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-1/log CHANGED
@@ -8,14 +8,14 @@ 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-1/input-seqs.fa --msa-format FASTA
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  Analysis options:
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  run mode: ML tree search
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  start tree(s): random (10) + parsimony (10)
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- random seed: 1755385698
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+ random seed: 1755531114
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  tip-inner: OFF
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- [00:00:00] [worker #0] ML tree search #15, logLikelihood: -519.076351
155
+ [00:00:00] [worker #0] ML tree search #13, logLikelihood: -519.076351
170
156
 
171
157
  [00:00:00 -829.173726] Initial branch length optimization
172
158
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
173
- [00:00:00] [worker #1] ML tree search #18, logLikelihood: -519.076351
174
- [00:00:00 -519.078738] AUTODETECT spr round 1 (radius: 5)
175
- [00:00:00 -519.078738] SPR radius for FAST iterations: 5 (autodetect)
176
- [00:00:00 -519.078738] Model parameter optimization (eps = 3.000000)
159
+ [00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
160
+ [00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
161
+ [00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
162
+ [00:00:00] [worker #1] ML tree search #14, logLikelihood: -519.076351
177
163
  [00:00:00 -519.076352] FAST spr round 1 (radius: 5)
178
164
  [00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
179
165
  [00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
180
166
  [00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
181
167
 
182
- [00:00:00] [worker #0] ML tree search #17, logLikelihood: -519.076351
168
+ [00:00:00] [worker #0] ML tree search #15, logLikelihood: -519.076351
169
+
170
+ [00:00:00 -829.173912] Initial branch length optimization
171
+ [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
172
+ [00:00:00] [worker #1] ML tree search #16, logLikelihood: -519.076351
173
+ [00:00:00 -519.078738] AUTODETECT spr round 1 (radius: 5)
174
+ [00:00:00 -519.078736] SPR radius for FAST iterations: 5 (autodetect)
175
+ [00:00:00 -519.078736] Model parameter optimization (eps = 3.000000)
176
+ [00:00:00 -519.076349] FAST spr round 1 (radius: 5)
177
+ [00:00:00 -519.076349] Model parameter optimization (eps = 1.000000)
178
+ [00:00:00 -519.076349] SLOW spr round 1 (radius: 5)
179
+ [00:00:00 -519.076349] Model parameter optimization (eps = 0.100000)
180
+
181
+ [00:00:00] [worker #0] ML tree search #17, logLikelihood: -519.076349
183
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184
183
  [00:00:00 -829.173726] Initial branch length optimization
185
184
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
185
+ [00:00:00] [worker #1] ML tree search #18, logLikelihood: -519.076351
186
186
  [00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
187
187
  [00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
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188
  [00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
189
189
  [00:00:00 -519.076352] FAST spr round 1 (radius: 5)
190
- [00:00:00] [worker #1] ML tree search #20, logLikelihood: -519.076351
191
190
  [00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
192
191
  [00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
192
+ [00:00:00] [worker #1] ML tree search #20, logLikelihood: -519.076349
193
193
  [00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
194
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195
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  [00:00:00] [worker #0] ML tree search #19, logLikelihood: -519.076351
@@ -217,9 +217,9 @@ Optimized model saved to: /home/runner/work/partis/partis/test/ref-results/parti
217
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218
218
  Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log
219
219
 
220
- Analysis started: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:18
220
+ Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
221
221
 
222
- Elapsed time: 0.190 seconds
222
+ Elapsed time: 0.164 seconds
223
223
 
224
224
 
225
225
  RAxML-NG v. 1.2.1 released on 22.12.2023 by The Exelixis Lab.
@@ -230,14 +230,14 @@ Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!
230
230
 
231
231
  System: AMD EPYC 7763 64-Core Processor, 2 cores, 15 GB RAM
232
232
 
233
- RAxML-NG was called at 16-Aug-2025 23:08:18 as follows:
233
+ RAxML-NG was called at 18-Aug-2025 15:31:54 as follows:
234
234
 
235
235
  /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-1/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree
236
236
 
