partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

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

@@ -0,0 +1,282 @@
+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-0/input-seqs.fa
+Type of analysis: ModelFinder + tree reconstruction
+Random seed number: 769287
+
+REFERENCES
+----------
+
+To cite IQ-TREE 3 please use:
+
+Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger,
+Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn,
+Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025)
+IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.
+Submitted.
+
+Please also cite the following paper(s) for the feature(s) that you used:
+
+To cite ModelFinder please use: 
+
+Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
+and Lars S Jermiin (2017) ModelFinder: Fast model selection for
+accurate phylogenetic estimates. Nature Methods, 14:587–589.
+https://doi.org/10.1038/nmeth.4285
+
+SEQUENCE ALIGNMENT
+------------------
+
+Input data: 12 sequences with 352 nucleotide sites
+Number of constant sites: 324 (= 92.0455% of all sites)
+Number of invariant (constant or ambiguous constant) sites: 324 (= 92.0455% of all sites)
+Number of parsimony informative sites: 8
+Number of distinct site patterns: 29
+
+ModelFinder
+-----------
+
+Best-fit model according to BIC: JC
+
+List of models sorted by BIC scores: 
+
+Model                  LogL         AIC      w-AIC        AICc     w-AICc         BIC      w-BIC
+JC                 -667.319    1376.639 -   0.0474    1379.439 +   0.0688    1457.775 +     0.28
+JC                 -667.319    1376.639 -   0.0474    1379.439 +   0.0688    1457.775 +     0.28
+F81                -667.320    1376.639 -   0.0474    1379.439 +   0.0687    1457.775 +     0.28
+HKY                -667.283    1378.566 -   0.0181    1381.642 -   0.0229    1463.566 -   0.0155
+K2P                -667.283    1378.566 -   0.0181    1381.642 -   0.0228    1463.566 -   0.0155
+K2P                -667.283    1378.566 -   0.0181    1381.642 -   0.0228    1463.566 -   0.0155
+JC+I               -667.319    1378.639 -   0.0174    1381.715 -    0.022    1463.639 -    0.015
+JC+I               -667.319    1378.639 -   0.0174    1381.715 -    0.022    1463.639 -    0.015
+F81+I              -667.320    1378.639 -   0.0174    1381.715 -    0.022    1463.639 -   0.0149
+JC+G4              -667.320    1378.641 -   0.0174    1381.717 -    0.022    1463.640 -   0.0149
+JC+G4              -667.320    1378.641 -   0.0174    1381.717 -    0.022    1463.640 -   0.0149
+F81+G4             -667.320    1378.641 -   0.0174    1381.717 -    0.022    1463.641 -   0.0149
+F81+F              -663.546    1375.093 +    0.103    1378.763 +   0.0964    1467.820 -  0.00185
+K3Pu               -666.838    1379.676 -   0.0104    1383.041 -   0.0114    1468.539 -  0.00129
+K3P                -666.838    1379.676 -   0.0104    1383.042 -   0.0113    1468.539 -  0.00129
+K3P                -666.838    1379.676 -   0.0104    1383.042 -   0.0113    1468.539 -  0.00129
+TPM2u              -667.114    1380.228 -  0.00788    1383.594 -  0.00861    1469.092 - 0.000978
+TPM2               -667.114    1380.228 -  0.00788    1383.594 -  0.00861    1469.092 - 0.000978
+TPM2               -667.114    1380.228 -  0.00788    1383.594 -  0.00861    1469.092 - 0.000978
+TN                 -667.185    1380.371 -  0.00734    1383.737 -  0.00802    1469.234 - 0.000911
+TNe                -667.185    1380.371 -  0.00734    1383.737 -  0.00802    1469.234 - 0.000911
+TNe                -667.185    1380.371 -  0.00734    1383.737 -  0.00802    1469.234 - 0.000911
