partis-bcr 1.0.8.post1.dev1__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

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

@@ -1 +1 @@
-(XnaiveX:0.0000010000,13de8675ec:0.0000010000,(((20a0129b57:0.0027295720,97366cf0d8:0.0027295728)Node4:0.0000010000,4233d708fe:0.0000010000)Node3:0.0000010000,(31e052ee14:0.0000010000,(33aaa62e12:0.0000010000,91796617a0:0.0000010000)Node6:0.0000010000)Node5:0.0000010000)Node2:0.0000010000)Node1;
+(XnaiveX:0.0000010000,13de8675ec:0.0000010000,(((((20a0129b57:0.0027294000,97366cf0d8:0.0027294000)Node6:0.0000010000,33aaa62e12:0.0000010000)Node5:0.0000010000,31e052ee14:0.0000010000)Node4:0.0000010000,91796617a0:0.0000010000)Node3:0.0000010000,4233d708fe:0.0000010000)Node2:0.0000010000)Node1;

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

@@ -6,21 +6,21 @@ 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-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
-Seed:    617209 (Using SPRNG - Scalable Parallel Random Number Generator)
-Time:    Sat Aug 16 23:08:16 2025
+Seed:    801199 (Using SPRNG - Scalable Parallel Random Number Generator)
+Time:    Mon Aug 18 15:31:52 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-2/input-seqs.fa ... Fasta format detected
-Reading fasta file: done in 0.000877834 secs
+Reading fasta file: done in 7.8927e-05 secs using 98.83% CPU
 Alignment most likely contains DNA/RNA sequences
-Constructing alignment: done in 0.000427405 secs using 25.03% CPU
+Constructing alignment: done in 0.000400938 secs using 36.17% CPU
 Alignment has 8 sequences with 379 columns, 21 distinct patterns
 4 parsimony-informative, 17 singleton sites, 358 constant sites
             Gap/Ambiguity  Composition  p-value
-Analyzing sequences: done in 8.636e-06 secs using 92.64% CPU
+Analyzing sequences: done in 8.516e-06 secs
    1  XnaiveX       0.00%    passed     99.90%
    2  162cb1691f    0.00%    passed     99.94%
    3  17f57acf2e    0.00%    passed     99.94%
@@ -36,15 +36,15 @@ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000
 Perform fast likelihood tree search using GTR+I+G model...
 Estimate model parameters (epsilon = 5.000)
 Perform nearest neighbor interchange...
-Optimizing NNI: done in 0.000489232 secs using 66.84% CPU
+Optimizing NNI: done in 0.000480928 secs using 93.36% CPU
 Estimate model parameters (epsilon = 1.000)
 1. Initial log-likelihood: -668.906
 Optimal log-likelihood: -668.900
-Rate parameters:  A-C: 0.58043  A-G: 0.19277  A-T: 0.25950  C-G: 0.74204  C-T: 1.19038  G-T: 1.00000
+Rate parameters:  A-C: 0.58043  A-G: 0.19277  A-T: 0.25950  C-G: 0.74204  C-T: 1.19039  G-T: 1.00000
 Base frequencies:  A: 0.219  C: 0.280  G: 0.285  T: 0.216
 Proportion of invariable sites: 0.470
 Gamma shape alpha: 998.448
-Parameters optimization took 1 rounds (0.002 sec)
+Parameters optimization took 1 rounds (0.001 sec)
 Time for fast ML tree search: 0.004 seconds
 
 NOTE: ModelFinder requires 0 MB RAM!
@@ -56,7 +56,7 @@ ModelFinder will test up to 968 DNA models (sample size: 379 epsilon: 0.100) ...
   4  JC+I+G4       674.940      15  1379.879     1381.201     1438.942
   5  JC+R2         674.481      15  1378.963     1380.285     1438.026
   6  JC+R3         674.481      17  1382.962     1384.658     1449.900
- 14  JC+I+R2       674.942      16  1381.884     1383.387     1444.884
+ 14  JC+I+R2       674.942      16  1381.884     1383.386     1444.884
  15  JC+I+R3       674.935      18  1385.870     1387.770     1456.746
  23  JC            674.481      13  1374.962     1375.959     1426.150
  24  JC+I          674.481      14  1376.962     1378.116     1432.088
@@ -193,8 +193,8 @@ 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-2/out.model.gz
-CPU time for ModelFinder: 0.105 seconds (0h:0m:0s)
-Wall-clock time for ModelFinder: 0.108 seconds (0h:0m:0s)
+CPU time for ModelFinder: 0.066 seconds (0h:0m:0s)
+Wall-clock time for ModelFinder: 0.075 seconds (0h:0m:0s)
 
