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-0/input-seqs.fa.raxml.ancestralStates

@@ -0,0 +1,10 @@
+Node1	GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node2	GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node3	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node4	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node5	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node6	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node7	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node8	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node9	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+Node10	GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree

@@ -0,0 +1 @@
+(((((5fb484a8a6:0.014574,(((XnaiveX:0.000001,(822801f8ab:0.000001,d024e5cab0:0.000001)Node1:0.000001)Node2:0.005798,efdea248af:0.008730)Node3:0.000001,308de1d739:0.011636)Node4:0.000001)Node5:0.000001,(ee25049b92:0.005817,9c3cedb840:0.002896)Node6:0.011689)Node7:0.000001,18f4019708:0.014595)Node8:0.005797,8024ed1a22:0.000001)Node9:0.000001,648902c3e5:0.000001,f47122f1f5:0.000001)Node10;

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel

@@ -0,0 +1 @@
+GTR{0.976979/0.982855/0.461252/0.700964/0.796581/1.000000}+FU{0.218410/0.257146/0.305095/0.219349}+G4m{99.862254}, noname = 1-346

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree

@@ -0,0 +1 @@
+(((18f4019708:0.014599,5fb484a8a6:0.014574):0.000001,(((f47122f1f5:0.000001,648902c3e5:0.000001):0.000001,8024ed1a22:0.000001):0.005797,308de1d739:0.011643):0.000001):0.000001,(efdea248af:0.008730,(ee25049b92:0.005819,9c3cedb840:0.002893):0.011684):0.000001,((d024e5cab0:0.000001,822801f8ab:0.000001):0.000001,XnaiveX:0.000001):0.005800);

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed

@@ -0,0 +1 @@
+(308de1d739:0.011643,efdea248af:0.008730,(ee25049b92:0.005819,9c3cedb840:0.002893):0.011684,(d024e5cab0:0.000001,822801f8ab:0.000001,XnaiveX:0.000001):0.005800,18f4019708:0.014599,5fb484a8a6:0.014574,(f47122f1f5:0.000001,648902c3e5:0.000001,8024ed1a22:0.000001):0.005797);

