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

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Files changed (95) hide show
  1. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +95 -95
  3. test/new-results/get-selection-metrics-new-simu.yaml +1 -1
  4. test/new-results/test.log +2 -2
  5. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  8. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  9. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  25. test/paired/new-results/run-times.csv +6 -6
  26. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -6
  27. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  28. test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  32. test/paired/new-results/test.log +33 -33
  33. test/ref-results/partition-new-simu/iqtree/iclust-0/log +187 -151
  34. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  35. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +34 -34
  36. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +187 -151
  37. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  38. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +2820 -2820
  39. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -1
  40. test/ref-results/partition-new-simu/iqtree/iclust-1/log +166 -207
  41. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  42. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +151 -151
  43. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +166 -207
  44. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  45. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +740 -740
  46. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -1
  47. test/ref-results/partition-new-simu/iqtree/iclust-2/log +134 -135
  48. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  49. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +17 -17
  50. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +134 -135
  51. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  52. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +763 -763
  53. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -1
  54. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -1
  55. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +30 -30
  56. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +7 -7
  57. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -1
  58. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -1
  59. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -1
  60. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  61. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +87 -87
  62. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -20
  63. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -20
  64. test/ref-results/partition-new-simu/raxml/iclust-0/log +198 -197
  65. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -1
  66. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -1
  67. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  68. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +54 -54
  69. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -20
  70. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -20
  71. test/ref-results/partition-new-simu/raxml/iclust-1/log +112 -112
  72. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +22 -22
  73. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -6
  74. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -1
  75. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -1
  76. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -1
  77. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  78. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +84 -84
  79. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -20
  80. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -20
  81. test/ref-results/partition-new-simu/raxml/iclust-2/log +182 -182
  82. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -1
  83. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  84. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  85. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  86. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  87. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  88. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  89. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  90. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  91. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  92. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  93. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  94. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  95. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel CHANGED
@@ -1 +1 @@
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- GTR{0.615177/0.198624/0.258666/0.788804/1.245919/1.000000}+FU{0.220278/0.272199/0.286214/0.221308}+G4m{99.846068}, noname = 1-379
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+ GTR{0.615226/0.198610/0.258677/0.788773/1.245925/1.000000}+FU{0.220278/0.272199/0.286215/0.221308}+G4m{99.846063}, noname = 1-379
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree CHANGED
@@ -1 +1 @@
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- (c8a90cc3d7:0.016009,XnaiveX:0.002638,(73d6c6e558:0.007949,((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308):0.000001):0.002641):0.000001);
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+ ((((948b83fb4d:0.005308,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.002641,73d6c6e558:0.007949):0.000001,c8a90cc3d7:0.016009,XnaiveX:0.002638);
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed CHANGED
@@ -1 +1 @@
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- (c8a90cc3d7:0.016009,XnaiveX:0.002638,73d6c6e558:0.007949,((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308):0.002641);
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+ (73d6c6e558:0.007949,c8a90cc3d7:0.016009,XnaiveX:0.002638,(948b83fb4d:0.005308,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.002641);
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log CHANGED
@@ -7,14 +7,14 @@ Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!
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  System: AMD EPYC 7763 64-Core Processor, 2 cores, 15 GB RAM
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- RAxML-NG was called at 16-Aug-2025 23:08:18 as follows:
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+ RAxML-NG was called at 18-Aug-2025 15:31:54 as follows:
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  /home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree
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  Analysis options:
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  run mode: Ancestral state reconstruction
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  start tree(s): user
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- random seed: 1755385698
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+ random seed: 1755531114
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  tip-inner: ON
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  pattern compression: OFF
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  Starting ML tree search with 20 distinct starting trees
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- [00:00:00] Tree #1, initial LogLikelihood: -940.256414
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- [00:00:00] Tree #1, final logLikelihood: -678.993028
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- [00:00:00] Tree #12, final logLikelihood: -668.362574
132
+ [00:00:00] Tree #12, final logLikelihood: -668.362318
133
133
 