 NOTE: 0 MB RAM (0 GB) is required!
 Estimate model parameters (epsilon = 0.100)
@@ -205,145 +205,144 @@ 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 0.000171813 secs using 99.53% CPU
-Computing ML distances took 0.000190 sec (of wall-clock time) 0.000193 sec (of CPU time)
-Setting up auxiliary I and S matrices: done in 2.6009e-05 secs using 92.28% CPU
-Constructing RapidNJ tree: done in 3.2872e-05 secs using 91.26% CPU
-Computing RapidNJ tree took 0.000080 sec (of wall-clock time) 0.000076 sec (of CPU time)
+Calculating distance matrix: done in 0.000124302 secs using 89.3% CPU
+Computing ML distances took 0.000140 sec (of wall-clock time) 0.000127 sec (of CPU time)
+Setting up auxiliary I and S matrices: done in 2.667e-05 secs using 86.24% CPU
+Constructing RapidNJ tree: done in 3.232e-05 secs using 86.63% CPU
+Computing RapidNJ tree took 0.000079 sec (of wall-clock time) 0.000071 sec (of CPU time)
 Log-likelihood of RapidNJ tree: -680.247
 --------------------------------------------------------------------
 |             INITIALIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Generating 98 parsimony trees... 0.021 second
-Computing log-likelihood of 72 initial trees ... 0.009 seconds
+Generating 98 parsimony trees... 0.015 second
+Computing log-likelihood of 66 initial trees ... 0.005 seconds
 Current best score: -674.481
 