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log

@@ -0,0 +1,216 @@
+
+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-0/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/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-0/input-seqs.fa
+[00:00:00] Loaded alignment with 12 taxa and 346 sites
+
+WARNING: Sequences XnaiveX and 822801f8ab are exactly identical!
+WARNING: Sequences XnaiveX and d024e5cab0 are exactly identical!
+WARNING: Sequences 648902c3e5 and 8024ed1a22 are exactly identical!
+WARNING: Sequences 648902c3e5 and f47122f1f5 are exactly identical!
+WARNING: Duplicate sequences found: 4
+
+NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
+NOTE: was saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy
+
+Alignment comprises 1 partitions and 346 sites
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites: 346
+Gaps: 0.00 %
+Invariant sites: 91.91 %
+
+
+NOTE: Binary MSA file already exists: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/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 / 173 / 2768
+[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: -1045.659744
+
+[00:00:00 -1045.659744] Initial branch length optimization
+[00:00:00 -738.752348] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -725.000046
+
+[00:00:00] Tree #2, initial LogLikelihood: -1046.886052
+
+[00:00:00 -1046.886052] Initial branch length optimization
+[00:00:00 -738.757373] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -725.000021
+
+[00:00:00] Tree #3, initial LogLikelihood: -1042.987303
+
+[00:00:00 -1042.987303] Initial branch length optimization
+[00:00:00 -738.758082] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -721.511501
+
+[00:00:00] Tree #4, initial LogLikelihood: -1040.663132
+
+[00:00:00 -1040.663132] Initial branch length optimization
+[00:00:00 -725.744207] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -714.338568
+
+[00:00:00] Tree #5, initial LogLikelihood: -1044.242985
+
+[00:00:00 -1044.242985] Initial branch length optimization
+[00:00:00 -738.762719] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -725.000032
+
+[00:00:00] Tree #6, initial LogLikelihood: -1030.578002
+
+[00:00:00 -1030.578002] Initial branch length optimization
+[00:00:00 -720.999971] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -706.156329
+
+[00:00:00] Tree #7, initial LogLikelihood: -1040.620761
+
+[00:00:00 -1040.620761] Initial branch length optimization
+[00:00:00 -725.746446] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -714.021094
+
+[00:00:00] Tree #8, initial LogLikelihood: -1045.340747
+
+[00:00:00 -1045.340747] Initial branch length optimization
+[00:00:00 -734.508881] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -721.148652
+
+[00:00:00] Tree #9, initial LogLikelihood: -1046.979195
+
+[00:00:00 -1046.979195] Initial branch length optimization
+[00:00:00 -738.760469] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -725.000035
+
+[00:00:00] Tree #10, initial LogLikelihood: -1045.773389
+
+[00:00:00 -1045.773389] Initial branch length optimization
+[00:00:00 -738.762327] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -724.999796
+
+[00:00:00] Tree #11, initial LogLikelihood: -1004.317870
+
+[00:00:00 -1004.317870] Initial branch length optimization
+[00:00:00 -668.056483] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -662.853098
+
+[00:00:00] Tree #12, initial LogLikelihood: -1004.319632
+
+[00:00:00 -1004.319632] Initial branch length optimization
+[00:00:00 -668.056544] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -662.853087
+
+[00:00:00] Tree #13, initial LogLikelihood: -1004.317937
+
+[00:00:00 -1004.317937] Initial branch length optimization
+[00:00:00 -668.056736] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #13, final logLikelihood: -662.852930
+
+[00:00:00] Tree #14, initial LogLikelihood: -1004.320321
+
+[00:00:00 -1004.320321] Initial branch length optimization
+[00:00:00 -668.056272] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -662.853214
+
+[00:00:00] Tree #15, initial LogLikelihood: -1004.319559
+
+[00:00:00 -1004.319559] Initial branch length optimization
+[00:00:00 -668.056446] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #15, final logLikelihood: -662.853134
+
+[00:00:00] Tree #16, initial LogLikelihood: -1004.326398
+
+[00:00:00 -1004.326398] Initial branch length optimization
+[00:00:00 -668.058705] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -662.852320
+
+[00:00:00] Tree #17, initial LogLikelihood: -1004.325322
+
+[00:00:00 -1004.325322] Initial branch length optimization
+[00:00:00 -668.056408] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -662.853188
+
+[00:00:00] Tree #18, initial LogLikelihood: -1004.328189
+
+[00:00:00 -1004.328189] Initial branch length optimization
+[00:00:00 -668.057815] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -662.852694
+
+[00:00:00] Tree #19, initial LogLikelihood: -1004.322428
+
+[00:00:00 -1004.322428] Initial branch length optimization
+[00:00:00 -668.058423] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -662.852359
+
+[00:00:00] Tree #20, initial LogLikelihood: -1004.319412
+
+[00:00:00 -1004.319412] Initial branch length optimization
+[00:00:00 -668.056741] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -662.852953
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.862246 (ML),  weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.219082 0.257002 0.304229 0.219686 
+   Substitution rates (ML): 0.897311 0.970592 0.393839 0.763217 0.745304 1.000000 
+
+Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs
+Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates
+Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log
+
+Analysis started: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:19
+
+Elapsed time: 0.371 seconds
+