237
237
  Analysis options:
238
238
  run mode: Ancestral state reconstruction
239
239
  start tree(s): user
240
- random seed: 1755385698
240
+ random seed: 1755531114
241
241
  tip-inner: ON
242
242
  pattern compression: OFF
243
243
  per-rate scalers: OFF
@@ -280,103 +280,103 @@ Parallel reduction/worker buffer size: 1 KB / 0 KB
280
280
 
281
281
  Starting ML tree search with 20 distinct starting trees
282
282
 
283
- [00:00:00] Tree #1, initial LogLikelihood: -829.173113
283
+ [00:00:00] Tree #1, initial LogLikelihood: -829.175292
284
284
 
285
- [00:00:00 -829.173113] Initial branch length optimization
285
+ [00:00:00 -829.175292] Initial branch length optimization
286
286
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
287
287
 
288
- [00:00:00] Tree #1, final logLikelihood: -519.078737
288
+ [00:00:00] Tree #1, final logLikelihood: -519.078739
289
289
 
290
- [00:00:00] Tree #2, initial LogLikelihood: -829.175906
290
+ [00:00:00] Tree #2, initial LogLikelihood: -829.173726
291
291
 
292
- [00:00:00 -829.175906] Initial branch length optimization
292
+ [00:00:00 -829.173726] Initial branch length optimization
293
293
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
294
294
 
295
295
  [00:00:00] Tree #2, final logLikelihood: -519.078739
296
296
 
297
- [00:00:00] Tree #3, initial LogLikelihood: -829.173113
297
+ [00:00:00] Tree #3, initial LogLikelihood: -829.175772
298
298
 
299
- [00:00:00 -829.173113] Initial branch length optimization
299
+ [00:00:00 -829.175772] Initial branch length optimization
300
300
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
301
301
 
302
302
  [00:00:00] Tree #3, final logLikelihood: -519.078739
303
303
 
304
- [00:00:00] Tree #4, initial LogLikelihood: -829.173432
304
+ [00:00:00] Tree #4, initial LogLikelihood: -829.173726
305
305
 
306
- [00:00:00 -829.173432] Initial branch length optimization
306
+ [00:00:00 -829.173726] Initial branch length optimization
307
307
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
308
308
 
309
- [00:00:00] Tree #4, final logLikelihood: -519.078739
309
+ [00:00:00] Tree #4, final logLikelihood: -519.078738
310
310
 
311
- [00:00:00] Tree #5, initial LogLikelihood: -829.171437
311
+ [00:00:00] Tree #5, initial LogLikelihood: -829.175587
312
312
 
313
- [00:00:00 -829.171437] Initial branch length optimization
313
+ [00:00:00 -829.175587] Initial branch length optimization
314
314
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
315
315
 
316
- [00:00:00] Tree #5, final logLikelihood: -519.078738
316
+ [00:00:00] Tree #5, final logLikelihood: -519.078739
317
317
 
318
- [00:00:00] Tree #6, initial LogLikelihood: -829.175906
318
+ [00:00:00] Tree #6, initial LogLikelihood: -829.170958
319
319
 
320
- [00:00:00 -829.175906] Initial branch length optimization
320
+ [00:00:00 -829.170958] Initial branch length optimization
321
321
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
322
322
 
323
- [00:00:00] Tree #6, final logLikelihood: -519.078739
323
+ [00:00:00] Tree #6, final logLikelihood: -519.078737
324
324
 
325
- [00:00:00] Tree #7, initial LogLikelihood: -829.176201
325
+ [00:00:00] Tree #7, initial LogLikelihood: -829.175772
326
326
 
327
- [00:00:00 -829.176201] Initial branch length optimization
327
+ [00:00:00 -829.175772] Initial branch length optimization
328
328
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
329
329
 
330
- [00:00:00] Tree #7, final logLikelihood: -519.078739
330
+ [00:00:00] Tree #7, final logLikelihood: -519.078738
331
331
 
332
- [00:00:00] Tree #8, initial LogLikelihood: -829.173468
332
+ [00:00:00] Tree #8, initial LogLikelihood: -829.175587
333
333
 