 Do NNI search on 20 best initial trees
-Optimizing NNI: done in 0.000353666 secs using 99.53% CPU
+Optimizing NNI: done in 0.000217055 secs using 90.76% CPU
 Estimate model parameters (epsilon = 0.100)
 BETTER TREE FOUND at iteration 1: -674.481
-Optimizing NNI: done in 0.000267734 secs using 99.35% CPU
-Optimizing NNI: done in 0.000343177 secs using 99.37% CPU
-Optimizing NNI: done in 0.000320664 secs using 99.48% CPU
-Optimizing NNI: done in 0.000338298 secs using 99.62% CPU
-Optimizing NNI: done in 0.000331074 secs using 99.68% CPU
-Optimizing NNI: done in 0.000309172 secs using 99.62% CPU
-Optimizing NNI: done in 0.000346473 secs using 99.57% CPU
-Optimizing NNI: done in 0.000333158 secs using 99.65% CPU
-Optimizing NNI: done in 0.00070038 secs using 99.8% CPU
+Optimizing NNI: done in 0.000177983 secs
+Optimizing NNI: done in 0.000207597 secs
+Optimizing NNI: done in 0.000200935 secs
+Optimizing NNI: done in 0.000228316 secs using 91.1% CPU
+Optimizing NNI: done in 0.000206866 secs using 89.91% CPU
+Optimizing NNI: done in 0.000225581 secs using 89.99% CPU
+Optimizing NNI: done in 0.000206025 secs using 90.28% CPU
+Optimizing NNI: done in 0.000223937 secs using 99.58% CPU
+Optimizing NNI: done in 0.000442726 secs using 99.84% CPU
 Iteration 10 / LogL: -674.481 / Time: 0h:0m:0s
-Optimizing NNI: done in 0.000697384 secs using 99.8% CPU
-Optimizing NNI: done in 0.000297149 secs using 99.61% CPU
-Optimizing NNI: done in 0.000684049 secs using 99.85% CPU
-Optimizing NNI: done in 0.000706851 secs using 99.88% CPU
-Optimizing NNI: done in 0.000688758 secs using 99.74% CPU
-Optimizing NNI: done in 0.000666826 secs using 99.88% CPU
-Optimizing NNI: done in 0.00032399 secs using 99.69% CPU
-Optimizing NNI: done in 0.000901418 secs using 99.84% CPU
-Optimizing NNI: done in 0.000308531 secs using 99.5% CPU
-Optimizing NNI: done in 0.000606072 secs using 99.66% CPU
+Optimizing NNI: done in 0.000450561 secs
+Optimizing NNI: done in 0.000436274 secs
+Optimizing NNI: done in 0.000435944 secs using 51.38% CPU
+Optimizing NNI: done in 0.000434852 secs using 99.8% CPU
+Optimizing NNI: done in 0.000196477 secs using 99.25% CPU
+Optimizing NNI: done in 0.000475437 secs using 99.7% CPU
+Optimizing NNI: done in 0.000667235 secs using 99.96% CPU
+Optimizing NNI: done in 0.000832193 secs using 99.86% CPU
+Optimizing NNI: done in 0.000882326 secs using 99.85% CPU
+Optimizing NNI: done in 0.000560486 secs using 99.91% CPU
 Iteration 20 / LogL: -674.482 / Time: 0h:0m:0s
-Finish initializing candidate tree set (7)
-Current best tree score: -674.481 / CPU time: 0.042
+Finish initializing candidate tree set (5)
+Current best tree score: -674.481 / CPU time: 0.029
 Number of iterations: 20
 --------------------------------------------------------------------
 |               OPTIMIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Optimizing NNI: done in 0.000697163 secs using 99.69% CPU
-Optimizing NNI: done in 0.000681163 secs using 98.51% CPU
+Optimizing NNI: done in 0.000679819 secs using 99.73% CPU
+Optimizing NNI: done in 0.000644582 secs
+Optimizing NNI: done in 0.000658519 secs using 70.16% CPU
+Optimizing NNI: done in 0.000650203 secs using 99.81% CPU
+Optimizing NNI: done in 0.000673918 secs using 99.86% CPU
 UPDATE BEST LOG-LIKELIHOOD: -674.481
-Optimizing NNI: done in 0.0006056 secs
-UPDATE BEST LOG-LIKELIHOOD: -674.481
-Optimizing NNI: done in 0.000208623 secs
-UPDATE BEST LOG-LIKELIHOOD: -674.481
-Optimizing NNI: done in 0.000528726 secs using 84.54% CPU
-Optimizing NNI: done in 0.000453484 secs using 93.72% CPU
-Optimizing NNI: done in 0.00043496 secs
-Optimizing NNI: done in 0.000415462 secs using 15.16% CPU
-Optimizing NNI: done in 0.000422236 secs using 99.71% CPU
-Optimizing NNI: done in 0.000670524 secs
-Iteration 30 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000465767 secs using 0.6441% CPU
-Optimizing NNI: done in 0.000492578 secs
-Optimizing NNI: done in 0.000460006 secs
-Optimizing NNI: done in 0.000169329 secs
-Optimizing NNI: done in 0.000384344 secs
-Optimizing NNI: done in 0.000184748 secs using 89.85% CPU
-Optimizing NNI: done in 0.000423297 secs using 91.43% CPU
-Optimizing NNI: done in 0.000498488 secs
-Optimizing NNI: done in 0.000436763 secs
-Optimizing NNI: done in 0.000451471 secs
