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

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

@@ -0,0 +1,279 @@
+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-1/input-seqs.fa
+Type of analysis: ModelFinder + tree reconstruction
+Random seed number: 596149
+
+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: 8 sequences with 370 nucleotide sites
+Number of constant sites: 368 (= 99.4595% of all sites)
+Number of invariant (constant or ambiguous constant) sites: 368 (= 99.4595% of all sites)
+Number of parsimony informative sites: 0
+Number of distinct site patterns: 7
+
+ModelFinder
+-----------
+
+Best-fit model according to BIC: F81
+
+List of models sorted by BIC scores: 
+
+Model                  LogL         AIC      w-AIC        AICc     w-AICc         BIC      w-BIC
+F81                -524.779    1075.559 -   0.0357    1076.581 -   0.0464    1126.434 +    0.278
+JC                 -524.779    1075.559 -   0.0357    1076.581 -   0.0464    1126.434 +    0.278
+JC                 -524.779    1075.559 -   0.0357    1076.581 -   0.0464    1126.434 +    0.278
+HKY                -524.663    1077.325 -   0.0148    1078.508 -   0.0177    1132.114 -   0.0162
+K2P                -524.663    1077.326 -   0.0148    1078.509 -   0.0177    1132.115 -   0.0162
+K2P                -524.663    1077.326 -   0.0148    1078.509 -   0.0177    1132.115 -   0.0162
+F81+I              -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+JC+I               -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+JC+I               -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+F81+G4             -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+JC+G4              -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+JC+G4              -524.779    1077.559 -   0.0131    1078.742 -   0.0158    1132.348 -   0.0144
+TPM3               -523.895    1077.791 -   0.0117    1079.147 -   0.0129    1136.493 -  0.00182
+TPM3               -523.895    1077.791 -   0.0117    1079.147 -   0.0129    1136.493 -  0.00182
+TPM3u              -523.895    1077.791 -   0.0117    1079.147 -   0.0129    1136.493 -  0.00182
+K3Pu               -523.971    1077.941 -   0.0109    1079.297 -   0.0119    1136.644 -  0.00168
+K3P                -523.994    1077.988 -   0.0106    1079.344 -   0.0117    1136.690 -  0.00165
+K3P                -523.994    1077.988 -   0.0106    1079.344 -   0.0117    1136.690 -  0.00165
+TPM2u              -524.023    1078.046 -   0.0103    1079.402 -   0.0113    1136.749 -   0.0016
+TPM2               -524.023    1078.046 -   0.0103    1079.402 -   0.0113    1136.749 -   0.0016
+TPM2               -524.023    1078.046 -   0.0103    1079.402 -   0.0113    1136.749 -   0.0016
+TNe                -524.028    1078.055 -   0.0103    1079.411 -   0.0113    1136.758 -  0.00159
+TNe                -524.028    1078.055 -   0.0103    1079.411 -   0.0113    1136.758 -  0.00159
+TN                 -524.028    1078.055 -   0.0103    1079.411 -   0.0113    1136.758 -  0.00159
+F81+F              -521.218    1074.437 +   0.0626    1075.978 +   0.0628    1137.053 -  0.00137
+HKY+I              -524.663    1079.325 -  0.00544    1080.681 -  0.00598    1138.028 - 0.000843
+HKY+G4             -524.663    1079.325 -  0.00544    1080.681 -  0.00598    1138.028 - 0.000843
+K2P+I              -524.663    1079.326 -  0.00543    1080.682 -  0.00598    1138.028 - 0.000843
+K2P+I              -524.663    1079.326 -  0.00543    1080.682 -  0.00598    1138.028 - 0.000843
+K2P+G4             -524.663    1079.326 -  0.00543    1080.682 -  0.00598    1138.028 - 0.000843
+K2P+G4             -524.663    1079.326 -  0.00543    1080.682 -  0.00598    1138.028 - 0.000843
+JC+R2              -524.779    1079.559 -  0.00484    1080.914 -  0.00532    1138.261 -  0.00075