+TPM3u              -667.241    1380.482 -  0.00694    1383.848 -  0.00758    1469.346 - 0.000862
+TPM3               -667.241    1380.482 -  0.00694    1383.848 -  0.00758    1469.346 - 0.000862
+TPM3               -667.241    1380.482 -  0.00694    1383.848 -  0.00758    1469.346 - 0.000862
+HKY+I              -667.283    1380.566 -  0.00665    1383.932 -  0.00727    1469.430 - 0.000826
+K2P+I              -667.283    1380.566 -  0.00665    1383.932 -  0.00727    1469.430 - 0.000826
+K2P+I              -667.283    1380.566 -  0.00665    1383.932 -  0.00727    1469.430 - 0.000826
+HKY+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
+K2P+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
+K2P+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
+JC+R2              -667.320    1380.640 -  0.00641    1384.006 -  0.00701    1469.503 - 0.000796
+JC+I+G4            -668.194    1382.388 -  0.00268    1385.753 -  0.00292    1471.251 - 0.000332
+HKY+F              -663.502    1377.004 -   0.0395    1380.992 -   0.0316    1473.595 - 0.000103
+F81+F+I            -663.546    1377.093 -   0.0378    1381.081 -   0.0303    1473.684 - 9.85e-05
+F81+F+G4           -663.547    1377.095 -   0.0377    1381.082 -   0.0302    1473.685 - 9.84e-05
+TIM                -666.740    1381.480 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
+TIMe               -666.740    1381.481 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
+TIMe               -666.740    1381.481 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
+K3Pu+I             -666.838    1381.676 -  0.00382    1385.345 -  0.00359    1474.403 - 6.88e-05
+K3P+I              -666.838    1381.676 -  0.00382    1385.345 -  0.00359    1474.403 - 6.88e-05
+K3P+I              -666.838    1381.676 -  0.00382    1385.345 -  0.00359    1474.403 - 6.88e-05
+K3Pu+G4            -666.839    1381.677 -  0.00382    1385.347 -  0.00358    1474.404 - 6.87e-05
+K3P+G4             -666.839    1381.677 -  0.00382    1385.347 -  0.00358    1474.405 - 6.87e-05
+K3P+G4             -666.839    1381.677 -  0.00382    1385.347 -  0.00358    1474.405 - 6.87e-05
+TIM2               -667.017    1382.033 -   0.0032    1385.703 -    0.003    1474.760 - 5.75e-05
+TIM2e              -667.017    1382.033 -   0.0032    1385.703 -    0.003    1474.760 - 5.75e-05
+TIM2e              -667.017    1382.033 -   0.0032    1385.703 -    0.003    1474.760 - 5.75e-05
+TPM2u+I            -667.114    1382.228 -   0.0029    1385.898 -  0.00272    1474.955 - 5.22e-05
+TPM2+I             -667.114    1382.228 -   0.0029    1385.898 -  0.00272    1474.955 - 5.22e-05
+TPM2+I             -667.114    1382.228 -   0.0029    1385.898 -  0.00272    1474.955 - 5.22e-05
+TPM2u+G4           -667.115    1382.230 -   0.0029    1385.900 -  0.00272    1474.957 - 5.21e-05
+TPM2+G4            -667.115    1382.230 -   0.0029    1385.900 -  0.00272    1474.957 - 5.21e-05
+TPM2+G4            -667.115    1382.230 -   0.0029    1385.900 -  0.00272    1474.957 - 5.21e-05
+TIM3               -667.144    1382.287 -  0.00281    1385.957 -  0.00264    1475.014 - 5.06e-05
+TIM3e              -667.144    1382.287 -  0.00281    1385.957 -  0.00264    1475.014 - 5.06e-05
+TIM3e              -667.144    1382.287 -  0.00281    1385.957 -  0.00264    1475.014 - 5.06e-05
+TN+I               -667.185    1382.371 -   0.0027    1386.041 -  0.00253    1475.098 - 4.86e-05
+TNe+I              -667.185    1382.371 -   0.0027    1386.041 -  0.00253    1475.098 - 4.86e-05
+TNe+I              -667.185    1382.371 -   0.0027    1386.041 -  0.00253    1475.098 - 4.86e-05