334
- [00:00:00 -829.173468] Initial branch length optimization
335
- [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
334
+ [00:00:00 -829.175587] Initial branch length optimization
335
+ [00:00:00 -524.781299] Model parameter optimization (eps = 10.000000)
336
336
 
337
- [00:00:00] Tree #8, final logLikelihood: -519.078738
337
+ [00:00:00] Tree #8, final logLikelihood: -519.078736
338
338
 
339
- [00:00:00] Tree #9, initial LogLikelihood: -829.175292
339
+ [00:00:00] Tree #9, initial LogLikelihood: -829.170958
340
340
 
341
- [00:00:00 -829.175292] Initial branch length optimization
341
+ [00:00:00 -829.170958] Initial branch length optimization
342
342
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
343
343
 
344
344
  [00:00:00] Tree #9, final logLikelihood: -519.078738
345
345
 
346
- [00:00:00] Tree #10, initial LogLikelihood: -829.173726
346
+ [00:00:00] Tree #10, initial LogLikelihood: -829.175721
347
347
 
348
- [00:00:00 -829.173726] Initial branch length optimization
348
+ [00:00:00 -829.175721] Initial branch length optimization
349
349
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
350
350
 
351
351
  [00:00:00] Tree #10, final logLikelihood: -519.078738
352
352
 
353
- [00:00:00] Tree #11, initial LogLikelihood: -829.173912
353
+ [00:00:00] Tree #11, initial LogLikelihood: -829.173726
354
354
 
355
- [00:00:00 -829.173912] Initial branch length optimization
355
+ [00:00:00 -829.173726] Initial branch length optimization
356
356
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
357
357
 
358
358
  [00:00:00] Tree #11, final logLikelihood: -519.078739
359
359
 
360
- [00:00:00] Tree #12, initial LogLikelihood: -829.173912
360
+ [00:00:00] Tree #12, initial LogLikelihood: -829.176201
361
361
 
362
- [00:00:00 -829.173912] Initial branch length optimization
362
+ [00:00:00 -829.176201] Initial branch length optimization
363
363
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
364
364
 
365
- [00:00:00] Tree #12, final logLikelihood: -519.078738
365
+ [00:00:00] Tree #12, final logLikelihood: -519.078733
366
366
 
367
- [00:00:00] Tree #13, initial LogLikelihood: -829.176201
367
+ [00:00:00] Tree #13, initial LogLikelihood: -829.173726
368
368
 
369
- [00:00:00 -829.176201] Initial branch length optimization
369
+ [00:00:00 -829.173726] Initial branch length optimization
370
370
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
371
371
 
372
- [00:00:00] Tree #13, final logLikelihood: -519.078733
372
+ [00:00:00] Tree #13, final logLikelihood: -519.078739
373
373
 
374
- [00:00:00] Tree #14, initial LogLikelihood: -829.173726
374
+ [00:00:00] Tree #14, initial LogLikelihood: -829.176201
375
375
 
376
- [00:00:00 -829.173726] Initial branch length optimization
376
+ [00:00:00 -829.176201] Initial branch length optimization
377
377
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
378
378
 
379
- [00:00:00] Tree #14, final logLikelihood: -519.078739
379
+ [00:00:00] Tree #14, final logLikelihood: -519.078738
380
380
 
381
381
  [00:00:00] Tree #15, initial LogLikelihood: -829.173726
382
382
 
@@ -385,26 +385,26 @@ Starting ML tree search with 20 distinct starting trees
385
385
 
386
386
  [00:00:00] Tree #15, final logLikelihood: -519.078739
387
387
 
388
- [00:00:00] Tree #16, initial LogLikelihood: -829.173912
388
+ [00:00:00] Tree #16, initial LogLikelihood: -829.173726
389
389
 
390
- [00:00:00 -829.173912] Initial branch length optimization
390
+ [00:00:00 -829.173726] Initial branch length optimization
391
391
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
392
392
 