+JC+I+G4            -524.782    1079.564 -  0.00482    1080.920 -  0.00531    1138.267 - 0.000748
+TIM3e              -523.262    1078.523 -  0.00812    1080.064 -  0.00814    1141.139 - 0.000178
+TIM3               -523.262    1078.523 -  0.00812    1080.064 -  0.00814    1141.139 - 0.000178
+TIM3e              -523.262    1078.523 -  0.00812    1080.064 -  0.00814    1141.139 - 0.000178
+TIM2e              -523.390    1078.779 -  0.00714    1080.320 -  0.00716    1141.395 - 0.000157
+TIM2e              -523.390    1078.779 -  0.00714    1080.320 -  0.00716    1141.395 - 0.000157
+TIM2               -523.390    1078.779 -  0.00714    1080.320 -  0.00716    1141.395 - 0.000157
+TIM                -523.733    1079.466 -  0.00507    1081.007 -  0.00508    1142.082 - 0.000111
+TIMe               -523.740    1079.479 -  0.00503    1081.021 -  0.00505    1142.096 -  0.00011
+TIMe               -523.740    1079.479 -  0.00503    1081.021 -  0.00505    1142.096 -  0.00011
+TPM3+I             -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+TPM3+I             -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+TPM3u+I            -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+TPM3+G4            -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+TPM3u+G4           -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+TPM3+G4            -523.895    1079.791 -  0.00431    1081.332 -  0.00432    1142.407 - 9.44e-05
+K3Pu+G4            -523.970    1079.940 -    0.004    1081.481 -  0.00401    1142.556 - 8.76e-05
+K3Pu+I             -523.970    1079.940 -    0.004    1081.481 -  0.00401    1142.556 - 8.76e-05
+K3P+G4             -523.996    1079.992 -  0.00389    1081.533 -  0.00391    1142.608 - 8.54e-05
+K3P+G4             -523.996    1079.992 -  0.00389    1081.533 -  0.00391    1142.608 - 8.54e-05
+K3P+I              -523.998    1079.996 -  0.00389    1081.537 -   0.0039    1142.612 - 8.52e-05
+K3P+I              -523.998    1079.996 -  0.00389    1081.537 -   0.0039    1142.612 - 8.52e-05
+TPM2u+I            -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TPM2u+G4           -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TPM2+I             -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TPM2+I             -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TPM2+G4            -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TPM2+G4            -524.023    1080.046 -  0.00379    1081.587 -   0.0038    1142.662 - 8.31e-05
+TNe+I              -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+TN+I               -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+TNe+I              -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+TN+G4              -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+TNe+G4             -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+TNe+G4             -524.028    1080.055 -  0.00377    1081.596 -  0.00378    1142.671 - 8.27e-05
+HKY+F              -521.099    1076.198 -    0.026    1077.937 -   0.0236    1142.728 - 8.04e-05
+F81+F+I            -521.218    1076.437 -    0.023    1078.175 -   0.0209    1142.966 - 7.14e-05
+F81+F+G4           -521.218    1076.437 -    0.023    1078.175 -   0.0209    1142.966 - 7.14e-05
+JC+I+R2            -524.782    1081.564 -  0.00177    1083.105 -  0.00178    1144.180 - 3.89e-05
+TPM3u+F            -520.242    1076.484 -   0.0225    1078.433 -   0.0184    1146.927 - 9.85e-06
+TVM                -523.261    1080.522 -  0.00299    1082.261 -  0.00271    1147.052 - 9.26e-06
+TVMe               -523.261    1080.522 -  0.00299    1082.261 -  0.00271    1147.052 - 9.26e-06
+TVMe               -523.261    1080.522 -  0.00299    1082.261 -  0.00271    1147.052 - 9.26e-06