+TN+G4              -667.186    1382.373 -   0.0027    1386.042 -  0.00253    1475.100 - 4.85e-05
+TNe+G4             -667.186    1382.373 -   0.0027    1386.042 -  0.00253    1475.100 - 4.85e-05
+TNe+G4             -667.186    1382.373 -   0.0027    1386.042 -  0.00253    1475.100 - 4.85e-05
+TPM3u+I            -667.241    1382.482 -  0.00255    1386.152 -   0.0024    1475.209 - 4.59e-05
+TPM3+I             -667.241    1382.482 -  0.00255    1386.152 -   0.0024    1475.209 - 4.59e-05
+TPM3+I             -667.241    1382.482 -  0.00255    1386.152 -   0.0024    1475.209 - 4.59e-05
+TPM3u+G4           -667.242    1382.484 -  0.00255    1386.154 -  0.00239    1475.211 - 4.59e-05
+TPM3+G4            -667.242    1382.484 -  0.00255    1386.154 -  0.00239    1475.211 - 4.59e-05
+TPM3+G4            -667.242    1382.484 -  0.00255    1386.154 -  0.00239    1475.211 - 4.59e-05
+JC+I+R2            -668.203    1384.405 - 0.000976    1388.075 - 0.000916    1477.133 - 1.76e-05
+K3Pu+F             -662.995    1377.990 -   0.0241    1382.310 -   0.0164    1478.445 - 9.11e-06
+TN+F               -663.461    1378.923 -   0.0151    1383.243 -   0.0103    1479.377 - 5.72e-06
+TPM2u+F            -663.468    1378.936 -    0.015    1383.256 -   0.0102    1479.391 - 5.68e-06
+TPM3u+F            -663.499    1378.998 -   0.0146    1383.318 -  0.00989    1479.452 - 5.51e-06
+HKY+F+I            -663.502    1379.004 -   0.0145    1383.324 -  0.00985    1479.458 - 5.49e-06
+HKY+F+G4           -663.503    1379.006 -   0.0145    1383.326 -  0.00985    1479.460 - 5.48e-06
+TVM                -666.493    1382.987 -  0.00198    1386.975 -  0.00159    1479.578 - 5.17e-06
+TVMe               -666.493    1382.987 -  0.00198    1386.975 -  0.00159    1479.578 - 5.17e-06
+TVMe               -666.493    1382.987 -  0.00198    1386.975 -  0.00159    1479.578 - 5.17e-06
+TIM+I              -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
+TIMe+I             -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
+TIMe+I             -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
+TIM+G4             -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
+TIMe+G4            -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
+TIMe+G4            -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
+TIM2e+I            -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
+TIM2+I             -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
+TIM2e+I            -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
+TIM2+G4            -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
+TIM2e+G4           -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
+TIM2e+G4           -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
+TIM3+I             -667.143    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
+TIM3e+I            -667.144    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
+TIM3e+I            -667.144    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
+TIM3+G4            -667.144    1384.289 -  0.00103    1388.276 - 0.000828    1480.879 -  2.7e-06
+TIM3e+G4           -667.144    1384.289 -  0.00103    1388.276 - 0.000828    1480.879 -  2.7e-06
+TIM3e+G4           -667.144    1384.289 -  0.00103    1388.276 - 0.000828    1480.879 -  2.7e-06
+JC+R3              -667.320    1384.639 - 0.000868    1388.627 - 0.000695    1481.230 - 2.26e-06
+TIM+F              -662.954    1379.909 -  0.00924    1384.575 -  0.00527    1484.227 - 5.06e-07
+K3Pu+F+I           -662.995    1379.990 -  0.00887    1384.657 -  0.00506    1484.308 - 4.86e-07
