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

test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out

@@ -0,0 +1 @@
+((648902c3e5:0.0,8024ed1a22:0.0,f47122f1f5:0.0):0.00600,(ee25049b92:0.00602,9c3cedb840:0.00300)0.965:0.01209,(((5fb484a8a6:0.01508,efdea248af:0.00903)0.613:0.00055,(18f4019708:0.01511,308de1d739:0.01204)0.878:0.00055)0.544:0.00055,(XnaiveX:0.0,822801f8ab:0.0,d024e5cab0:0.0):0.00600)0.076:0.00055);

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

@@ -0,0 +1,24 @@
+>XnaiveX
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>18f4019708
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>308de1d739
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>5fb484a8a6
+NNNNNNGAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG
+>648902c3e5
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>8024ed1a22
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>822801f8ab
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>d024e5cab0
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>ee25049b92
+NNNNNNGAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>efdea248af
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>f47122f1f5
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>9c3cedb840
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/fasttree/iclust-0/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 48 times)
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.082 after 0.00 sec
+ML-NNI round 1: LogLk = -668.065 NNIs 2 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2215 0.2569 0.3074 0.2143
+GTR rates(ac ag at cg ct gt) 0.9755 0.9620 0.4555 0.6885 0.8030 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.641 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -655.501 Time 0.04
+Total time: 0.05 seconds Unique: 8/12 Bad splits: 0/5

test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out

@@ -0,0 +1 @@
+((XnaiveX:0.0,13de8675ec:0.0,31e052ee14:0.0,33aaa62e12:0.0,4233d708fe:0.0,91796617a0:0.0):0.00055,20a0129b57:0.00286,97366cf0d8:0.00286);

test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa

@@ -0,0 +1,16 @@
+>XnaiveX
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>13de8675ec
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>20a0129b57
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG
+>31e052ee14
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>33aaa62e12
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>4233d708fe
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>91796617a0
+NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>97366cf0d8
+NNNCAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/fasttree/iclust-1/log

@@ -0,0 +1,23 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Ignored unknown character X (seen 9 times)
+Initial topology in 0.00 seconds
+Refining topology: 6 rounds ME-NNIs, 2 rounds ME-SPRs, 3 rounds ML-NNIs
+Total branch-length 0.005 after 0.00 sec
+ML-NNI round 1: LogLk = -524.975 NNIs 0 max delta 0.00 Time 0.00
+GTR Frequencies: 0.2380 0.2697 0.2923 0.2000
+GTR rates(ac ag at cg ct gt) 0.0104 0.7989 0.0104 0.0104 0.0104 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.624 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -518.679 NNIs 0 max delta 0.00 Time 0.01
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -518.679 NNIs 0 max delta 0.00 Time 0.01 (final)
+Optimize all lengths: LogLk = -518.679 Time 0.01
+Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0

test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out

@@ -0,0 +1 @@
+((73431a9b10:0.00542,bf50fa2017:0.00055)0.819:0.00269,(73d6c6e558:0.00815,(XnaiveX:0.00270,c8a90cc3d7:0.01640)0.240:0.00055)0.802:0.00270,(948b83fb4d:0.00544,(162cb1691f:0.00544,17f57acf2e:0.00269)0.891:0.00545)0.051:0.00055);

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

@@ -0,0 +1,16 @@
+>XnaiveX
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>162cb1691f
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG
+>17f57acf2e
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73431a9b10
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73d6c6e558
+CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>948b83fb4d
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>bf50fa2017
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>c8a90cc3d7
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/fasttree/iclust-2/log