+TIM3e+I            -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+TIM3+I             -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+TIM3e+I            -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+TIM3e+G4           -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+TIM3e+G4           -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+TIM3+G4            -523.262    1080.523 -  0.00299    1082.262 -  0.00271    1147.053 - 9.25e-06
+K3Pu+F             -520.390    1076.780 -   0.0194    1078.729 -   0.0159    1147.223 -  8.5e-06
+TIM2e+I            -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TIM2+I             -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TIM2e+I            -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TIM2+G4            -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TIM2e+G4           -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TIM2e+G4           -523.390    1080.779 -  0.00263    1082.518 -  0.00239    1147.309 - 8.14e-06
+TPM2u+F            -520.505    1077.011 -   0.0173    1078.959 -   0.0141    1147.454 - 7.57e-06
+TN+F               -520.525    1077.050 -    0.017    1078.999 -   0.0139    1147.494 - 7.42e-06
+TIM+G4             -523.719    1081.439 -  0.00189    1083.177 -  0.00172    1147.968 - 5.85e-06
+TIM+I              -523.726    1081.452 -  0.00188    1083.191 -   0.0017    1147.982 - 5.81e-06
+TIMe+G4            -523.726    1081.452 -  0.00188    1083.191 -   0.0017    1147.982 - 5.81e-06
+TIMe+G4            -523.726    1081.452 -  0.00188    1083.191 -   0.0017    1147.982 - 5.81e-06
+TIMe+I             -523.733    1081.466 -  0.00186    1083.205 -  0.00169    1147.996 - 5.77e-06
+TIMe+I             -523.733    1081.466 -  0.00186    1083.205 -  0.00169    1147.996 - 5.77e-06
+HKY+F+I            -521.099    1078.198 -  0.00955    1080.147 -  0.00781    1148.641 - 4.18e-06
+HKY+F+G4           -521.099    1078.198 -  0.00955    1080.147 -  0.00781    1148.641 - 4.18e-06
+JC+R3              -524.779    1083.559 - 0.000655    1085.297 - 0.000595    1150.088 - 2.03e-06
+TIM3+F             -519.669    1077.338 -   0.0147    1079.510 -   0.0107    1151.695 - 9.08e-07
+SYM                -522.627    1081.254 -  0.00207    1083.203 -  0.00169    1151.697 - 9.07e-07
+GTR                -522.627    1081.254 -  0.00207    1083.203 -  0.00169    1151.697 - 9.07e-07
+SYM                -522.627    1081.254 -  0.00207    1083.203 -  0.00169    1151.697 - 9.07e-07
+TIM+F              -519.817    1077.635 -   0.0127    1079.806 -  0.00926    1151.991 - 7.83e-07
+TIM2+F             -519.933    1077.866 -   0.0113    1080.037 -  0.00825    1152.222 - 6.98e-07
+TPM3u+F+I          -520.242    1078.484 -  0.00828    1080.656 -  0.00606    1152.841 - 5.12e-07
+TPM3u+F+G4         -520.242    1078.484 -  0.00828    1080.656 -  0.00606    1152.841 - 5.12e-07
+TVM+I              -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+TVMe+I             -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+TVMe+I             -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+TVMe+G4            -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+TVMe+G4            -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+TVM+G4             -523.261    1082.522 -   0.0011    1084.471 - 0.000899    1152.965 - 4.81e-07
+K3Pu+F+I           -520.390    1078.780 -  0.00714    1080.952 -  0.00522    1153.137 - 4.42e-07
+K3Pu+F+G4          -520.390    1078.780 -  0.00714    1080.952 -  0.00522    1153.137 - 4.42e-07
+TPM2u+F+G4         -520.505    1079.010 -  0.00636    1081.181 -  0.00466    1153.367 - 3.94e-07
+TPM2u+F+I          -520.505    1079.010 -  0.00636    1081.182 -  0.00466    1153.367 - 3.94e-07
+TN+F+G4            -520.525    1079.050 -  0.00624    1081.222 -  0.00456    1153.407 - 3.86e-07
