6577576bb8_contig_igh+igk':0.01135)doq:0.00273)dst:0.01304,('c2cc9da0c3_contig_igh+igk':0.02928,('665985d2d1_contig_igh+igk':0.00459,('c0fcfe005f_contig_igh+igk':0.0043,'d1ee7f9ce6_contig_igh+igk':0.00142)eov:0.00114)flx:0.01031)npq:0.00336)ily:0.00263)XnaiveX;\n", "aa-lbi": {"6cf028b770_contig_igh+igk": 1.590387216565321e-07, "4f03967793_contig_igh+igk": 2.2726179576187187e-07, "6577576bb8_contig_igh+igk": 5.749401503946767e-05, "doq": 0.423730155600042, "dst": 0.42378771362700035, "c2cc9da0c3_contig_igh+igk": 1.1576295368507477e-10, "665985d2d1_contig_igh+igk": 0.008819474476511727, "c0fcfe005f_contig_igh+igk": 0.009194049754989489, "d1ee7f9ce6_contig_igh+igk": 0.09699719743663368, "eov": 0.4010009955272404, "flx": 0.44175344158797664, "npq": 0.4139302316133695, "ily": 0.4138233482832746, "XnaiveX": 0.23000539938349435}, "aa-lbr": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 1.7592800484341533, "dst": 2.1364638240684584, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.1272941502962917, "flx": 2.225392437032795, "npq": 1.8416442198661118, "ily": 2.086498058247843, "XnaiveX": 0.0}, "aa-lbf": {"6cf028b770_contig_igh+igk": 0.0, "4f03967793_contig_igh+igk": 0.0, "6577576bb8_contig_igh+igk": 0.0, "doq": 2.013494523777629, "dst": 2.1513283427006487, "c2cc9da0c3_contig_igh+igk": 0.0, "665985d2d1_contig_igh+igk": 0.0, "c0fcfe005f_contig_igh+igk": 0.0, "d1ee7f9ce6_contig_igh+igk": 0.0, "eov": 1.6123357113964245, "flx": 2.2420195367507216, "npq": 2.014424618766412, "ily": 2.1008311286083865, "XnaiveX": 1.1676960129739724}}}, {"unique_ids": ["3a07b6f0a9_contig_igh+igk", "453132f3ab_contig_igh+igk", "7334912e1e_contig_igh+igk", "f094dfd68a_contig_igh+igk", "f3509e0ef3_contig_igh+igk"], "lb": {"tree": "[&R] ((('f094dfd68a_contig_igh+igk':0.01324,('3a07b6f0a9_contig_igh+igk':0.00734,'7334912e1e_contig_igh+igk':0.01329)uvx:0.00148)eyz:0.00576,('453132f3ab_contig_igh+igk':0.01929,'f3509e0ef3_contig_igh+igk':0.01351)dhq:0.00274)fnv:0.00055)XnaiveX;\n", "cons-dist-aa": {"3a07b6f0a9_contig_igh+igk": -5, "453132f3ab_contig_igh+igk": -11, "7334912e1e_contig_igh+igk": -10, "f094dfd68a_contig_igh+igk": -6, "f3509e0ef3_contig_igh+igk": -10}, "lbi": {"f094dfd68a_contig_igh+igk": 2.050866983277052e-05, "3a07b6f0a9_contig_igh+igk": 0.001374411202362295, "7334912e1e_contig_igh+igk": 1.9562560251718753e-05, "uvx": 0.450154598614648, "eyz": 0.4531519486851458, "453132f3ab_contig_igh+igk": 2.2885298790203233e-07, "f3509e0ef3_contig_igh+igk": 1.4186632447257765e-05, "dhq": 0.41100339894213805, "fnv": 0.4146330697528938, "XnaiveX": 0.34221438379828345}, "lbr": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "uvx": 1.4730733331150867, "eyz": 2.3026411553149893, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "dhq": 1.7474597519815334, "fnv": 2.1634499940251217, "XnaiveX": 0.0}, "lbf": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "uvx": 3.0629662022340693, "eyz": 3.601995649805839, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "dhq": 3.071114424124445, "fnv": 3.322108562065492, "XnaiveX": 2.7419089660598637}, "aa-tree": "[&R] ((('f094dfd68a_contig_igh+igk':0.01324,('3a07b6f0a9_contig_igh+igk':0.00734,'7334912e1e_contig_igh+igk':0.01329)uvx:0.00148)eyz:0.00576,('453132f3ab_contig_igh+igk':0.01929,'f3509e0ef3_contig_igh+igk':0.01351)dhq:0.00274)fnv:0.00055)XnaiveX;\n", "aa-lbi": {"f094dfd68a_contig_igh+igk": 2.050866983277052e-05, "3a07b6f0a9_contig_igh+igk": 0.001374411202362295, "7334912e1e_contig_igh+igk": 1.9562560251718753e-05, "uvx": 0.450154598614648, "eyz": 0.4531519486851458, "453132f3ab_contig_igh+igk": 2.2885298790203233e-07, "f3509e0ef3_contig_igh+igk": 1.4186632447257765e-05, "dhq": 0.41100339894213805, "fnv": 0.4146330697528938, "XnaiveX": 0.34221438379828345}, "aa-lbr": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "uvx": 1.4730733331150867, "eyz": 2.3026411553149893, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "dhq": 1.7474597519815334, "fnv": 2.1634499940251217, "XnaiveX": 0.0}, "aa-lbf": {"f094dfd68a_contig_igh+igk": 0.0, "3a07b6f0a9_contig_igh+igk": 0.0, "7334912e1e_contig_igh+igk": 0.0, "uvx": 3.0629662022340693, "eyz": 3.601995649805839, "453132f3ab_contig_igh+igk": 0.0, "f3509e0ef3_contig_igh+igk": 0.0, "dhq": 3.071114424124445, "fnv": 3.322108562065492, "XnaiveX": 2.7419089660598637}}}]