134
- [00:00:00] Tree #13, initial LogLikelihood: -934.232575
134
+ [00:00:00] Tree #13, initial LogLikelihood: -934.239923
135
135
 
136
- [00:00:00 -934.232575] Initial branch length optimization
136
+ [00:00:00 -934.239923] Initial branch length optimization
137
137
  [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
138
138
 
139
- [00:00:00] Tree #13, final logLikelihood: -668.362653
139
+ [00:00:00] Tree #13, final logLikelihood: -668.362656
140
140
 
141
- [00:00:00] Tree #14, initial LogLikelihood: -934.237524
141
+ [00:00:00] Tree #14, initial LogLikelihood: -934.237570
142
142
 
143
- [00:00:00 -934.237524] Initial branch length optimization
144
- [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
143
+ [00:00:00 -934.237570] Initial branch length optimization
144
+ [00:00:00 -674.849060] Model parameter optimization (eps = 10.000000)
145
145
 
146
- [00:00:00] Tree #14, final logLikelihood: -668.362660
146
+ [00:00:00] Tree #14, final logLikelihood: -668.362613
147
147
 
148
- [00:00:00] Tree #15, initial LogLikelihood: -934.232575
148
+ [00:00:00] Tree #15, initial LogLikelihood: -934.234974
149
149
 
150
- [00:00:00 -934.232575] Initial branch length optimization
150
+ [00:00:00 -934.234974] Initial branch length optimization
151
151
  [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
152
152
 
153
- [00:00:00] Tree #15, final logLikelihood: -668.362653
153
+ [00:00:00] Tree #15, final logLikelihood: -668.362655
154
154
 
155
- [00:00:00] Tree #16, initial LogLikelihood: -934.239923
155
+ [00:00:00] Tree #16, initial LogLikelihood: -934.225153
156
156
 
157
- [00:00:00 -934.239923] Initial branch length optimization
158
- [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
157
+ [00:00:00 -934.225153] Initial branch length optimization
158
+ [00:00:00 -674.849336] Model parameter optimization (eps = 10.000000)
159
159
 
160
- [00:00:00] Tree #16, final logLikelihood: -668.362655
160
+ [00:00:00] Tree #16, final logLikelihood: -668.362399
161
161
 
162
- [00:00:00] Tree #17, initial LogLikelihood: -934.234974
162
+ [00:00:00] Tree #17, initial LogLikelihood: -934.237570
163
163
 
164
- [00:00:00 -934.234974] Initial branch length optimization
164
+ [00:00:00 -934.237570] Initial branch length optimization
165
165
  [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
166
166
 
167
- [00:00:00] Tree #17, final logLikelihood: -668.362656
167
+ [00:00:00] Tree #17, final logLikelihood: -668.362659
168
168
 
169
- [00:00:00] Tree #18, initial LogLikelihood: -934.232575
169
+ [00:00:00] Tree #18, initial LogLikelihood: -934.239923
170
170
 
171
- [00:00:00 -934.232575] Initial branch length optimization
172
- [00:00:00 -674.849046] Model parameter optimization (eps = 10.000000)
171
+ [00:00:00 -934.239923] Initial branch length optimization
172
+ [00:00:00 -674.849193] Model parameter optimization (eps = 10.000000)
173
173
 
174
- [00:00:00] Tree #18, final logLikelihood: -668.362643
174
+ [00:00:00] Tree #18, final logLikelihood: -668.362454
175
175
 
176
- [00:00:00] Tree #19, initial LogLikelihood: -934.237524
176
+ [00:00:00] Tree #19, initial LogLikelihood: -934.225153
177
177
 
178
- [00:00:00 -934.237524] Initial branch length optimization
179
- [00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
178
+ [00:00:00 -934.225153] Initial branch length optimization
179
+ [00:00:00 -674.849233] Model parameter optimization (eps = 10.000000)
180
180
 
181
- [00:00:00] Tree #19, final logLikelihood: -668.362658
181
+ [00:00:00] Tree #19, final logLikelihood: -668.362478
182
182
 