+TN+F+I             -520.525    1079.050 -  0.00624    1081.222 -  0.00456    1153.407 - 3.86e-07
+JC+I+R3            -524.782    1085.564 -  0.00024    1087.513 - 0.000196    1156.007 - 1.05e-07
+TVM+F              -519.650    1079.299 -  0.00551    1081.706 -  0.00358    1157.569 - 4.81e-08
+TIM3+F+I           -519.669    1079.338 -   0.0054    1081.745 -  0.00351    1157.608 - 4.72e-08
+TIM3+F+G4          -519.669    1079.339 -   0.0054    1081.746 -  0.00351    1157.609 - 4.72e-08
+SYM+I              -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+GTR+I              -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+SYM+I              -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+SYM+G4             -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+GTR+G4             -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+SYM+G4             -522.627    1083.254 - 0.000762    1085.425 - 0.000558    1157.611 - 4.72e-08
+TIM+F+G4           -519.817    1079.635 -  0.00466    1082.042 -  0.00303    1157.905 - 4.07e-08
+TIM+F+I            -519.818    1079.635 -  0.00466    1082.042 -  0.00303    1157.905 - 4.07e-08
+TIM2+F+G4          -519.933    1079.866 -  0.00415    1082.273 -   0.0027    1158.136 - 3.63e-08
+TIM2+F+I           -519.933    1079.866 -  0.00415    1082.273 -   0.0027    1158.136 - 3.63e-08
+GTR+F              -519.077    1080.154 -  0.00359    1082.809 -  0.00206    1162.338 - 4.44e-09
+TVM+F+I            -519.650    1081.299 -  0.00203    1083.954 -  0.00116    1163.483 -  2.5e-09
+TVM+F+G4           -519.650    1081.299 -  0.00203    1083.954 -  0.00116    1163.483 -  2.5e-09
+GTR+F+I            -519.077    1082.154 -  0.00132    1085.070 - 0.000666    1168.251 - 2.31e-10
+GTR+F+G4           -519.077    1082.154 -  0.00132    1085.071 - 0.000666    1168.251 - 2.31e-10
+
+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: F81+F
+
+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: (empirical counts from alignment)
+
+  pi(A) = 0.2374
+  pi(C) = 0.2698
+  pi(G) = 0.2936
+  pi(T) = 0.1993
+
+Rate matrix Q:
+
+  A    -1.024    0.3621    0.3941    0.2675
+  C    0.3187   -0.9802    0.3941    0.2675
+  G    0.3187    0.3621   -0.9482    0.2675
+  T    0.3187    0.3621    0.3941    -1.075
+
+Model of rate heterogeneity: Uniform
+
+MAXIMUM LIKELIHOOD TREE
+-----------------------
+
+Log-likelihood of the tree: -521.2183 (s.e. 10.5164)
+Unconstrained log-likelihood (without tree): -533.7213
+Number of free parameters (#branches + #model parameters): 16
+Akaike information criterion (AIC) score: 1074.4366
+Corrected Akaike information criterion (AICc) score: 1075.9776
+Bayesian information criterion (BIC) score: 1137.0526
+
+Total tree length (sum of branch lengths): 0.0055
+Sum of internal branch lengths: 0.0000 (0.0548% of tree length)
+
+WARNING: 5 near-zero internal branches (<0.0027) 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)
++**13de8675ec
+|
+|        +----------------------------------------------------------20a0129b57
+|     +**| (Node4)
+|     |  +----------------------------------------------------------97366cf0d8
+|  +**| (Node3)
+|  |  +**4233d708fe
++**| (Node2)
+   |  +**31e052ee14
+   +**| (Node5)
+      |  +**33aaa62e12
+      +**| (Node6)
+         +**91796617a0
+
+Tree in newick format:
+
+(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;
+
+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-1/out.treefile -m "F81+F{0.237398,0.269755,0.293597,0.199251}" --length 370
+
+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-1/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-1/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: Sat Aug 16 23:08:16 2025
+Total CPU time used: 0.148368 seconds (0h:0m:0s)
+Total wall-clock time used: 0.158447 seconds (0h:0m:0s)
+