@@ -0,0 +1,22 @@
+run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+FastTree Version 2.1.10 SSE3
+Alignment: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
+Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
+TopHits: 1.00*sqrtN close=default refresh=0.80
+ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
+Initial topology in 0.00 seconds
+Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
+Total branch-length 0.056 after 0.00 sec
+ML-NNI round 1: LogLk = -675.096 NNIs 1 max delta 0.00 Time 0.01
+GTR Frequencies: 0.2187 0.2796 0.2852 0.2164
+GTR rates(ac ag at cg ct gt) 0.5930 0.1945 0.2547 0.7730 1.2348 1.0000
+Switched to using 20 rate categories (CAT approximation)
+Rate categories were divided by 0.636 so that average rate = 1.0
+CAT-based log-likelihoods may not be comparable across runs
+Use -gamma for approximate but comparable Gamma(20) log-likelihoods
+ML-NNI round 2: LogLk = -662.808 NNIs 2 max delta 0.00 Time 0.03
+Turning off heuristics for final round of ML NNIs (converged)
+ML-NNI round 3: LogLk = -662.808 NNIs 1 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -662.808 Time 0.04
+Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5

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

@@ -0,0 +1,24 @@
+>XnaiveX
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>18f4019708
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>308de1d739
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>5fb484a8a6
+NNNNNNGAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG
+>648902c3e5
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>8024ed1a22
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>822801f8ab
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>d024e5cab0
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>ee25049b92
+NNNNNNGAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>efdea248af
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>f47122f1f5
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>9c3cedb840
+NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/iqtree/iclust-0/log