393
393
  [00:00:00] Tree #16, final logLikelihood: -519.078739
394
394
 
395
- [00:00:00] Tree #17, initial LogLikelihood: -829.173726
395
+ [00:00:00] Tree #17, initial LogLikelihood: -829.173912
396
396
 
397
- [00:00:00 -829.173726] Initial branch length optimization
397
+ [00:00:00 -829.173912] Initial branch length optimization
398
398
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
399
399
 
400
400
  [00:00:00] Tree #17, final logLikelihood: -519.078738
401
401
 
402
- [00:00:00] Tree #18, initial LogLikelihood: -829.171437
402
+ [00:00:00] Tree #18, initial LogLikelihood: -829.176201
403
403
 
404
- [00:00:00 -829.171437] Initial branch length optimization
404
+ [00:00:00 -829.176201] Initial branch length optimization
405
405
  [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
406
406
 
407
- [00:00:00] Tree #18, final logLikelihood: -519.078739
407
+ [00:00:00] Tree #18, final logLikelihood: -519.078737
408
408
 
409
409
  [00:00:00] Tree #19, initial LogLikelihood: -829.173726
410
410
 
@@ -413,12 +413,12 @@ Starting ML tree search with 20 distinct starting trees
413
413
 
414
414
  [00:00:00] Tree #19, final logLikelihood: -519.078739
415
415
 
416
- [00:00:00] Tree #20, initial LogLikelihood: -829.173726
416
+ [00:00:00] Tree #20, initial LogLikelihood: -829.176201
417
417
 
418
- [00:00:00 -829.173726] Initial branch length optimization
419
- [00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
418
+ [00:00:00 -829.176201] Initial branch length optimization
419
+ [00:00:00 -524.781299] Model parameter optimization (eps = 10.000000)
420
420
 
421
- [00:00:00] Tree #20, final logLikelihood: -519.078738
421
+ [00:00:00] Tree #20, final logLikelihood: -519.078735
422
422
 
423
423
 
424
424
  Optimized model parameters:
@@ -426,7 +426,7 @@ Optimized model parameters:
426
426
  Partition 0: noname
427
427
  Rate heterogeneity: GAMMA (4 cats, mean), alpha: 99.862657 (ML), weights&rates: (0.250000,0.875823) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897)
428
428
  Base frequencies (ML): 0.238369 0.269737 0.291569 0.200326
429
- Substitution rates (ML): 0.001000 0.929837 0.001000 0.001000 0.001000 1.000000
429
+ Substitution rates (ML): 0.001000 0.929845 0.001000 0.001000 0.001000 1.000000
430
430
 
431
431
  Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs
432
432
  Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates
@@ -434,7 +434,7 @@ Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/par
434
434
 
435
435
  Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log
436
436
 
437
- Analysis started: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:18
437
+ Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
438
438
 