+K3Pu+F+G4          -662.996    1379.992 -  0.00887    1384.658 -  0.00506    1484.310 - 4.85e-07
+TIM2+F             -663.427    1380.854 -  0.00576    1385.521 -  0.00329    1485.172 - 3.15e-07
+TIM3+F             -663.458    1380.916 -  0.00559    1385.583 -  0.00319    1485.234 - 3.06e-07
+TN+F+I             -663.461    1380.923 -  0.00557    1385.589 -  0.00317    1485.241 - 3.05e-07
+TN+F+G4            -663.462    1380.924 -  0.00556    1385.591 -  0.00317    1485.242 - 3.04e-07
+GTR                -666.396    1384.792 - 0.000804    1389.112 - 0.000545    1485.247 - 3.04e-07
+SYM                -666.396    1384.793 - 0.000804    1389.113 - 0.000545    1485.247 - 3.04e-07
+SYM                -666.396    1384.793 - 0.000804    1389.113 - 0.000545    1485.247 - 3.04e-07
+TPM2u+F+I          -663.468    1380.936 -  0.00553    1385.603 -  0.00315    1485.254 - 3.03e-07
+TPM2u+F+G4         -663.469    1380.938 -  0.00552    1385.604 -  0.00315    1485.256 - 3.02e-07
+TPM3u+F+I          -663.499    1380.998 -  0.00536    1385.664 -  0.00306    1485.316 - 2.93e-07
+TPM3u+F+G4         -663.500    1380.999 -  0.00536    1385.666 -  0.00306    1485.317 - 2.93e-07
+TVM+I              -666.493    1384.987 -  0.00073    1389.307 - 0.000495    1485.441 - 2.76e-07
+TVMe+I             -666.493    1384.987 -  0.00073    1389.307 - 0.000495    1485.441 - 2.76e-07
+TVMe+I             -666.493    1384.987 -  0.00073    1389.307 - 0.000495    1485.441 - 2.76e-07
+TVM+G4             -666.494    1384.988 - 0.000729    1389.308 - 0.000494    1485.443 - 2.75e-07
+TVMe+G4            -666.494    1384.988 - 0.000729    1389.308 - 0.000494    1485.443 - 2.75e-07
+TVMe+G4            -666.494    1384.988 - 0.000729    1389.308 - 0.000494    1485.443 - 2.75e-07
+JC+I+R3            -668.176    1388.352 - 0.000136    1392.672 -  9.2e-05    1488.806 - 5.12e-08
+TVM+F              -662.870    1381.740 -   0.0037    1386.768 -  0.00176    1489.922 - 2.93e-08
+TIM+F+I            -662.954    1381.909 -   0.0034    1386.937 -  0.00162    1490.090 -  2.7e-08
+TIM+F+G4           -662.955    1381.910 -   0.0034    1386.938 -  0.00162    1490.092 - 2.69e-08
+TIM2+F+I           -663.427    1382.854 -  0.00212    1387.882 -  0.00101    1491.036 - 1.68e-08
+TIM2+F+G4          -663.428    1382.856 -  0.00212    1387.884 -  0.00101    1491.037 - 1.68e-08
+TIM3+F+I           -663.458    1382.916 -  0.00205    1387.944 - 0.000978    1491.098 - 1.63e-08
+TIM3+F+G4          -663.459    1382.918 -  0.00205    1387.946 - 0.000977    1491.099 - 1.63e-08
+GTR+I              -666.396    1386.792 - 0.000296    1391.459 - 0.000169    1491.110 - 1.62e-08
+SYM+I              -666.396    1386.793 - 0.000296    1391.459 - 0.000169    1491.111 - 1.62e-08
+SYM+I              -666.396    1386.793 - 0.000296    1391.459 - 0.000169    1491.111 - 1.62e-08
+GTR+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.112 - 1.62e-08
+SYM+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.113 - 1.62e-08
+SYM+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.113 - 1.62e-08
+GTR+F              -662.829    1383.659 -  0.00142    1389.062 - 0.000559    1495.704 - 1.63e-09
+TVM+F+I            -662.870    1383.740 -  0.00136    1389.144 - 0.000537    1495.786 - 1.56e-09
+TVM+F+G4           -662.871    1383.742 -  0.00136    1389.146 - 0.000536    1495.787 - 1.56e-09
+GTR+F+I            -662.829    1385.659 - 0.000521    1391.453 - 0.000169    1501.568 - 8.68e-11
+GTR+F+G4           -662.830    1385.660 - 0.000521    1391.455 - 0.000169    1501.569 - 8.67e-11
+
+AIC, w-AIC   : Akaike information criterion scores and weights.