@@ -0,0 +1,394 @@
+run /home/runner/work/partis/partis/bin/iqtree-3-linux -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out -o XnaiveX
+IQ-TREE version 3.0.1 for Linux x86 64-bit built May  5 2025
+Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
+Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
+Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
+
+Host:    pkrvmubgrv54qmi (AVX2, FMA3, 15 GB RAM)
+Command: /home/runner/work/partis/partis/bin/iqtree3_intel -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out -o XnaiveX
+Seed:    580837 (Using SPRNG - Scalable Parallel Random Number Generator)
+Time:    Sat Aug 16 23:08:16 2025
+Kernel:  AVX+FMA - 1 threads (4 CPU cores detected)
+
+HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
+HINT: -nt AUTO will automatically determine the best number of threads to use.
+
+Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa ... Fasta format detected
+Reading fasta file: done in 0.000107562 secs using 59.5% CPU
+Alignment most likely contains DNA/RNA sequences
+Constructing alignment: done in 0.000288013 secs using 60.07% CPU
+WARNING: 6 sites contain only gaps or ambiguous characters.
+Alignment has 12 sequences with 352 columns, 29 distinct patterns
+8 parsimony-informative, 20 singleton sites, 324 constant sites
+            Gap/Ambiguity  Composition  p-value
+Analyzing sequences: done in 5.541e-06 secs using 54.14% CPU
+   1  XnaiveX       1.70%    passed     99.41%
+   2  18f4019708    1.70%    passed     99.75%
+   3  308de1d739    1.70%    passed     98.96%
+   4  5fb484a8a6    1.70%    passed     99.94%
+   5  648902c3e5    1.70%    passed     99.27%
+   6  8024ed1a22    1.70%    passed     99.27%
+   7  822801f8ab    1.70%    passed     99.41%
+   8  d024e5cab0    1.70%    passed     99.41%
+   9  ee25049b92    1.70%    passed     97.94%
+  10  efdea248af    1.70%    passed     99.57%
+  11  f47122f1f5    1.70%    passed     99.27%
+  12  9c3cedb840    1.70%    passed     99.78%
+****  TOTAL         1.70%  0 sequences failed composition chi2 test (p-value<5%; df=3)
+
+
+Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
+Perform fast likelihood tree search using GTR+I+G model...
+Estimate model parameters (epsilon = 5.000)
+Perform nearest neighbor interchange...
+Optimizing NNI: done in 0.000604378 secs
+Estimate model parameters (epsilon = 1.000)
+1. Initial log-likelihood: -663.729
+Optimal log-likelihood: -663.717
+Rate parameters:  A-C: 0.93501  A-G: 0.93474  A-T: 0.45114  C-G: 0.67930  C-T: 0.80175  G-T: 1.00000
+Base frequencies:  A: 0.222  C: 0.257  G: 0.308  T: 0.213
+Proportion of invariable sites: 0.455
+Gamma shape alpha: 998.447
+Parameters optimization took 1 rounds (0.001 sec)
+Time for fast ML tree search: 0.004 seconds
+
+NOTE: ModelFinder requires 0 MB RAM!
+ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
+ No. Model         -LnL         df  AIC          AICc         BIC
+  1  JC            667.319      21  1376.639     1379.439     1457.775
+  2  JC+I          667.319      22  1378.639     1381.715     1463.639
+  3  JC+G4         667.320      22  1378.641     1381.717     1463.640
+  4  JC+I+G4       668.194      23  1382.388     1385.754     1471.251
+  5  JC+R2         667.320      23  1380.640     1384.006     1469.503
+  6  JC+R3         667.320      25  1384.639     1388.627     1481.230
+ 14  JC+I+R2       668.203      24  1384.405     1388.075     1477.133
+ 15  JC+I+R3       668.176      26  1388.352     1392.672     1488.806
+ 23  JC            667.319      21  1376.639     1379.439     1457.775
+ 24  JC+I          667.319      22  1378.639     1381.715     1463.639
+ 25  JC+G4         667.320      22  1378.641     1381.717     1463.640
+ 45  F81           667.320      21  1376.639     1379.439     1457.775
+ 46  F81+I         667.320      22  1378.639     1381.715     1463.639
+ 47  F81+G4        667.320      22  1378.641     1381.717     1463.641
+ 67  F81+F         663.546      24  1375.093     1378.763     1467.820