439
- Elapsed time: 0.251 seconds
439
+ Elapsed time: 0.322 seconds
440
440
 
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs CHANGED
@@ -195,11 +195,11 @@ Node1 193 C 0.00000 1.00000 0.00000 0.00000
195
195
  Node1 194 T 0.00000 0.00000 0.00000 1.00000
196
196
  Node1 195 C 0.00000 1.00000 0.00000 0.00000
197
197
  Node1 196 A 1.00000 0.00000 0.00000 0.00000
198
- Node1 197 G 0.00000 0.00000 1.00000 0.00000
198
+ Node1 197 A 1.00000 0.00000 0.00000 0.00000
199
199
  Node1 198 G 0.00000 0.00000 1.00000 0.00000
200
200
  Node1 199 A 1.00000 0.00000 0.00000 0.00000
201
201
  Node1 200 G 0.00000 0.00000 1.00000 0.00000
202
- Node1 201 G 0.00000 0.00000 1.00000 0.00000
202
+ Node1 201 T 0.00000 0.00000 0.00002 0.99998
203
203
  Node1 202 C 0.00000 1.00000 0.00000 0.00000
204
204
  Node1 203 G 0.00000 0.00000 1.00000 0.00000
205
205
  Node1 204 A 1.00000 0.00000 0.00000 0.00000
@@ -322,7 +322,7 @@ Node1 320 G 0.00000 0.00000 1.00000 0.00000
322
322
  Node1 321 T 0.00000 0.00000 0.00000 1.00000
323
323
  Node1 322 T 0.00000 0.00000 0.00000 1.00000
324
324
  Node1 323 A 1.00000 0.00000 0.00000 0.00000
325
- Node1 324 C 0.00000 1.00000 0.00000 0.00000
325
+ Node1 324 C 0.00000 0.99994 0.00000 0.00005
326
326
  Node1 325 T 0.00000 0.00000 0.00000 1.00000
327
327
  Node1 326 A 1.00000 0.00000 0.00000 0.00000
328
328
  Node1 327 C 0.00000 1.00000 0.00000 0.00000
@@ -574,11 +574,11 @@ Node2 193 C 0.00000 1.00000 0.00000 0.00000
574
574
  Node2 194 T 0.00000 0.00000 0.00000 1.00000
575
575
  Node2 195 C 0.00000 1.00000 0.00000 0.00000
576
576
  Node2 196 A 1.00000 0.00000 0.00000 0.00000
577
- Node2 197 A 1.00000 0.00000 0.00000 0.00000
577
+ Node2 197 G 0.00000 0.00000 1.00000 0.00000
578
578
  Node2 198 G 0.00000 0.00000 1.00000 0.00000
579
579
  Node2 199 A 1.00000 0.00000 0.00000 0.00000
580
580
  Node2 200 G 0.00000 0.00000 1.00000 0.00000
581
- Node2 201 G 0.00000 0.00000 0.99999 0.00001
581
+ Node2 201 G 0.00000 0.00000 1.00000 0.00000
582
582
  Node2 202 C 0.00000 1.00000 0.00000 0.00000
583
583
  Node2 203 G 0.00000 0.00000 1.00000 0.00000
584
584
  Node2 204 A 1.00000 0.00000 0.00000 0.00000
@@ -861,7 +861,7 @@ Node3 101 A 1.00000 0.00000 0.00000 0.00000
861
861
  Node3 102 C 0.00000 1.00000 0.00000 0.00000
862
862
  Node3 103 T 0.00000 0.00000 0.00000 1.00000
863
863
  Node3 104 A 1.00000 0.00000 0.00000 0.00000
864
- Node3 105 C 0.00000 1.00000 0.00000 0.00000
864
+ Node3 105 G 0.00000 0.00125 0.99875 0.00000
865
865
  Node3 106 T 0.00000 0.00000 0.00000 1.00000
866
866
  Node3 107 G 0.00000 0.00000 1.00000 0.00000
867
867
  Node3 108 G 0.00000 0.00000 1.00000 0.00000
@@ -895,7 +895,7 @@ Node3 135 G 0.00000 0.00000 1.00000 0.00000
895
895
  Node3 136 G 0.00000 0.00000 1.00000 0.00000
896
896
  Node3 137 G 0.00000 0.00000 1.00000 0.00000
897
897
  Node3 138 A 1.00000 0.00000 0.00000 0.00000
898
- Node3 139 C 0.00000 1.00000 0.00000 0.00000
898
+ Node3 139 C 0.00000 0.99329 0.00001 0.00670