+AICc, w-AICc : Corrected AIC scores and weights.
+BIC, w-BIC   : Bayesian information criterion scores and weights.
+
+Plus signs denote the 95% confidence sets.
+Minus signs denote significant exclusion.
+
+SUBSTITUTION PROCESS
+--------------------
+
+Model of substitution: JC
+
+Rate parameter R:
+
+  A-C: 1.0000
+  A-G: 1.0000
+  A-T: 1.0000
+  C-G: 1.0000
+  C-T: 1.0000
+  G-T: 1.0000
+
+State frequencies: (equal frequencies)
+
+Rate matrix Q:
+
+  A        -1    0.3333    0.3333    0.3333
+  C    0.3333        -1    0.3333    0.3333
+  G    0.3333    0.3333        -1    0.3333
+  T    0.3333    0.3333    0.3333        -1
+
+Model of rate heterogeneity: Uniform
+
+MAXIMUM LIKELIHOOD TREE
+-----------------------
+
+Log-likelihood of the tree: -667.3194 (s.e. 29.3999)
+Unconstrained log-likelihood (without tree): -653.0565
+Number of free parameters (#branches + #model parameters): 21
+Akaike information criterion (AIC) score: 1376.6388
+Corrected Akaike information criterion (AICc) score: 1379.4388
+Bayesian information criterion (BIC) score: 1457.7751
+
+Total tree length (sum of branch lengths): 0.0816
+Sum of internal branch lengths: 0.0175 (21.4403% of tree length)
+
+WARNING: 6 near-zero internal branches (<0.0028) should be treated with caution
+         Such branches are denoted by '**' in the figure below
+
+NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
+
++**XnaiveX
+| (Node1)
+|                +------------------------------------18f4019708
+|  +-------------| (Node3)
+|  |             |     +----------------------------308de1d739
+|  |             |  +**| (Node5)
+|  |             |  |  +---------------------efdea248af
+|  |             +**| (Node4)
+|  |                |     +------------------------------------5fb484a8a6
+|  |                |  +**| (Node7)
+|  |                |  |  |                             +-------------ee25049b92
+|  |                |  |  +-----------------------------| (Node8)
+|  |                |  |                                +------9c3cedb840
+|  |                +**| (Node6)
+|  |                   |             +**648902c3e5
+|  |                   +-------------| (Node9)
+|  |                                 |  +**8024ed1a22
+|  |                                 +**| (Node10)
+|  |                                    +**f47122f1f5
++**| (Node2)
+|  +**d024e5cab0
+|
++**822801f8ab
+
+Tree in newick format:
+
+(XnaiveX:0.0000010000,((18f4019708:0.0145918999,((308de1d739:0.0116507178,efdea248af:0.0087210277)Node5:0.0000010000,((5fb484a8a6:0.0145918997,(ee25049b92:0.0058202340,9c3cedb840:0.0028896479)Node8:0.0116795079)Node7:0.0000010000,(648902c3e5:0.0000010000,(8024ed1a22:0.0000010000,f47122f1f5:0.0000010000)Node10:0.0000010000)Node9:0.0058027364)Node6:0.0000010000)Node4:0.0000010000)Node3:0.0058027364,d024e5cab0:0.0000010000)Node2:0.0000010000,822801f8ab:0.0000010000)Node1;
+
+ALISIM COMMAND
+--------------
+To simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis, you can use the following command:
+
+--alisim simulated_MSA -t /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile -m "JC" --length 352
+
+To mimic the alignment used to produce this analysis, i.e. simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis *and* copying the same gap positions as the original alignment, you can use the following command:
+
+iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa --alisim mimicked_MSA
+
+To simulate any number of alignments in either of the two commandlines above, use the --num-alignments options, for example mimic 100 alignments you would use the command line:
+
+iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa --alisim mimicked_MSA --num-alignments 100
+
+For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
+
+TIME STAMP
+----------
+
+Date and time: Mon Aug 18 15:31:53 2025
+Total CPU time used: 0.317828 seconds (0h:0m:0s)
+Total wall-clock time used: 0.34555 seconds (0h:0m:0s)
+