+ 68  F81+F+I       663.546      25  1377.093     1381.081     1473.684
+ 69  F81+F+G4      663.547      25  1377.095     1381.082     1473.685
+ 89  K2P           667.283      22  1378.566     1381.642     1463.566
+ 90  K2P+I         667.283      23  1380.566     1383.932     1469.430
+ 91  K2P+G4        667.284      23  1380.568     1383.934     1469.431
+111  K2P           667.283      22  1378.566     1381.642     1463.566
+112  K2P+I         667.283      23  1380.566     1383.932     1469.430
+113  K2P+G4        667.284      23  1380.568     1383.934     1469.431
+133  HKY           667.283      22  1378.566     1381.642     1463.566
+134  HKY+I         667.283      23  1380.566     1383.932     1469.430
+135  HKY+G4        667.284      23  1380.568     1383.934     1469.431
+155  HKY+F         663.502      25  1377.004     1380.992     1473.595
+156  HKY+F+I       663.502      26  1379.004     1383.324     1479.458
+157  HKY+F+G4      663.503      26  1379.006     1383.326     1479.460
+177  TNe           667.185      23  1380.371     1383.737     1469.234
+178  TNe+I         667.185      24  1382.371     1386.041     1475.098
+179  TNe+G4        667.186      24  1382.373     1386.042     1475.100
+199  TNe           667.185      23  1380.371     1383.737     1469.234
+200  TNe+I         667.185      24  1382.371     1386.041     1475.098
+201  TNe+G4        667.186      24  1382.373     1386.042     1475.100
+221  TN            667.185      23  1380.371     1383.737     1469.234
+222  TN+I          667.185      24  1382.371     1386.041     1475.098
+223  TN+G4         667.186      24  1382.373     1386.042     1475.100
+243  TN+F          663.461      26  1378.923     1383.243     1479.377
+244  TN+F+I        663.461      27  1380.923     1385.589     1485.241
+245  TN+F+G4       663.462      27  1380.924     1385.591     1485.242
+265  K3P           666.838      23  1379.676     1383.042     1468.539
+266  K3P+I         666.838      24  1381.676     1385.345     1474.403
+267  K3P+G4        666.839      24  1381.677     1385.347     1474.405
+287  K3P           666.838      23  1379.676     1383.042     1468.539
+288  K3P+I         666.838      24  1381.676     1385.345     1474.403
+289  K3P+G4        666.839      24  1381.677     1385.347     1474.405
+309  K3Pu          666.838      23  1379.676     1383.042     1468.539
+310  K3Pu+I        666.838      24  1381.676     1385.345     1474.403
+311  K3Pu+G4       666.839      24  1381.677     1385.347     1474.404
+331  K3Pu+F        662.995      26  1377.990     1382.310     1478.445
+332  K3Pu+F+I      662.995      27  1379.990     1384.657     1484.308
+333  K3Pu+F+G4     662.996      27  1379.992     1384.658     1484.310
+353  TPM2          667.114      23  1380.228     1383.594     1469.092
+354  TPM2+I        667.114      24  1382.228     1385.898     1474.955
+355  TPM2+G4       667.115      24  1382.230     1385.900     1474.957
+375  TPM2          667.114      23  1380.228     1383.594     1469.092
+376  TPM2+I        667.114      24  1382.228     1385.898     1474.955
+377  TPM2+G4       667.115      24  1382.230     1385.900     1474.957
+397  TPM2u         667.114      23  1380.228     1383.594     1469.092
+398  TPM2u+I       667.114      24  1382.228     1385.898     1474.955
+399  TPM2u+G4      667.115      24  1382.230     1385.900     1474.957
+419  TPM2u+F       663.468      26  1378.936     1383.256     1479.391
+420  TPM2u+F+I     663.468      27  1380.936     1385.603     1485.254
+421  TPM2u+F+G4    663.469      27  1380.938     1385.604     1485.256
+441  TPM3          667.241      23  1380.482     1383.848     1469.346
+442  TPM3+I        667.241      24  1382.482     1386.152     1475.209
+443  TPM3+G4       667.242      24  1382.484     1386.154     1475.211
+463  TPM3          667.241      23  1380.482     1383.848     1469.346
+464  TPM3+I        667.241      24  1382.482     1386.152     1475.209