-Iteration 40 / LogL: -680.246 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000448715 secs
-Optimizing NNI: done in 0.000414591 secs using 99.86% CPU
-Optimizing NNI: done in 0.000444667 secs using 98.05% CPU
-Optimizing NNI: done in 0.000416995 secs using 99.76% CPU
-Optimizing NNI: done in 0.000489281 secs using 99.74% CPU
-Optimizing NNI: done in 0.000629957 secs using 99.85% CPU
-Optimizing NNI: done in 0.000478532 secs using 99.89% CPU
-Optimizing NNI: done in 0.000695891 secs using 99.15% CPU
-Optimizing NNI: done in 0.000615019 secs using 99.83% CPU
-Optimizing NNI: done in 0.000458724 secs using 99.84% CPU
+Optimizing NNI: done in 0.00122079 secs using 99.94% CPU
+Optimizing NNI: done in 0.000625246 secs using 99.8% CPU
+Optimizing NNI: done in 0.000833606 secs using 99.93% CPU
+Optimizing NNI: done in 0.000204742 secs using 99.64% CPU
+Optimizing NNI: done in 0.000206194 secs using 99.42% CPU
+Iteration 30 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000249656 secs using 99.34% CPU
+Optimizing NNI: done in 0.000666033 secs using 99.84% CPU
+Optimizing NNI: done in 0.000633072 secs using 99.83% CPU
+Optimizing NNI: done in 0.000508219 secs
+Optimizing NNI: done in 0.000685609 secs using 45.8% CPU
+Optimizing NNI: done in 0.000708683 secs using 99.48% CPU
+Optimizing NNI: done in 0.000466461 secs using 99.9% CPU
+Optimizing NNI: done in 0.000424231 secs using 99.71% CPU
+Optimizing NNI: done in 0.000520872 secs using 99.64% CPU
+Optimizing NNI: done in 0.000988114 secs using 1.214% CPU
+Iteration 40 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000623232 secs using 99.8% CPU
+Optimizing NNI: done in 0.000663117 secs using 99.83% CPU
+Optimizing NNI: done in 0.00054122 secs using 99.77% CPU
+Optimizing NNI: done in 0.000631208 secs using 99.81% CPU
+Optimizing NNI: done in 0.00065394 secs using 99.86% CPU
+Optimizing NNI: done in 0.000645064 secs using 99.84% CPU
+Optimizing NNI: done in 0.000288789 secs using 98.34% CPU
+Optimizing NNI: done in 0.000603405 secs using 99.77% CPU
+Optimizing NNI: done in 0.000654271 secs
+Optimizing NNI: done in 0.000659972 secs using 81.82% CPU
 Iteration 50 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000480496 secs using 99.69% CPU
-Optimizing NNI: done in 0.000480025 secs using 99.79% CPU
-Optimizing NNI: done in 0.000470066 secs using 99.77% CPU
-Optimizing NNI: done in 0.000434528 secs using 99.88% CPU
-Optimizing NNI: done in 0.000486737 secs
-Optimizing NNI: done in 0.000423918 secs using 5.426% CPU
-Optimizing NNI: done in 0.000419811 secs using 99.81% CPU
-Optimizing NNI: done in 0.000387069 secs using 99.21% CPU
-Optimizing NNI: done in 0.000581656 secs using 99.72% CPU
-Optimizing NNI: done in 0.000437735 secs using 98.92% CPU
-Iteration 60 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000426413 secs using 99.67% CPU
-Optimizing NNI: done in 0.000671686 secs
-Optimizing NNI: done in 0.000690701 secs
-Optimizing NNI: done in 0.000205397 secs
-Optimizing NNI: done in 0.000484994 secs using 83.09% CPU
-Optimizing NNI: done in 0.000719526 secs using 92.98% CPU
-Optimizing NNI: done in 0.000425782 secs using 99.82% CPU
-Optimizing NNI: done in 0.000510622 secs using 96.74% CPU
-Optimizing NNI: done in 0.000726909 secs using 99.87% CPU
-Optimizing NNI: done in 0.000933598 secs using 99.94% CPU
+Optimizing NNI: done in 0.000421727 secs using 89.16% CPU
+Optimizing NNI: done in 0.000464126 secs using 99.76% CPU
+Optimizing NNI: done in 0.000668187 secs
+Optimizing NNI: done in 0.000209701 secs
+Optimizing NNI: done in 0.000208549 secs using 32.61% CPU
+Optimizing NNI: done in 0.000460509 secs using 99.89% CPU
+Optimizing NNI: done in 0.000645956 secs using 99.85% CPU
+Optimizing NNI: done in 0.000427648 secs using 99.85% CPU
+UPDATE BEST LOG-LIKELIHOOD: -674.481
+Optimizing NNI: done in 0.000517596 secs using 99.69% CPU
+Optimizing NNI: done in 0.000511264 secs using 99.56% CPU
+Iteration 60 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000703683 secs using 98.91% CPU
+Optimizing NNI: done in 0.000458335 secs using 99.71% CPU
+Optimizing NNI: done in 0.000451051 secs using 99.77% CPU
+Optimizing NNI: done in 0.000454178 secs using 99.74% CPU
+Optimizing NNI: done in 0.000536741 secs using 99.86% CPU
+Optimizing NNI: done in 0.00043974 secs using 99.83% CPU