183
- [00:00:00] Tree #20, initial LogLikelihood: -934.225153
183
+ [00:00:00] Tree #20, initial LogLikelihood: -934.232961
184
184
 
185
- [00:00:00 -934.225153] Initial branch length optimization
186
- [00:00:00 -674.849340] Model parameter optimization (eps = 10.000000)
185
+ [00:00:00 -934.232961] Initial branch length optimization
186
+ [00:00:00 -674.849080] Model parameter optimization (eps = 10.000000)
187
187
 
188
- [00:00:00] Tree #20, final logLikelihood: -668.362395
188
+ [00:00:00] Tree #20, final logLikelihood: -668.362545
189
189
 
190
190
 
191
191
  Optimized model parameters:
192
192
 
193
193
  Partition 0: noname
194
- Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.862306 (ML), weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897)
195
- Base frequencies (ML): 0.220277 0.272445 0.285559 0.221719
196
- Substitution rates (ML): 0.584621 0.196468 0.229582 0.860189 1.199731 1.000000
194
+ Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.862356 (ML), weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897)
195
+ Base frequencies (ML): 0.220521 0.272281 0.285569 0.221629
196
+ Substitution rates (ML): 0.586335 0.197169 0.228769 0.865038 1.202222 1.000000
197
197
 
198
198
  Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs
199
199
  Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates
@@ -201,7 +201,7 @@ Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/par
201
201
 
202
202
  Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log
203
203
 
204
- Analysis started: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:18
204
+ Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:55
205
205
 