+465  TPM3+G4       667.242      24  1382.484     1386.154     1475.211
+485  TPM3u         667.241      23  1380.482     1383.848     1469.346
+486  TPM3u+I       667.241      24  1382.482     1386.152     1475.209
+487  TPM3u+G4      667.242      24  1382.484     1386.154     1475.211
+507  TPM3u+F       663.499      26  1378.998     1383.318     1479.452
+508  TPM3u+F+I     663.499      27  1380.998     1385.664     1485.316
+509  TPM3u+F+G4    663.500      27  1380.999     1385.666     1485.317
+529  TIMe          666.740      24  1381.481     1385.150     1474.208
+530  TIMe+I        666.740      25  1383.481     1387.468     1480.071
+531  TIMe+G4       666.741      25  1383.482     1387.470     1480.073
+551  TIMe          666.740      24  1381.481     1385.150     1474.208
+552  TIMe+I        666.740      25  1383.481     1387.468     1480.071
+553  TIMe+G4       666.741      25  1383.482     1387.470     1480.073
+573  TIM           666.740      24  1381.481     1385.150     1474.208
+574  TIM+I         666.740      25  1383.480     1387.468     1480.071
+575  TIM+G4        666.741      25  1383.482     1387.470     1480.073
+595  TIM+F         662.954      27  1379.909     1384.575     1484.227
+596  TIM+F+I       662.954      28  1381.909     1386.937     1490.090
+597  TIM+F+G4      662.955      28  1381.910     1386.938     1490.092
+617  TIM2e         667.017      24  1382.033     1385.703     1474.760
+618  TIM2e+I       667.017      25  1384.033     1388.021     1480.624
+619  TIM2e+G4      667.017      25  1384.035     1388.023     1480.626
+639  TIM2e         667.017      24  1382.033     1385.703     1474.760
+640  TIM2e+I       667.017      25  1384.033     1388.021     1480.624
+641  TIM2e+G4      667.017      25  1384.035     1388.023     1480.626
+661  TIM2          667.017      24  1382.033     1385.703     1474.760
+662  TIM2+I        667.017      25  1384.033     1388.021     1480.624
+663  TIM2+G4       667.017      25  1384.035     1388.023     1480.626
+683  TIM2+F        663.427      27  1380.854     1385.521     1485.172
+684  TIM2+F+I      663.427      28  1382.854     1387.882     1491.036
+685  TIM2+F+G4     663.428      28  1382.856     1387.884     1491.037
+705  TIM3e         667.144      24  1382.287     1385.957     1475.014
+706  TIM3e+I       667.144      25  1384.287     1388.275     1480.878
+707  TIM3e+G4      667.144      25  1384.289     1388.276     1480.879
+727  TIM3e         667.144      24  1382.287     1385.957     1475.014
+728  TIM3e+I       667.144      25  1384.287     1388.275     1480.878
+729  TIM3e+G4      667.144      25  1384.289     1388.276     1480.879
+749  TIM3          667.144      24  1382.287     1385.957     1475.014
+750  TIM3+I        667.143      25  1384.287     1388.275     1480.878
+751  TIM3+G4       667.144      25  1384.289     1388.276     1480.879
+771  TIM3+F        663.458      27  1380.916     1385.583     1485.234
+772  TIM3+F+I      663.458      28  1382.916     1387.944     1491.098
+773  TIM3+F+G4     663.459      28  1382.918     1387.946     1491.099
+793  TVMe          666.493      25  1382.987     1386.975     1479.578
+794  TVMe+I        666.493      26  1384.987     1389.307     1485.441
+795  TVMe+G4       666.494      26  1384.988     1389.308     1485.443
+815  TVMe          666.493      25  1382.987     1386.975     1479.578
+816  TVMe+I        666.493      26  1384.987     1389.307     1485.441
+817  TVMe+G4       666.494      26  1384.988     1389.308     1485.443
+837  TVM           666.493      25  1382.987     1386.975     1479.578
+838  TVM+I         666.493      26  1384.987     1389.307     1485.441
+839  TVM+G4        666.494      26  1384.988     1389.308     1485.443
+859  TVM+F         662.870      28  1381.740     1386.768     1489.922
+860  TVM+F+I       662.870      29  1383.740     1389.144     1495.786
+861  TVM+F+G4      662.871      29  1383.742     1389.146     1495.787
+881  SYM           666.396      26  1384.793     1389.113     1485.247