899
899
  Node3 140 T 0.00000 0.00000 0.00000 1.00000
900
900
  Node3 141 G 0.00000 0.00000 1.00000 0.00000
901
901
  Node3 142 G 0.00000 0.00000 1.00000 0.00000
@@ -941,7 +941,7 @@ Node3 181 T 0.00000 0.00000 0.00000 1.00000
941
941
  Node3 182 A 1.00000 0.00000 0.00000 0.00000
942
942
  Node3 183 C 0.00000 1.00000 0.00000 0.00000
943
943
  Node3 184 A 1.00000 0.00000 0.00000 0.00000
944
- Node3 185 A 1.00000 0.00000 0.00000 0.00000
944
+ Node3 185 C 0.00081 0.99919 0.00000 0.00000
945
945
  Node3 186 C 0.00000 1.00000 0.00000 0.00000
946
946
  Node3 187 C 0.00000 1.00000 0.00000 0.00000
947
947
  Node3 188 C 0.00000 1.00000 0.00000 0.00000
@@ -957,7 +957,7 @@ Node3 197 A 1.00000 0.00000 0.00000 0.00000
957
957
  Node3 198 G 0.00000 0.00000 1.00000 0.00000
958
958
  Node3 199 A 1.00000 0.00000 0.00000 0.00000
959
959
  Node3 200 G 0.00000 0.00000 1.00000 0.00000
960
- Node3 201 T 0.00000 0.00000 0.00002 0.99998
960
+ Node3 201 G 0.00000 0.00000 1.00000 0.00000
961
961
  Node3 202 C 0.00000 1.00000 0.00000 0.00000
962
962
  Node3 203 G 0.00000 0.00000 1.00000 0.00000
963
963
  Node3 204 A 1.00000 0.00000 0.00000 0.00000
@@ -1080,10 +1080,10 @@ Node3 320 G 0.00000 0.00000 1.00000 0.00000
1080
1080
  Node3 321 T 0.00000 0.00000 0.00000 1.00000
1081
1081
  Node3 322 T 0.00000 0.00000 0.00000 1.00000
1082
1082
  Node3 323 A 1.00000 0.00000 0.00000 0.00000
1083
- Node3 324 C 0.00000 0.99995 0.00000 0.00005
1083
+ Node3 324 C 0.00000 1.00000 0.00000 0.00000
1084
1084
  Node3 325 T 0.00000 0.00000 0.00000 1.00000
1085
1085
  Node3 326 A 1.00000 0.00000 0.00000 0.00000
1086
- Node3 327 C 0.00000 1.00000 0.00000 0.00000
1086
+ Node3 327 C 0.00081 0.99918 0.00000 0.00000
1087
1087
  Node3 328 T 0.00000 0.00000 0.00000 1.00000
1088
1088
  Node3 329 A 1.00000 0.00000 0.00000 0.00000
1089
1089
  Node3 330 C 0.00000 1.00000 0.00000 0.00000
@@ -1115,7 +1115,7 @@ Node3 355 G 0.00000 0.00000 1.00000 0.00000
1115
1115
  Node3 356 G 0.00000 0.00000 1.00000 0.00000
1116
1116
  Node3 357 C 0.00000 1.00000 0.00000 0.00000
1117
1117
  Node3 358 A 1.00000 0.00000 0.00000 0.00000
1118
- Node3 359 C 0.00000 1.00000 0.00000 0.00000
1118
+ Node3 359 C 0.00000 0.99834 0.00000 0.00166
1119
1119
  Node3 360 C 0.00000 1.00000 0.00000 0.00000
1120
1120
  Node3 361 C 0.00000 1.00000 0.00000 0.00000
1121
1121
  Node3 362 T 0.00000 0.00000 0.00000 1.00000
@@ -1336,7 +1336,7 @@ Node4 197 A 1.00000 0.00000 0.00000 0.00000
1336
1336
  Node4 198 G 0.00000 0.00000 1.00000 0.00000
1337
1337
  Node4 199 A 1.00000 0.00000 0.00000 0.00000
1338
1338
  Node4 200 G 0.00000 0.00000 1.00000 0.00000
1339
- Node4 201 T 0.00000 0.00000 0.00003 0.99997
1339
+ Node4 201 G 0.00000 0.00000 0.99999 0.00001
1340
1340
  Node4 202 C 0.00000 1.00000 0.00000 0.00000
1341
1341
  Node4 203 G 0.00000 0.00000 1.00000 0.00000
1342
1342
  Node4 204 A 1.00000 0.00000 0.00000 0.00000
@@ -1459,7 +1459,7 @@ Node4 320 G 0.00000 0.00000 1.00000 0.00000