206
- Elapsed time: 0.358 seconds
206
+ Elapsed time: 0.393 seconds
207
207
 
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees CHANGED
@@ -1,20 +1,20 @@
1
- ((948b83fb4d:0.005308,((XnaiveX:0.002638,(c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001):0.002641,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001):0.005311,162cb1691f:0.005307,17f57acf2e:0.002632);
2
- (c8a90cc3d7:0.016009,XnaiveX:0.002638,(73d6c6e558:0.007949,(((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,948b83fb4d:0.005308):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.002641):0.000001);
3
- (bf50fa2017:0.000001,73431a9b10:0.005285,(((73d6c6e558:0.007949,(XnaiveX:0.002638,c8a90cc3d7:0.016009):0.000001):0.002641,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001,948b83fb4d:0.005308):0.002645);
4
- (c8a90cc3d7:0.016009,XnaiveX:0.002638,(73d6c6e558:0.007949,((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308):0.000001):0.002641):0.000001);
5
- (948b83fb4d:0.005308,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311,((XnaiveX:0.002638,(c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001):0.002641,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.000001);
6
- ((73d6c6e558:0.007949,(c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001):0.002641,948b83fb4d:0.005308,((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001);
7
- ((73d6c6e558:0.007949,XnaiveX:0.002638):0.000001,c8a90cc3d7:0.016009,(948b83fb4d:0.005308,((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001):0.002641);
8
- (c8a90cc3d7:0.016009,XnaiveX:0.002638,(73d6c6e558:0.007949,((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,(948b83fb4d:0.005308,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.000001):0.002641):0.000001);
9
- (948b83fb4d:0.005308,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,((XnaiveX:0.002638,(c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001):0.002641,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001);
10
- ((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,((948b83fb4d:0.005308,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.000001,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.002641,73d6c6e558:0.007949);
11
- ((((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(948b83fb4d:0.005308,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001):0.002641,XnaiveX:0.002638):0.000001,73d6c6e558:0.007949,c8a90cc3d7:0.016009);
12
- ((73d6c6e558:0.007949,XnaiveX:0.002638):0.000001,c8a90cc3d7:0.016009,(((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,948b83fb4d:0.005308):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.002641);
13
- (((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311,((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,73d6c6e558:0.007949):0.002641);
14
- (73431a9b10:0.005285,bf50fa2017:0.000001,((((73d6c6e558:0.007949,c8a90cc3d7:0.016009):0.000001,XnaiveX:0.002638):0.002641,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.000001,948b83fb4d:0.005308):0.002645);
15
- (((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,((XnaiveX:0.002638,c8a90cc3d7:0.016009):0.000001,73d6c6e558:0.007949):0.002641);
16
- (((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,((c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001,XnaiveX:0.002638):0.002641):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308);
17
- (((((XnaiveX:0.002638,c8a90cc3d7:0.016009):0.000001,73d6c6e558:0.007949):0.002641,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001,948b83fb4d:0.005308):0.005311,162cb1691f:0.005307,17f57acf2e:0.002632);
18
- ((XnaiveX:0.002638,c8a90cc3d7:0.016009):0.000001,73d6c6e558:0.007949,(((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.002641);
19
- ((((c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001,XnaiveX:0.002638):0.002641,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001,948b83fb4d:0.005308,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645);
20
- (((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001,((73d6c6e558:0.007949,XnaiveX:0.002638):0.000001,c8a90cc3d7:0.016009):0.002641,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311);