+882  SYM+I         666.396      27  1386.793     1391.459     1491.111
+883  SYM+G4        666.397      27  1386.794     1391.461     1491.113
+903  SYM           666.396      26  1384.793     1389.113     1485.247
+904  SYM+I         666.396      27  1386.793     1391.459     1491.111
+905  SYM+G4        666.397      27  1386.794     1391.461     1491.113
+925  GTR           666.396      26  1384.792     1389.112     1485.247
+926  GTR+I         666.396      27  1386.792     1391.459     1491.110
+927  GTR+G4        666.397      27  1386.794     1391.461     1491.112
+947  GTR+F         662.829      29  1383.659     1389.063     1495.704
+948  GTR+F+I       662.829      30  1385.659     1391.453     1501.568
+949  GTR+F+G4      662.830      30  1385.660     1391.455     1501.569
+Akaike Information Criterion:           F81+F
+Corrected Akaike Information Criterion: F81+F
+Bayesian Information Criterion:         JC
+Best-fit model: JC chosen according to BIC
+
+All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz
+CPU time for ModelFinder: 0.120 seconds (0h:0m:0s)
+Wall-clock time for ModelFinder: 0.131 seconds (0h:0m:0s)
+
+NOTE: 0 MB RAM (0 GB) is required!
+Estimate model parameters (epsilon = 0.100)
+1. Initial log-likelihood: -667.320
+Optimal log-likelihood: -667.320
+Rate parameters:  A-C: 1.00000  A-G: 1.00000  A-T: 1.00000  C-G: 1.00000  C-T: 1.00000  G-T: 1.00000
+Base frequencies:  A: 0.250  C: 0.250  G: 0.250  T: 0.250
+Parameters optimization took 1 rounds (0.000 sec)
+Wrote distance file to... 
+Computing ML distances based on estimated model parameters...
+Calculating distance matrix: done in 0.000415974 secs using 95.44% CPU
+Computing ML distances took 0.000445 sec (of wall-clock time) 0.000430 sec (of CPU time)
+Setting up auxiliary I and S matrices: done in 3.6279e-05 secs using 96.47% CPU
+Constructing RapidNJ tree: done in 5.6416e-05 secs using 97.49% CPU
+Computing RapidNJ tree took 0.000115 sec (of wall-clock time) 0.000115 sec (of CPU time)
+Log-likelihood of RapidNJ tree: -667.322
+--------------------------------------------------------------------
+|             INITIALIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Generating 98 parsimony trees... 0.023 second
+Computing log-likelihood of 98 initial trees ... 0.021 seconds
+Current best score: -667.319
+
+Do NNI search on 20 best initial trees
+Optimizing NNI: done in 0.000608887 secs using 94.27% CPU
+Estimate model parameters (epsilon = 0.100)
+BETTER TREE FOUND at iteration 1: -667.319
+Optimizing NNI: done in 0.000595683 secs using 98.37% CPU
+Optimizing NNI: done in 0.000607454 secs
+BETTER TREE FOUND at iteration 3: -667.319
+Optimizing NNI: done in 0.000607845 secs using 65.64% CPU
+BETTER TREE FOUND at iteration 4: -667.319
+Optimizing NNI: done in 0.000580934 secs using 99.67% CPU
+Optimizing NNI: done in 0.000583148 secs using 96.54% CPU
+Optimizing NNI: done in 0.000633383 secs
+Optimizing NNI: done in 0.000584451 secs using 67.93% CPU
+Optimizing NNI: done in 0.000567198 secs using 93.27% CPU
+Optimizing NNI: done in 0.000575274 secs using 99.78% CPU
+Iteration 10 / LogL: -667.319 / Time: 0h:0m:0s
+Optimizing NNI: done in 0.00060517 secs using 99.81% CPU
+Optimizing NNI: done in 0.000586796 secs using 99.86% CPU
+Optimizing NNI: done in 0.000563982 secs using 99.83% CPU
+BETTER TREE FOUND at iteration 13: -667.319
+Optimizing NNI: done in 0.000541149 secs using 99.79% CPU
+BETTER TREE FOUND at iteration 14: -667.319
+Optimizing NNI: done in 0.000550627 secs
+Optimizing NNI: done in 0.000536621 secs using 41% CPU
+Optimizing NNI: done in 0.000570264 secs using 99.78% CPU
+Optimizing NNI: done in 0.000611872 secs using 99.69% CPU
+Optimizing NNI: done in 0.000581445 secs using 97% CPU
+Optimizing NNI: done in 0.000601262 secs using 99.79% CPU
+Iteration 20 / LogL: -667.319 / Time: 0h:0m:0s
+Finish initializing candidate tree set (20)
+Current best tree score: -667.319 / CPU time: 0.059
+Number of iterations: 20