+Optimizing NNI: done in 0.000646577 secs using 99.76% CPU
+Optimizing NNI: done in 0.000493791 secs using 99.84% CPU
+Optimizing NNI: done in 0.000204842 secs using 99.59% CPU
+Optimizing NNI: done in 0.000464186 secs
 Iteration 70 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000464304 secs using 99.72% CPU
-Optimizing NNI: done in 0.000424309 secs using 99.93% CPU
-Optimizing NNI: done in 0.000480495 secs using 99.69% CPU
-Optimizing NNI: done in 0.000672577 secs using 99.91% CPU
-Optimizing NNI: done in 0.000682015 secs using 99.85% CPU
-Optimizing NNI: done in 0.000653111 secs using 99.83% CPU
-Optimizing NNI: done in 0.000401807 secs using 99.8% CPU
-Optimizing NNI: done in 0.000668379 secs using 99.94% CPU
-Optimizing NNI: done in 0.000454627 secs using 99.64% CPU
-Optimizing NNI: done in 0.000450088 secs using 99.76% CPU
-Iteration 80 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.00020158 secs using 99.22% CPU
-Optimizing NNI: done in 0.000415042 secs using 99.75% CPU
-Optimizing NNI: done in 0.000427195 secs using 99.72% CPU
-Optimizing NNI: done in 0.000582096 secs using 99.81% CPU
-Optimizing NNI: done in 0.000463854 secs using 99.82% CPU
-Optimizing NNI: done in 0.000469805 secs using 99.83% CPU
-Optimizing NNI: done in 0.000657859 secs using 99.87% CPU
-Optimizing NNI: done in 0.000657339 secs using 99.8% CPU
-Optimizing NNI: done in 0.000474103 secs using 99.77% CPU
-Optimizing NNI: done in 0.000673439 secs using 99.93% CPU
-Iteration 90 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000193876 secs using 99.55% CPU
-Optimizing NNI: done in 0.000205647 secs using 99.2% CPU
-Optimizing NNI: done in 0.000439999 secs using 99.77% CPU
+Optimizing NNI: done in 0.00047201 secs
+Optimizing NNI: done in 0.00045498 secs using 98.47% CPU
+Optimizing NNI: done in 0.000373878 secs using 88.8% CPU
+Optimizing NNI: done in 0.000722138 secs using 99.84% CPU
+Optimizing NNI: done in 0.000205603 secs using 97.27% CPU
+Optimizing NNI: done in 0.00064866 secs using 99.9% CPU
+Optimizing NNI: done in 0.000501025 secs using 99.8% CPU
+Optimizing NNI: done in 0.000722497 secs using 99.79% CPU
+Optimizing NNI: done in 0.00043945 secs using 99.9% CPU
+Optimizing NNI: done in 0.000196998 secs using 99.49% CPU
 UPDATE BEST LOG-LIKELIHOOD: -674.481
-Optimizing NNI: done in 0.000688607 secs using 99.91% CPU
-Optimizing NNI: done in 0.000462341 secs using 99.71% CPU
-Optimizing NNI: done in 0.000466289 secs
-Optimizing NNI: done in 0.000434639 secs
+Iteration 80 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000201355 secs using 99.33% CPU
+Optimizing NNI: done in 0.000454559 secs using 99.66% CPU
+Optimizing NNI: done in 0.000518768 secs using 99.85% CPU
+Optimizing NNI: done in 0.000204713 secs using 99.16% CPU
+Optimizing NNI: done in 0.000481629 secs using 99.87% CPU
+Optimizing NNI: done in 0.000195625 secs using 99.68% CPU
+Optimizing NNI: done in 0.00043947 secs using 99.89% CPU
 UPDATE BEST LOG-LIKELIHOOD: -674.481
-Optimizing NNI: done in 0.000492878 secs using 99.82% CPU
-Optimizing NNI: done in 0.000201219 secs using 99.39% CPU
-Optimizing NNI: done in 0.000403871 secs using 94.34% CPU
-Iteration 100 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000428498 secs using 99.88% CPU
-Optimizing NNI: done in 0.000653541 secs using 99.76% CPU
+Optimizing NNI: done in 0.000517165 secs using 99.77% CPU
+Optimizing NNI: done in 0.00049828 secs using 99.74% CPU
+Optimizing NNI: done in 0.000421847 secs using 99.8% CPU
+Iteration 90 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000205774 secs using 99.62% CPU
+Optimizing NNI: done in 0.000674708 secs
+Optimizing NNI: done in 0.000457274 secs
+Optimizing NNI: done in 0.000385929 secs using 99.76% CPU
+Optimizing NNI: done in 0.000474164 secs using 99.75% CPU
+Optimizing NNI: done in 0.000494753 secs using 99.65% CPU
+Optimizing NNI: done in 0.000419853 secs
+Optimizing NNI: done in 0.000715395 secs using 35.92% CPU
+Optimizing NNI: done in 0.000683946 secs using 99.57% CPU
+Optimizing NNI: done in 0.000729591 secs using 99.92% CPU
+Iteration 100 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00022019 secs using 99.46% CPU
+Optimizing NNI: done in 0.000455971 secs using 99.79% CPU
 TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
 