1
+ ((c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001,((948b83fb4d:0.005308,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.002641,XnaiveX:0.002638);
2
+ (((948b83fb4d:0.005308,((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001):0.002641,c8a90cc3d7:0.016009):0.000001,73d6c6e558:0.007949,XnaiveX:0.002638);
3
+ (XnaiveX:0.002638,(73d6c6e558:0.007949,c8a90cc3d7:0.016009):0.000001,((948b83fb4d:0.005308,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.002641);
4
+ (73431a9b10:0.005285,((((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,73d6c6e558:0.007949):0.002641,948b83fb4d:0.005308):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.002645,bf50fa2017:0.000001);
5
+ ((73d6c6e558:0.007949,XnaiveX:0.002638):0.000001,c8a90cc3d7:0.016009,((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,(948b83fb4d:0.005308,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001):0.002641);
6
+ ((73d6c6e558:0.007949,(c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001):0.002641,(948b83fb4d:0.005308,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311);
7
+ ((((948b83fb4d:0.005308,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.002641,73d6c6e558:0.007949):0.000001,c8a90cc3d7:0.016009,XnaiveX:0.002638);
8
+ (XnaiveX:0.002638,(((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001):0.002641,73d6c6e558:0.007949):0.000001,c8a90cc3d7:0.016009);
9
+ ((73431a9b10:0.005285,bf50fa2017:0.000001):0.002645,(((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,73d6c6e558:0.007949):0.002641,948b83fb4d:0.005308):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311);
10
+ ((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311,(948b83fb4d:0.005308,((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,73d6c6e558:0.007949):0.002641):0.000001);
11
+ ((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,(((162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308):0.000001,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.002641,73d6c6e558:0.007949);
12
+ (162cb1691f:0.005307,(((c8a90cc3d7:0.016009,(XnaiveX:0.002638,73d6c6e558:0.007949):0.000001):0.002641,(bf50fa2017:0.000001,73431a9b10:0.005285):0.002645):0.000001,948b83fb4d:0.005308):0.005311,17f57acf2e:0.002632);
13
+ ((((73d6c6e558:0.007949,c8a90cc3d7:0.016009):0.000001,XnaiveX:0.002638):0.002641,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311,948b83fb4d:0.005308);
14
+ (162cb1691f:0.005307,17f57acf2e:0.002632,(((XnaiveX:0.002638,(c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001):0.002641,948b83fb4d:0.005308):0.000001,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.005311);
15
+ (((73d6c6e558:0.007949,(XnaiveX:0.002638,c8a90cc3d7:0.016009):0.000001):0.002641,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.000001,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311,948b83fb4d:0.005308);
16
+ (((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,948b83fb4d:0.005308):0.000001,((XnaiveX:0.002638,73d6c6e558:0.007949):0.000001,c8a90cc3d7:0.016009):0.002641,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311);
17
+ (((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.000001,((73d6c6e558:0.007949,c8a90cc3d7:0.016009):0.000001,XnaiveX:0.002638):0.002641,948b83fb4d:0.005308);
18
+ ((c8a90cc3d7:0.016009,73d6c6e558:0.007949):0.000001,XnaiveX:0.002638,(((17f57acf2e:0.002632,162cb1691f:0.005307):0.005311,948b83fb4d:0.005308):0.000001,(73431a9b10:0.005285,bf50fa2017:0.000001):0.002645):0.002641);
19
+ (bf50fa2017:0.000001,(((c8a90cc3d7:0.016009,(73d6c6e558:0.007949,XnaiveX:0.002638):0.000001):0.002641,(162cb1691f:0.005307,17f57acf2e:0.002632):0.005311):0.000001,948b83fb4d:0.005308):0.002645,73431a9b10:0.005285);
20
+ ((c8a90cc3d7:0.016009,XnaiveX:0.002638):0.000001,(((bf50fa2017:0.000001,73431a9b10:0.005285):0.002645,(17f57acf2e:0.002632,162cb1691f:0.005307):0.005311):0.000001,948b83fb4d:0.005308):0.002641,73d6c6e558:0.007949);
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree CHANGED
@@ -1,20 +1,20 @@
1