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees

@@ -0,0 +1,20 @@
+(((5fb484a8a6:0.014574,efdea248af:0.008730):0.000001,((((f47122f1f5:0.000001,8024ed1a22:0.000001):0.000001,648902c3e5:0.000001):0.005797,(9c3cedb840:0.002893,ee25049b92:0.005819):0.011684):0.000001,((XnaiveX:0.000001,d024e5cab0:0.000001):0.000001,822801f8ab:0.000001):0.005800):0.000001):0.000001,18f4019708:0.014599,308de1d739:0.011643);
+(8024ed1a22:0.000001,f47122f1f5:0.000001,((((((d024e5cab0:0.000001,822801f8ab:0.000001):0.000001,XnaiveX:0.000001):0.005800,18f4019708:0.014599):0.000001,(5fb484a8a6:0.014574,(ee25049b92:0.005819,9c3cedb840:0.002893):0.011684):0.000001):0.000001,(308de1d739:0.011643,efdea248af:0.008730):0.000001):0.005797,648902c3e5:0.000001):0.000001);
+(((((648902c3e5:0.000001,8024ed1a22:0.000001):0.000001,f47122f1f5:0.000001):0.005797,((d024e5cab0:0.000001,822801f8ab:0.000001):0.000001,XnaiveX:0.000001):0.005800):0.000001,(308de1d739:0.011643,(ee25049b92:0.005819,9c3cedb840:0.002893):0.011684):0.000001):0.000001,5fb484a8a6:0.014574,(efdea248af:0.008730,18f4019708:0.014599):0.000001);
+(((9c3cedb840:0.002893,ee25049b92:0.005819):0.011684,5fb484a8a6:0.014574):0.000001,((((822801f8ab:0.000001,d024e5cab0:0.000001):0.000001,XnaiveX:0.000001):0.005800,(8024ed1a22:0.000001,(648902c3e5:0.000001,f47122f1f5:0.000001):0.000001):0.005797):0.000001,(efdea248af:0.008730,18f4019708:0.014599):0.000001):0.000001,308de1d739:0.011643);
+(efdea248af:0.008730,18f4019708:0.014599,((((XnaiveX:0.000001,d024e5cab0:0.000001):0.000001,822801f8ab:0.000001):0.005800,((648902c3e5:0.000001,8024ed1a22:0.000001):0.000001,f47122f1f5:0.000001):0.005797):0.000001,((5fb484a8a6:0.014574,(ee25049b92:0.005819,9c3cedb840:0.002893):0.011684):0.000001,308de1d739:0.011643):0.000001):0.000001);
+((9c3cedb840:0.002893,ee25049b92:0.005819):0.011684,(((((f47122f1f5:0.000001,8024ed1a22:0.000001):0.000001,648902c3e5:0.000001):0.005797,efdea248af:0.008730):0.000001,(XnaiveX:0.000001,(822801f8ab:0.000001,d024e5cab0:0.000001):0.000001):0.005800):0.000001,(5fb484a8a6:0.014574,308de1d739:0.011643):0.000001):0.000001,18f4019708:0.014599);
+(efdea248af:0.008730,((8024ed1a22:0.000001,(648902c3e5:0.000001,f47122f1f5:0.000001):0.000001):0.005797,18f4019708:0.014599):0.000001,(((XnaiveX:0.000001,(822801f8ab:0.000001,d024e5cab0:0.000001):0.000001):0.005800,5fb484a8a6:0.014574):0.000001,((ee25049b92:0.005819,9c3cedb840:0.002893):0.011684,308de1d739:0.011643):0.000001):0.000001);
+(((((308de1d739:0.011643,efdea248af:0.008730):0.000001,(822801f8ab:0.000001,(XnaiveX:0.000001,d024e5cab0:0.000001):0.000001):0.005800):0.000001,(((8024ed1a22:0.000001,f47122f1f5:0.000001):0.000001,648902c3e5:0.000001):0.005797,5fb484a8a6:0.014574):0.000001):0.000001,18f4019708:0.014599):0.011684,9c3cedb840:0.002893,ee25049b92:0.005819);
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test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy

@@ -0,0 +1,9 @@
+8 346
+XnaiveX GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+18f4019708 GAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG
+308de1d739 GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+5fb484a8a6 GAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG
+648902c3e5 GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+ee25049b92 GAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+efdea248af GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+9c3cedb840 GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree

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