 --------------------------------------------------------------------
@@ -361,10 +360,10 @@ Ancestral state probabilities printed to /home/runner/work/partis/partis/test/re
 Total tree length: 0.056
 
 Total number of iterations: 102
-CPU time used for tree search: 0.087 sec (0h:0m:0s)
-Wall-clock time used for tree search: 0.092 sec (0h:0m:0s)
-Total CPU time used: 0.204 sec (0h:0m:0s)
-Total wall-clock time used: 0.215 sec (0h:0m:0s)
+CPU time used for tree search: 0.080 sec (0h:0m:0s)
+Wall-clock time used for tree search: 0.082 sec (0h:0m:0s)
+Total CPU time used: 0.154 sec (0h:0m:0s)
+Total wall-clock time used: 0.169 sec (0h:0m:0s)
 
 Analysis results written to: 
   IQ-TREE report:                /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree
@@ -373,4 +372,4 @@ Analysis results written to:
   Ancestral state:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
   Screen log file:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.log
 
-Date and Time: Sat Aug 16 23:08:16 2025
+Date and Time: Mon Aug 18 15:31:52 2025

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

@@ -2,7 +2,7 @@ IQ-TREE 3.0.1 built May  5 2025
 
 Input file name: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa
 Type of analysis: ModelFinder + tree reconstruction
-Random seed number: 617209
+Random seed number: 801199
 
 REFERENCES
 ----------
@@ -73,9 +73,9 @@ HKY+I              -674.481    1378.962 -  0.00384    1380.284 -  0.00424    143
 K2P+I              -674.481    1378.962 -  0.00384    1380.284 -  0.00424    1438.025 - 0.000731
 K2P+I              -674.481    1378.962 -  0.00384    1380.284 -  0.00424    1438.025 - 0.000731
 JC+R2              -674.481    1378.963 -  0.00384    1380.285 -  0.00424    1438.026 - 0.000731
-K2P+G4             -674.481    1378.963 -  0.00384    1380.285 -  0.00423    1438.026 - 0.000731
 HKY+G4             -674.481    1378.963 -  0.00384    1380.285 -  0.00423    1438.026 - 0.000731
 K2P+G4             -674.481    1378.963 -  0.00384    1380.285 -  0.00423    1438.026 - 0.000731
+K2P+G4             -674.481    1378.963 -  0.00384    1380.285 -  0.00423    1438.026 - 0.000731
 JC+I+G4            -674.940    1379.879 -  0.00243    1381.201 -  0.00268    1438.942 - 0.000462
 TIM                -672.315    1376.630 -   0.0123    1378.133 -   0.0124    1439.630 - 0.000328
 TIMe               -672.315    1376.630 -   0.0123    1378.133 -   0.0124    1439.630 - 0.000328
@@ -86,9 +86,9 @@ TIM3e              -672.415    1376.831 -   0.0111    1378.333 -   0.0112    143
 TN+I               -672.458    1376.916 -   0.0107    1378.419 -   0.0108    1439.917 - 0.000284
 TNe+I              -672.458    1376.916 -   0.0107    1378.419 -   0.0108    1439.917 - 0.000284
 TNe+I              -672.458    1376.916 -   0.0107    1378.419 -   0.0108    1439.917 - 0.000284
-TNe+G4             -672.458    1376.917 -   0.0107    1378.420 -   0.0108    1439.917 - 0.000284
 TN+G4              -672.458    1376.917 -   0.0107    1378.420 -   0.0108    1439.917 - 0.000284
 TNe+G4             -672.458    1376.917 -   0.0107    1378.420 -   0.0108    1439.917 - 0.000284
+TNe+G4             -672.458    1376.917 -   0.0107    1378.420 -   0.0108    1439.917 - 0.000284
 TPM2u+I            -673.519    1379.038 -  0.00369    1380.541 -  0.00373    1442.038 - 9.83e-05
 TPM2+I             -673.519    1379.038 -  0.00369    1380.541 -  0.00373    1442.039 - 9.82e-05
 TPM2+I             -673.519    1379.038 -  0.00369    1380.541 -  0.00373    1442.039 - 9.82e-05
@@ -116,7 +116,7 @@ TIM2e+I            -671.494    1376.988 -   0.0103    1378.683 -  0.00943    144
 TIM2+G4            -671.494    1376.989 -   0.0103    1378.684 -  0.00943    1443.927 - 3.82e-05
 TIM2e+G4           -671.494    1376.989 -   0.0103    1378.684 -  0.00943    1443.927 - 3.82e-05
 TIM2e+G4           -671.494    1376.989 -   0.0103    1378.684 -  0.00943    1443.927 - 3.82e-05
-JC+I+R2            -674.942    1381.884 -  0.00089    1383.387 - 0.000898    1444.884 - 2.37e-05
+JC+I+R2            -674.942    1381.884 -  0.00089    1383.386 - 0.000898    1444.884 - 2.37e-05
 TIM+I              -672.315    1378.630 -  0.00453    1380.325 -  0.00415    1445.568 - 1.68e-05
 TIMe+I             -672.315    1378.630 -  0.00453    1380.325 -  0.00415    1445.568 - 1.68e-05
 TIMe+I             -672.315    1378.630 -  0.00453    1380.325 -  0.00415    1445.568 - 1.68e-05
@@ -222,7 +222,7 @@ Corrected Akaike information criterion (AICc) score: 1375.9593
 Bayesian information criterion (BIC) score: 1426.1500
 