- (((948b83fb4d:0.100000,73431a9b10:0.100000):0.100000,(c8a90cc3d7:0.100000,(bf50fa2017:0.100000,(73d6c6e558:0.100000,XnaiveX:0.100000):0.100000):0.100000):0.100000):0.100000,162cb1691f:0.100000,17f57acf2e:0.100000);
2
- (XnaiveX:0.100000,((73d6c6e558:0.100000,(c8a90cc3d7:0.100000,73431a9b10:0.100000):0.100000):0.100000,(bf50fa2017:0.100000,162cb1691f:0.100000):0.100000):0.100000,(948b83fb4d:0.100000,17f57acf2e:0.100000):0.100000);
3
- (XnaiveX:0.100000,(73431a9b10:0.100000,162cb1691f:0.100000):0.100000,(((c8a90cc3d7:0.100000,948b83fb4d:0.100000):0.100000,(bf50fa2017:0.100000,73d6c6e558:0.100000):0.100000):0.100000,17f57acf2e:0.100000):0.100000);
4
- ((c8a90cc3d7:0.100000,XnaiveX:0.100000):0.100000,((bf50fa2017:0.100000,948b83fb4d:0.100000):0.100000,(73d6c6e558:0.100000,(73431a9b10:0.100000,162cb1691f:0.100000):0.100000):0.100000):0.100000,17f57acf2e:0.100000);
5
- ((948b83fb4d:0.100000,(73d6c6e558:0.100000,XnaiveX:0.100000):0.100000):0.100000,162cb1691f:0.100000,((c8a90cc3d7:0.100000,(bf50fa2017:0.100000,73431a9b10:0.100000):0.100000):0.100000,17f57acf2e:0.100000):0.100000);
6
- (XnaiveX:0.100000,((948b83fb4d:0.100000,73d6c6e558:0.100000):0.100000,(73431a9b10:0.100000,(c8a90cc3d7:0.100000,162cb1691f:0.100000):0.100000):0.100000):0.100000,(bf50fa2017:0.100000,17f57acf2e:0.100000):0.100000);
7
- (XnaiveX:0.100000,((bf50fa2017:0.100000,(((c8a90cc3d7:0.100000,948b83fb4d:0.100000):0.100000,73d6c6e558:0.100000):0.100000,73431a9b10:0.100000):0.100000):0.100000,162cb1691f:0.100000):0.100000,17f57acf2e:0.100000);
8
- ((c8a90cc3d7:0.100000,(73431a9b10:0.100000,XnaiveX:0.100000):0.100000):0.100000,162cb1691f:0.100000,((bf50fa2017:0.100000,948b83fb4d:0.100000):0.100000,(73d6c6e558:0.100000,17f57acf2e:0.100000):0.100000):0.100000);
9
- ((948b83fb4d:0.100000,XnaiveX:0.100000):0.100000,(73431a9b10:0.100000,162cb1691f:0.100000):0.100000,((c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000,(bf50fa2017:0.100000,17f57acf2e:0.100000):0.100000):0.100000);
10
- (((c8a90cc3d7:0.100000,948b83fb4d:0.100000):0.100000,XnaiveX:0.100000):0.100000,162cb1691f:0.100000,(((bf50fa2017:0.100000,73d6c6e558:0.100000):0.100000,73431a9b10:0.100000):0.100000,17f57acf2e:0.100000):0.100000);
11
- ((((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,(948b83fb4d:0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000):0.100000):0.100000,XnaiveX:0.100000):0.100000,73d6c6e558:0.100000,c8a90cc3d7:0.100000);
12
- ((73d6c6e558:0.100000,XnaiveX:0.100000):0.100000,c8a90cc3d7:0.100000,(((73431a9b10:0.100000,bf50fa2017:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000):0.100000);
13
- (((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000,((c8a90cc3d7:0.100000,XnaiveX:0.100000):0.100000,73d6c6e558:0.100000):0.100000);
14
- (73431a9b10:0.100000,bf50fa2017:0.100000,((((73d6c6e558:0.100000,c8a90cc3d7:0.100000):0.100000,XnaiveX:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000);
15
- (((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000,((XnaiveX:0.100000,c8a90cc3d7:0.100000):0.100000,73d6c6e558:0.100000):0.100000);
16
- (((73431a9b10:0.100000,bf50fa2017:0.100000):0.100000,((c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000,XnaiveX:0.100000):0.100000):0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000,948b83fb4d:0.100000);
17
- (((((XnaiveX:0.100000,c8a90cc3d7:0.100000):0.100000,73d6c6e558:0.100000):0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000,162cb1691f:0.100000,17f57acf2e:0.100000);
18
- ((XnaiveX:0.100000,c8a90cc3d7:0.100000):0.100000,73d6c6e558:0.100000,(((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000):0.100000);
19
- ((((c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000,XnaiveX:0.100000):0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000):0.100000,948b83fb4d:0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000);
20
- (((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,948b83fb4d:0.100000):0.100000,((73d6c6e558:0.100000,XnaiveX:0.100000):0.100000,c8a90cc3d7:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000);
1
