partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.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	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node2	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node3	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node4	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node5	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+Node6	CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG

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

@@ -0,0 +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;

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

@@ -0,0 +1 @@
+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

@@ -0,0 +1 @@
+((((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

@@ -0,0 +1 @@
+(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

@@ -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 18-Aug-2025 15:31:54 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: 1755531114
+  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: -950.326762
+
+[00:00:00 -950.326762] Initial branch length optimization
+[00:00:00 -697.593427] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -688.738075
+
+[00:00:00] Tree #2, initial LogLikelihood: -946.063936
+
+[00:00:00 -946.063936] Initial branch length optimization
+[00:00:00 -692.069744] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -683.141442
+
+[00:00:00] Tree #3, initial LogLikelihood: -950.215964
+
+[00:00:00 -950.215964] Initial branch length optimization
+[00:00:00 -697.593352] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -688.738138
+
+[00:00:00] Tree #4, initial LogLikelihood: -949.699412
+
+[00:00:00 -949.699412] Initial branch length optimization
+[00:00:00 -697.593535] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -688.738021
+
+[00:00:00] Tree #5, initial LogLikelihood: -946.313033
+
+[00:00:00 -946.313033] Initial branch length optimization
+[00:00:00 -695.420145] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -687.553906
+
+[00:00:00] Tree #6, initial LogLikelihood: -945.633568
+
+[00:00:00 -945.633568] Initial branch length optimization
+[00:00:00 -693.947960] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -686.112840
+
+[00:00:00] Tree #7, initial LogLikelihood: -947.519464
+
+[00:00:00 -947.519464] Initial branch length optimization
+[00:00:00 -693.948036] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -686.112815
+
+[00:00:00] Tree #8, initial LogLikelihood: -946.951370
+
+[00:00:00 -946.951370] Initial branch length optimization
+[00:00:00 -693.947803] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -686.112685
+
+[00:00:00] Tree #9, initial LogLikelihood: -950.242456
+
+[00:00:00 -950.242456] Initial branch length optimization
+[00:00:00 -697.593476] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -688.738031
+
+[00:00:00] Tree #10, initial LogLikelihood: -950.473031
+
+[00:00:00 -950.473031] Initial branch length optimization
+[00:00:00 -697.593583] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -688.737991
+
+[00:00:00] Tree #11, initial LogLikelihood: -934.234974
+
+[00:00:00 -934.234974] Initial branch length optimization
+[00:00:00 -674.849261] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -668.362419
+
+[00:00:00] Tree #12, initial LogLikelihood: -934.227552
+
+[00:00:00 -934.227552] Initial branch length optimization
+[00:00:00 -674.849503] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -668.362318
+
+[00:00:00] Tree #13, 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 #13, final logLikelihood: -668.362656
+
+[00:00:00] Tree #14, initial LogLikelihood: -934.237570
+
+[00:00:00 -934.237570] Initial branch length optimization
+[00:00:00 -674.849060] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -668.362613
+
+[00:00:00] Tree #15, 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 #15, final logLikelihood: -668.362655
+
+[00:00:00] Tree #16, initial LogLikelihood: -934.225153
+
+[00:00:00 -934.225153] Initial branch length optimization
+[00:00:00 -674.849336] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -668.362399
+
+[00:00:00] Tree #17, initial LogLikelihood: -934.237570
+
+[00:00:00 -934.237570] Initial branch length optimization
+[00:00:00 -674.849041] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -668.362659
+
+[00:00:00] Tree #18, initial LogLikelihood: -934.239923
+
+[00:00:00 -934.239923] Initial branch length optimization
+[00:00:00 -674.849193] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -668.362454
+
+[00:00:00] Tree #19, initial LogLikelihood: -934.225153
+
+[00:00:00 -934.225153] Initial branch length optimization
+[00:00:00 -674.849233] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -668.362478
+
+[00:00:00] Tree #20, initial LogLikelihood: -934.232961
+
+[00:00:00 -934.232961] Initial branch length optimization
+[00:00:00 -674.849080] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -668.362545
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   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) 
+   Base frequencies (ML): 0.220521 0.272281 0.285569 0.221629 
+   Substitution rates (ML): 0.586335 0.197169 0.228769 0.865038 1.202222 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: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:55
+
+Elapsed time: 0.393 seconds
+

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

@@ -0,0 +1,20 @@
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+(((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);
+(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);
+(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);
+((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);
+((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);
+((((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);
+(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);
+((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);
+((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);
+((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);
+(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);
+((((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);
+(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);
+(((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);
+(((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);
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+(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);
+((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

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