 Total tree length (sum of branch lengths): 0.0557
-Sum of internal branch lengths: 0.0106 (19.0067% of tree length)
+Sum of internal branch lengths: 0.0106 (19.0068% of tree length)
 
 WARNING: 2 near-zero internal branches (<0.0026) should be treated with caution
          Such branches are denoted by '**' in the figure below
@@ -231,15 +231,15 @@ NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
 
 +--------XnaiveX
 | (Node1)
-|                                 +------------------162cb1691f
-|              +------------------| (Node5)
-|              |                  +--------17f57acf2e
-|           +**| (Node4)
-|           |  |        +------------------73431a9b10
-|           |  +--------| (Node6)
-|           |           +**bf50fa2017
+|                              +------------------162cb1691f
+|           +------------------| (Node4)
+|           |                  +--------17f57acf2e
 |  +--------| (Node3)
-|  |        +------------------948b83fb4d
+|  |        |           +------------------73431a9b10
+|  |        |  +--------| (Node6)
+|  |        |  |        +**bf50fa2017
+|  |        +**| (Node5)
+|  |           +------------------948b83fb4d
 +**| (Node2)
 |  +----------------------------73d6c6e558
 |
@@ -247,7 +247,7 @@ NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
 
 Tree in newick format:
 
-(XnaiveX:0.0026431745,((((162cb1691f:0.0053051772,17f57acf2e:0.0026431497)Node5:0.0053051594,(73431a9b10:0.0052956972,bf50fa2017:0.0000010000)Node6:0.0026431782)Node4:0.0000010000,948b83fb4d:0.0052956972)Node3:0.0026431908,73d6c6e558:0.0079576343)Node2:0.0000010000,c8a90cc3d7:0.0160006069)Node1;
+(XnaiveX:0.0026431745,(((162cb1691f:0.0053051714,17f57acf2e:0.0026431546)Node4:0.0053051782,((73431a9b10:0.0052956972,bf50fa2017:0.0000010000)Node6:0.0026431789,948b83fb4d:0.0052957106)Node5:0.0000010000)Node3:0.0026431908,73d6c6e558:0.0079576343)Node2:0.0000010000,c8a90cc3d7:0.0160006069)Node1;
 
 ALISIM COMMAND
 --------------
@@ -268,7 +268,7 @@ For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
 TIME STAMP
 ----------
 
-Date and time: Sat Aug 16 23:08:16 2025
-Total CPU time used: 0.203751 seconds (0h:0m:0s)
-Total wall-clock time used: 0.216325 seconds (0h:0m:0s)
+Date and time: Mon Aug 18 15:31:52 2025
+Total CPU time used: 0.153605 seconds (0h:0m:0s)
+Total wall-clock time used: 0.170284 seconds (0h:0m:0s)