+ (XnaiveX:0.100000,162cb1691f:0.100000,((c8a90cc3d7:0.100000,948b83fb4d:0.100000):0.100000,((bf50fa2017:0.100000,73d6c6e558:0.100000):0.100000,(73431a9b10:0.100000,17f57acf2e:0.100000):0.100000):0.100000):0.100000);
2
+ (XnaiveX:0.100000,(73d6c6e558:0.100000,(948b83fb4d:0.100000,(c8a90cc3d7:0.100000,((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,162cb1691f:0.100000):0.100000):0.100000):0.100000):0.100000,17f57acf2e:0.100000);
3
+ (XnaiveX:0.100000,((73d6c6e558:0.100000,(948b83fb4d:0.100000,(c8a90cc3d7:0.100000,73431a9b10:0.100000):0.100000):0.100000):0.100000,(bf50fa2017:0.100000,162cb1691f:0.100000):0.100000):0.100000,17f57acf2e:0.100000);
4
+ ((73431a9b10:0.100000,XnaiveX:0.100000):0.100000,162cb1691f:0.100000,(bf50fa2017:0.100000,(c8a90cc3d7:0.100000,(73d6c6e558:0.100000,(948b83fb4d:0.100000,17f57acf2e:0.100000):0.100000):0.100000):0.100000):0.100000);
5
+ (XnaiveX:0.100000,(73431a9b10:0.100000,(bf50fa2017:0.100000,162cb1691f:0.100000):0.100000):0.100000,((c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000,(948b83fb4d:0.100000,17f57acf2e:0.100000):0.100000):0.100000);
6
+ (((c8a90cc3d7:0.100000,(948b83fb4d:0.100000,73431a9b10:0.100000):0.100000):0.100000,(73d6c6e558:0.100000,XnaiveX:0.100000):0.100000):0.100000,(bf50fa2017:0.100000,162cb1691f:0.100000):0.100000,17f57acf2e:0.100000);
7
+ ((73d6c6e558:0.100000,XnaiveX:0.100000):0.100000,(((c8a90cc3d7:0.100000,bf50fa2017:0.100000):0.100000,948b83fb4d:0.100000):0.100000,162cb1691f:0.100000):0.100000,(73431a9b10:0.100000,17f57acf2e:0.100000):0.100000);
8
+ ((73d6c6e558:0.100000,XnaiveX:0.100000):0.100000,(73431a9b10:0.100000,(948b83fb4d:0.100000,(bf50fa2017:0.100000,162cb1691f:0.100000):0.100000):0.100000):0.100000,(c8a90cc3d7:0.100000,17f57acf2e:0.100000):0.100000);
9
+ ((bf50fa2017:0.100000,XnaiveX:0.100000):0.100000,((c8a90cc3d7:0.100000,(948b83fb4d:0.100000,73431a9b10:0.100000):0.100000):0.100000,(73d6c6e558:0.100000,162cb1691f:0.100000):0.100000):0.100000,17f57acf2e:0.100000);
10
+ ((73431a9b10:0.100000,XnaiveX:0.100000):0.100000,162cb1691f:0.100000,((c8a90cc3d7:0.100000,948b83fb4d:0.100000):0.100000,(bf50fa2017:0.100000,(73d6c6e558:0.100000,17f57acf2e:0.100000):0.100000):0.100000):0.100000);
11
+ ((c8a90cc3d7:0.100000,XnaiveX:0.100000):0.100000,(((162cb1691f:0.100000,17f57acf2e:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(bf50fa2017:0.100000,73431a9b10:0.100000):0.100000):0.100000,73d6c6e558:0.100000);
12
+ (162cb1691f:0.100000,(((c8a90cc3d7:0.100000,(XnaiveX:0.100000,73d6c6e558:0.100000):0.100000):0.100000,(bf50fa2017:0.100000,73431a9b10:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000,17f57acf2e:0.100000);
13
+ ((((73d6c6e558:0.100000,c8a90cc3d7:0.100000):0.100000,XnaiveX:0.100000):0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000):0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000,948b83fb4d:0.100000);
14
+ (162cb1691f:0.100000,17f57acf2e:0.100000,(((XnaiveX:0.100000,(c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000):0.100000);
15
+ (((73d6c6e558:0.100000,(XnaiveX:0.100000,c8a90cc3d7:0.100000):0.100000):0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000,948b83fb4d:0.100000);
16
+ (((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,948b83fb4d:0.100000):0.100000,((XnaiveX:0.100000,73d6c6e558:0.100000):0.100000,c8a90cc3d7:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000);
17
+ (((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000):0.100000,((73d6c6e558:0.100000,c8a90cc3d7:0.100000):0.100000,XnaiveX:0.100000):0.100000,948b83fb4d:0.100000);
18
+ ((c8a90cc3d7:0.100000,73d6c6e558:0.100000):0.100000,XnaiveX:0.100000,(((17f57acf2e:0.100000,162cb1691f:0.100000):0.100000,948b83fb4d:0.100000):0.100000,(73431a9b10:0.100000,bf50fa2017:0.100000):0.100000):0.100000);
19
+ (bf50fa2017:0.100000,(((c8a90cc3d7:0.100000,(73d6c6e558:0.100000,XnaiveX:0.100000):0.100000):0.100000,(162cb1691f:0.100000,17f57acf2e:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000,73431a9b10:0.100000);
20
+ ((c8a90cc3d7:0.100000,XnaiveX:0.100000):0.100000,(((bf50fa2017:0.100000,73431a9b10:0.100000):0.100000,(17f57acf2e:0.100000,162cb1691f:0.100000):0.100000):0.100000,948b83fb4d:0.100000):0.100000,73d6c6e558:0.100000);