+--------------------------------------------------------------------
+|               OPTIMIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Optimizing NNI: done in 0.00134074 secs using 99.35% CPU
+Optimizing NNI: done in 0.000758749 secs using 99.11% CPU
+Optimizing NNI: done in 0.000368644 secs using 99.28% CPU
+Optimizing NNI: done in 0.00118484 secs using 99.93% CPU
+Optimizing NNI: done in 0.000346834 secs using 99.76% CPU
+Optimizing NNI: done in 0.00117798 secs using 99.92% CPU
+Optimizing NNI: done in 0.000798614 secs using 99.67% CPU
+Optimizing NNI: done in 0.00035576 secs using 99.79% CPU
+Optimizing NNI: done in 0.000346773 secs using 99.78% CPU
+Optimizing NNI: done in 0.000790299 secs using 99.84% CPU
+Iteration 30 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000343177 secs using 99.66% CPU
+Optimizing NNI: done in 0.000714375 secs using 99.81% CPU
+Optimizing NNI: done in 0.00106988 secs using 99.92% CPU
+Optimizing NNI: done in 0.000829973 secs using 99.88% CPU
+Optimizing NNI: done in 0.000333128 secs using 99.66% CPU
+Optimizing NNI: done in 0.000788896 secs
+Optimizing NNI: done in 0.000364797 secs using 84.16% CPU
+Optimizing NNI: done in 0.00119208 secs using 99.83% CPU
+Optimizing NNI: done in 0.00075415 secs using 99.85% CPU
+Optimizing NNI: done in 0.000856874 secs
+Iteration 40 / LogL: -667.321 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000758088 secs using 43.66% CPU
+Optimizing NNI: done in 0.000691823 secs using 96.41% CPU
+Optimizing NNI: done in 0.000343397 secs using 99.59% CPU
+Optimizing NNI: done in 0.00147757 secs using 99.96% CPU
+Optimizing NNI: done in 0.00105325 secs using 99.88% CPU
+Optimizing NNI: done in 0.000789788 secs using 99.9% CPU
+Optimizing NNI: done in 0.000745214 secs using 99.84% CPU
+Optimizing NNI: done in 0.000802211 secs using 99.85% CPU
+Optimizing NNI: done in 0.000730427 secs using 99.94% CPU
+Optimizing NNI: done in 0.000763078 secs using 99.99% CPU
+Iteration 50 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00090765 secs using 99.82% CPU
+Optimizing NNI: done in 0.000344679 secs using 99.8% CPU
+Optimizing NNI: done in 0.000882542 secs using 99.94% CPU
+Optimizing NNI: done in 0.0016301 secs using 38.71% CPU
+Optimizing NNI: done in 0.000741506 secs using 99.93% CPU
+Optimizing NNI: done in 0.00078036 secs using 99.83% CPU
+Optimizing NNI: done in 0.00090244 secs using 99.84% CPU
+Optimizing NNI: done in 0.000764611 secs using 99.79% CPU
+Optimizing NNI: done in 0.000351702 secs using 99.8% CPU
+Optimizing NNI: done in 0.000375086 secs using 99.71% CPU
+Iteration 60 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00070603 secs using 99.85% CPU
+Optimizing NNI: done in 0.000756785 secs using 99.9% CPU
+Optimizing NNI: done in 0.0007115 secs using 99.93% CPU
+Optimizing NNI: done in 0.000730345 secs using 99.82% CPU
+Optimizing NNI: done in 0.000788084 secs using 99.99% CPU
+Optimizing NNI: done in 0.000845403 secs using 99.83% CPU
+Optimizing NNI: done in 0.000362984 secs using 99.73% CPU
+Optimizing NNI: done in 0.00156261 secs using 99.9% CPU
+Optimizing NNI: done in 0.000876562 secs
+Optimizing NNI: done in 0.000346553 secs using 92.63% CPU
+Iteration 70 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000326074 secs using 92.92% CPU
+Optimizing NNI: done in 0.00118572 secs using 99.77% CPU
+Optimizing NNI: done in 0.00080144 secs
+Optimizing NNI: done in 0.000655575 secs using 14.34% CPU
+Optimizing NNI: done in 0.000726329 secs using 99.95% CPU
+Optimizing NNI: done in 0.000344188 secs
+Optimizing NNI: done in 0.000760743 secs using 43.12% CPU
+Optimizing NNI: done in 0.00153436 secs using 97.3% CPU
+Optimizing NNI: done in 0.00033425 secs using 99.63% CPU
+Optimizing NNI: done in 0.000330071 secs using 99.68% CPU
+Iteration 80 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000486075 secs using 99.78% CPU
+Optimizing NNI: done in 0.000779359 secs using 99.83% CPU
+Optimizing NNI: done in 0.00106454 secs using 99.86% CPU