1459
1459
  Node4 321 T 0.00000 0.00000 0.00000 1.00000
1460
1460
  Node4 322 T 0.00000 0.00000 0.00000 1.00000
1461
1461
  Node4 323 A 1.00000 0.00000 0.00000 0.00000
1462
- Node4 324 C 0.00000 0.99995 0.00000 0.00005
1462
+ Node4 324 C 0.00000 1.00000 0.00000 0.00000
1463
1463
  Node4 325 T 0.00000 0.00000 0.00000 1.00000
1464
1464
  Node4 326 A 1.00000 0.00000 0.00000 0.00000
1465
1465
  Node4 327 C 0.00000 1.00000 0.00000 0.00000
@@ -1619,7 +1619,7 @@ Node5 101 A 1.00000 0.00000 0.00000 0.00000
1619
1619
  Node5 102 C 0.00000 1.00000 0.00000 0.00000
1620
1620
  Node5 103 T 0.00000 0.00000 0.00000 1.00000
1621
1621
  Node5 104 A 1.00000 0.00000 0.00000 0.00000
1622
- Node5 105 G 0.00000 0.00125 0.99875 0.00000
1622
+ Node5 105 C 0.00000 1.00000 0.00000 0.00000
1623
1623
  Node5 106 T 0.00000 0.00000 0.00000 1.00000
1624
1624
  Node5 107 G 0.00000 0.00000 1.00000 0.00000
1625
1625
  Node5 108 G 0.00000 0.00000 1.00000 0.00000
@@ -1653,7 +1653,7 @@ Node5 135 G 0.00000 0.00000 1.00000 0.00000
1653
1653
  Node5 136 G 0.00000 0.00000 1.00000 0.00000
1654
1654
  Node5 137 G 0.00000 0.00000 1.00000 0.00000
1655
1655
  Node5 138 A 1.00000 0.00000 0.00000 0.00000
1656
- Node5 139 C 0.00000 0.99329 0.00001 0.00670
1656
+ Node5 139 C 0.00000 1.00000 0.00000 0.00000
1657
1657
  Node5 140 T 0.00000 0.00000 0.00000 1.00000
1658
1658
  Node5 141 G 0.00000 0.00000 1.00000 0.00000
1659
1659
  Node5 142 G 0.00000 0.00000 1.00000 0.00000
@@ -1699,7 +1699,7 @@ Node5 181 T 0.00000 0.00000 0.00000 1.00000
1699
1699
  Node5 182 A 1.00000 0.00000 0.00000 0.00000
1700
1700
  Node5 183 C 0.00000 1.00000 0.00000 0.00000
1701
1701
  Node5 184 A 1.00000 0.00000 0.00000 0.00000
1702
- Node5 185 C 0.00081 0.99919 0.00000 0.00000
1702
+ Node5 185 A 1.00000 0.00000 0.00000 0.00000
1703
1703
  Node5 186 C 0.00000 1.00000 0.00000 0.00000
1704
1704
  Node5 187 C 0.00000 1.00000 0.00000 0.00000
1705
1705
  Node5 188 C 0.00000 1.00000 0.00000 0.00000
@@ -1715,7 +1715,7 @@ Node5 197 A 1.00000 0.00000 0.00000 0.00000
1715
1715
  Node5 198 G 0.00000 0.00000 1.00000 0.00000
1716
1716
  Node5 199 A 1.00000 0.00000 0.00000 0.00000
1717
1717
  Node5 200 G 0.00000 0.00000 1.00000 0.00000
1718
- Node5 201 G 0.00000 0.00000 1.00000 0.00000
1718
+ Node5 201 G 0.00000 0.00000 0.99999 0.00001
1719
1719
  Node5 202 C 0.00000 1.00000 0.00000 0.00000
1720
1720
  Node5 203 G 0.00000 0.00000 1.00000 0.00000
1721
1721
  Node5 204 A 1.00000 0.00000 0.00000 0.00000
@@ -1841,7 +1841,7 @@ Node5 323 A 1.00000 0.00000 0.00000 0.00000
1841
1841
  Node5 324 C 0.00000 1.00000 0.00000 0.00000
1842
1842
  Node5 325 T 0.00000 0.00000 0.00000 1.00000
1843
1843
  Node5 326 A 1.00000 0.00000 0.00000 0.00000
1844
- Node5 327 C 0.00081 0.99918 0.00000 0.00000
1844
+ Node5 327 C 0.00000 1.00000 0.00000 0.00000
1845
1845
  Node5 328 T 0.00000 0.00000 0.00000 1.00000
1846
1846
  Node5 329 A 1.00000 0.00000 0.00000 0.00000
1847
