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

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates

@@ -0,0 +1,6 @@
+Node1	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node2	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node3	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node4	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node5	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node6	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree

@@ -0,0 +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;

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel

@@ -0,0 +1 @@
+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

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree

@@ -0,0 +1 @@
+(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);

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed

@@ -0,0 +1 @@
+(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);

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log

@@ -0,0 +1,207 @@
+
+RAxML-NG v. 1.2.1 released on 22.12.2023 by The Exelixis Lab.
+Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
+Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
+Latest version: https://github.com/amkozlov/raxml-ng
+Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
+
+System: AMD EPYC 7763 64-Core Processor, 2 cores, 15 GB RAM
+
+RAxML-NG was called at 16-Aug-2025 23:08:18 as follows:
+
+/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
+
+Analysis options:
+  run mode: Ancestral state reconstruction
+  start tree(s): user
+  random seed: 1755385698
+  tip-inner: ON
+  pattern compression: OFF
+  per-rate scalers: OFF
+  site repeats: OFF
+  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
+  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
+  SIMD kernels: AVX2
+  parallelization: coarse-grained (auto), PTHREADS (auto)
+
+[00:00:00] Reading alignment from file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa
+[00:00:00] Loaded alignment with 8 taxa and 379 sites
+
+Alignment comprises 1 partitions and 379 sites
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites: 379
+Gaps: 0.00 %
+Invariant sites: 94.46 %
+
+
+NOTE: Binary MSA file already exists: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.rba
+
+Parallelization scheme autoconfig: 1 worker(s) x 2 thread(s)
+
+Parallel reduction/worker buffer size: 1 KB  / 0 KB
+
+[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 190 / 3040
+[00:00:00] Data distribution: max. searches per worker: 20
+
+Starting ML tree search with 20 distinct starting trees
+
+[00:00:00] Tree #1, initial LogLikelihood: -940.256414
+
+[00:00:00 -940.256414] Initial branch length optimization
+[00:00:00 -685.977828] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -678.993028
+
+[00:00:00] Tree #2, initial LogLikelihood: -949.421829
+
+[00:00:00 -949.421829] Initial branch length optimization
+[00:00:00 -697.593753] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -688.737800
+
+[00:00:00] Tree #3, initial LogLikelihood: -950.265446
+
+[00:00:00 -950.265446] Initial branch length optimization
+[00:00:00 -697.593380] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -688.738192
+
+[00:00:00] Tree #4, initial LogLikelihood: -947.570123
+
+[00:00:00 -947.570123] Initial branch length optimization
+[00:00:00 -694.573838] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -686.736242
+
+[00:00:00] Tree #5, initial LogLikelihood: -942.860420
+
+[00:00:00 -942.860420] Initial branch length optimization
+[00:00:00 -688.360957] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -680.554813
+
+[00:00:00] Tree #6, initial LogLikelihood: -950.363794
+
+[00:00:00 -950.363794] Initial branch length optimization
+[00:00:00 -697.593306] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -688.738173
+
+[00:00:00] Tree #7, initial LogLikelihood: -947.813809
+
+[00:00:00 -947.813809] Initial branch length optimization
+[00:00:00 -697.592998] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -688.738217
+
+[00:00:00] Tree #8, initial LogLikelihood: -949.688470
+
+[00:00:00 -949.688470] Initial branch length optimization
+[00:00:00 -697.593383] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -688.737968
+
+[00:00:00] Tree #9, initial LogLikelihood: -947.585600
+
+[00:00:00 -947.585600] Initial branch length optimization
+[00:00:00 -695.422647] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -687.554038
+
+[00:00:00] Tree #10, initial LogLikelihood: -947.781745
+
+[00:00:00 -947.781745] Initial branch length optimization
+[00:00:00 -697.592838] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -688.737694
+
+[00:00:00] Tree #11, initial LogLikelihood: -934.239923
+
+[00:00:00 -934.239923] Initial branch length optimization
+[00:00:00 -675.639483] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -668.360350
+
+[00:00:00] Tree #12, initial LogLikelihood: -934.225153
+
+[00:00:00 -934.225153] Initial branch length optimization
+[00:00:00 -674.849075] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -668.362574
+
+[00:00:00] Tree #13, initial LogLikelihood: -934.232575
+
+[00:00:00 -934.232575] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #13, final logLikelihood: -668.362653
+
+[00:00:00] Tree #14, initial LogLikelihood: -934.237524
+
+[00:00:00 -934.237524] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -668.362660
+
+[00:00:00] Tree #15, initial LogLikelihood: -934.232575
+
+[00:00:00 -934.232575] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #15, final logLikelihood: -668.362653
+
+[00:00:00] Tree #16, initial LogLikelihood: -934.239923
+
+[00:00:00 -934.239923] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -668.362655
+
+[00:00:00] Tree #17, initial LogLikelihood: -934.234974
+
+[00:00:00 -934.234974] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -668.362656
+
+[00:00:00] Tree #18, initial LogLikelihood: -934.232575
+
+[00:00:00 -934.232575] Initial branch length optimization
+[00:00:00 -674.849046] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -668.362643
+
+[00:00:00] Tree #19, initial LogLikelihood: -934.237524
+
+[00:00:00 -934.237524] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -668.362658
+
+[00:00:00] Tree #20, initial LogLikelihood: -934.225153
+
+[00:00:00 -934.225153] Initial branch length optimization
+[00:00:00 -674.849340] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -668.362395
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   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) 
+   Base frequencies (ML): 0.220277 0.272445 0.285559 0.221719 
+   Substitution rates (ML): 0.584621 0.196468 0.229582 0.860189 1.199731 1.000000 
+
+Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs
+Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates
+Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log
+
+Analysis started: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:18
+
+Elapsed time: 0.358 seconds
+

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees

@@ -0,0 +1,20 @@
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+(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);
+(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);
+(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);
+(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);
+((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);
+((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);
+(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);
+(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);
+((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);
+((((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);
+((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);
+(((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);
+(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);
+(((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);
+(((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);
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test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree

@@ -0,0 +1,20 @@
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