+Optimizing NNI: done in 0.000331564 secs using 99.53% CPU
+Optimizing NNI: done in 0.000873555 secs using 99.82% CPU
+Optimizing NNI: done in 0.000833079 secs using 99.87% CPU
+Optimizing NNI: done in 0.000726369 secs using 99.81% CPU
+Optimizing NNI: done in 0.00141428 secs using 99.91% CPU
+Optimizing NNI: done in 0.000380376 secs using 99.64% CPU
+Optimizing NNI: done in 0.000736337 secs using 98.73% CPU
+Iteration 90 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000653691 secs using 99.89% CPU
+Optimizing NNI: done in 0.000725557 secs using 99.79% CPU
+Optimizing NNI: done in 0.000874427 secs using 99.84% CPU
+Optimizing NNI: done in 0.000835223 secs using 99.97% CPU
+Optimizing NNI: done in 0.000680301 secs using 99.96% CPU
+Optimizing NNI: done in 0.000755083 secs using 99.86% CPU
+Optimizing NNI: done in 0.001132 secs using 11.84% CPU
+Optimizing NNI: done in 0.000330262 secs using 99.62% CPU
+Optimizing NNI: done in 0.000321756 secs using 99.45% CPU
+Optimizing NNI: done in 0.000781652 secs using 99.79% CPU
+Iteration 100 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00089204 secs using 99.88% CPU
+Optimizing NNI: done in 0.00118078 secs using 69.11% CPU
+Optimizing NNI: done in 0.000814935 secs using 44.79% CPU
+Optimizing NNI: done in 0.000769389 secs using 97.35% CPU
+Optimizing NNI: done in 0.00108522 secs using 99.89% CPU
+Optimizing NNI: done in 0.000333828 secs using 98.85% CPU
+Optimizing NNI: done in 0.000667467 secs
+Optimizing NNI: done in 0.000810907 secs
+Optimizing NNI: done in 0.00150203 secs using 85.08% CPU
+Optimizing NNI: done in 0.000785881 secs using 99.89% CPU
+Iteration 110 / LogL: -677.602 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000341403 secs using 99.59% CPU
+Optimizing NNI: done in 0.000831426 secs using 99.83% CPU
+Optimizing NNI: done in 0.000757998 secs using 99.87% CPU
+Optimizing NNI: done in 0.00115071 secs using 13.64% CPU
+Optimizing NNI: done in 0.000726449 secs using 99.8% CPU
+TREE SEARCH COMPLETED AFTER 115 ITERATIONS / Time: 0h:0m:0s
+
+--------------------------------------------------------------------
+|                    FINALIZING TREE SEARCH                        |
+--------------------------------------------------------------------
+Performs final model parameters optimization
+Estimate model parameters (epsilon = 0.010)
+1. Initial log-likelihood: -667.319
+Optimal log-likelihood: -667.319
+Rate parameters:  A-C: 1.00000  A-G: 1.00000  A-T: 1.00000  C-G: 1.00000  C-T: 1.00000  G-T: 1.00000
+Base frequencies:  A: 0.250  C: 0.250  G: 0.250  T: 0.250
+Parameters optimization took 1 rounds (0.000 sec)
+BEST SCORE FOUND : -667.319
+Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.state
+Total tree length: 0.082
+
+Total number of iterations: 115
+CPU time used for tree search: 0.140 sec (0h:0m:0s)
+Wall-clock time used for tree search: 0.147 sec (0h:0m:0s)
+Total CPU time used: 0.274 sec (0h:0m:0s)
+Total wall-clock time used: 0.296 sec (0h:0m:0s)
+
+Analysis results written to: 
+  IQ-TREE report:                /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree
+  Maximum-likelihood tree:       /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile
+  Likelihood distances:          /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist
+  Ancestral state:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.state
+  Screen log file:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.log
+
+Date and Time: Sat Aug 16 23:08:16 2025

test/ref-results/partition-new-simu/iqtree/iclust-0/out.bionj

@@ -0,0 +1 @@
+(((((XnaiveX:5e-07,d024e5cab0:5e-07):-6.1993063e-08,822801f8ab:5.6199303e-07):0.005789578,5fb484a8a6:0.014719013):-0.002933681,(ee25049b92:0.00585389,9c3cedb840:0.0028671236):0.014806692):-4.6566129e-09,(18f4019708:0.014717257,((648902c3e5:5e-07,8024ed1a22:5e-07):-8.4655255e-08,f47122f1f5:5.8465525e-07):0.0057913344):1.321733e-05,(308de1d739:0.011743682,efdea248af:0.0087654078):1.4826655e-06);