1847
  Node5 330 C 0.00000 1.00000 0.00000 0.00000
@@ -1873,7 +1873,7 @@ Node5 355 G 0.00000 0.00000 1.00000 0.00000
1873
1873
  Node5 356 G 0.00000 0.00000 1.00000 0.00000
1874
1874
  Node5 357 C 0.00000 1.00000 0.00000 0.00000
1875
1875
  Node5 358 A 1.00000 0.00000 0.00000 0.00000
1876
- Node5 359 C 0.00000 0.99834 0.00000 0.00166
1876
+ Node5 359 C 0.00000 1.00000 0.00000 0.00000
1877
1877
  Node5 360 C 0.00000 1.00000 0.00000 0.00000
1878
1878
  Node5 361 C 0.00000 1.00000 0.00000 0.00000
1879
1879
  Node5 362 T 0.00000 0.00000 0.00000 1.00000
@@ -2094,7 +2094,7 @@ Node6 197 A 1.00000 0.00000 0.00000 0.00000
2094
2094
  Node6 198 G 0.00000 0.00000 1.00000 0.00000
2095
2095
  Node6 199 A 1.00000 0.00000 0.00000 0.00000
2096
2096
  Node6 200 G 0.00000 0.00000 1.00000 0.00000
2097
- Node6 201 G 0.00000 0.00000 0.99999 0.00001
2097
+ Node6 201 T 0.00000 0.00000 0.00002 0.99998
2098
2098
  Node6 202 C 0.00000 1.00000 0.00000 0.00000
2099
2099
  Node6 203 G 0.00000 0.00000 1.00000 0.00000
2100
2100
  Node6 204 A 1.00000 0.00000 0.00000 0.00000
@@ -2217,7 +2217,7 @@ Node6 320 G 0.00000 0.00000 1.00000 0.00000
2217
2217
  Node6 321 T 0.00000 0.00000 0.00000 1.00000
2218
2218
  Node6 322 T 0.00000 0.00000 0.00000 1.00000
2219
2219
  Node6 323 A 1.00000 0.00000 0.00000 0.00000
2220
- Node6 324 C 0.00000 1.00000 0.00000 0.00000
2220
+ Node6 324 C 0.00000 0.99995 0.00000 0.00005
2221
2221
  Node6 325 T 0.00000 0.00000 0.00000 1.00000
2222
2222
  Node6 326 A 1.00000 0.00000 0.00000 0.00000
2223
2223
  Node6 327 C 0.00000 1.00000 0.00000 0.00000
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates CHANGED
@@ -1,6 +1,6 @@
1
- Node1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
2
- Node2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
3
- Node3 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
4
- Node4 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
5
- Node5 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
6
- Node6 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
1
+ Node1 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
2
+ Node2 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
3
+ Node3 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
4
+ Node4 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
5
+ Node5 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
6
+ Node6 CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree CHANGED
@@ -1 +1 @@
1
- (((bf50fa2017:0.000001,73431a9b10:0.005284)Node1:0.002644,948b83fb4d:0.005307)Node2:0.000001,((73d6c6e558:0.007947,XnaiveX:0.002638)Node3:0.000001,c8a90cc3d7:0.016006)Node4:0.002640,(17f57acf2e:0.002631,162cb1691f:0.005305)Node5:0.005307)Node6;
1
+ ((c8a90cc3d7:0.016006,XnaiveX:0.002638)Node1:0.000001,(((bf50fa2017:0.000001,73431a9b10:0.005284)Node2:0.002644,(17f57acf2e:0.002632,162cb1691f:0.005305)Node3:0.005307)Node4:0.000001,948b83fb4d:0.005307)Node5:0.002640,73d6c6e558:0.007946)Node6;