IQ-TREE 2.1.2 COVID-edition built Mar 30 2021 Input file name: /data/dnb09/galaxy_db/files/f/5/1/dataset_f51e4d5c-d6dd-4660-b4d6-a8f6b204adcb.dat Type of analysis: ModelFinder + tree reconstruction Random seed number: 389313 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 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: 17 sequences with 1998 nucleotide sites Number of constant sites: 686 (= 34.3343% of all sites) Number of invariant (constant or ambiguous constant) sites: 686 (= 34.3343% of all sites) Number of parsimony informative sites: 1009 Number of distinct site patterns: 1152 ModelFinder ----------- Best-fit model according to AIC: GTR+F+I+G4 List of models sorted by AIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC GTR+F+I+G4 -21148.848 42379.696 + 0.392 42381.457 + 0.41 42609.292 - 0.0187 GTR+F+R3 -21147.208 42380.415 + 0.274 42382.352 + 0.262 42621.211 - 4.84e-05 GTR+F+R4 -21145.838 42381.676 + 0.146 42383.797 + 0.127 42633.672 - 9.52e-08 TIM2+F+I+G4 -21152.494 42382.987 + 0.0756 42384.581 + 0.086 42601.383 + 0.977 TIM2+F+R3 -21150.539 42383.078 + 0.0723 42384.838 + 0.0756 42612.674 - 0.00345 TIM2+F+R4 -21149.139 42384.279 - 0.0397 42386.215 - 0.038 42625.074 - 7.01e-06 GTR+F+G4 -21155.969 42391.939 - 0.000861 42393.615 - 0.000939 42615.935 - 0.000676 GTR+F+R2 -21235.664 42553.329 - 7.76e-39 42555.089 - 8.11e-39 42782.925 - 3.7e-40 TVM+F+R3 -21279.991 42643.983 - 1.6e-58 42645.830 - 1.6e-58 42879.179 - 4.65e-61 TPM2+F+R3 -21283.318 42646.637 - 4.25e-59 42648.313 - 4.63e-59 42870.633 - 3.34e-59 TPM2u+F+R3 -21283.318 42646.637 - 4.25e-59 42648.313 - 4.63e-59 42870.633 - 3.34e-59 TVM+F+R4 -21280.002 42648.004 - 2.14e-59 42650.031 - 1.96e-59 42894.399 - 2.3e-64 TPM2+F+R4 -21283.369 42650.738 - 5.46e-60 42652.585 - 5.47e-60 42885.933 - 1.59e-62 TPM2u+F+R4 -21283.369 42650.738 - 5.46e-60 42652.586 - 5.47e-60 42885.934 - 1.59e-62 TVM+F+I+G4 -21288.268 42656.537 - 3.01e-61 42658.213 - 3.28e-61 42880.533 - 2.36e-61 TPM2+F+I+G4 -21291.877 42659.753 - 6.02e-62 42661.266 - 7.13e-62 42872.550 - 1.28e-59 TPM2u+F+I+G4 -21291.877 42659.753 - 6.02e-62 42661.266 - 7.13e-62 42872.550 - 1.28e-59 SYM+R3 -21301.198 42682.396 - 7.29e-67 42684.072 - 7.96e-67 42906.392 - 5.73e-67 SYM+R4 -21299.575 42683.149 - 5.01e-67 42684.997 - 5.01e-67 42918.345 - 1.45e-69 TIM2e+R3 -21303.898 42683.796 - 3.62e-67 42685.309 - 4.29e-67 42896.592 - 7.7e-65 TIM2e+R4 -21302.244 42684.489 - 2.56e-67 42686.165 - 2.8e-67 42908.485 - 2.01e-67 SYM+I+G4 -21306.169 42688.337 - 3.74e-68 42689.850 - 4.43e-68 42901.133 - 7.94e-66 TIM2e+I+G4 -21309.135 42690.269 - 1.42e-68 42691.628 - 1.82e-68 42891.866 - 8.17e-64 TN+F+R4 -21355.818 42795.636 - 1.88e-91 42797.483 - 1.88e-91 43030.832 - 5.45e-94 TN+F+R3 -21357.891 42795.783 - 1.74e-91 42797.459 - 1.9e-91 43019.779 - 1.37e-91 TIM3+F+R4 -21354.988 42795.976 - 1.58e-91 42797.912 - 1.52e-91 43036.771 - 2.8e-95 TIM3+F+R3 -21357.139 42796.278 - 1.36e-91 42798.038 - 1.42e-91 43025.874 - 6.5e-93 TIM3+F+I+G4 -21359.483 42796.967 - 9.64e-92 42798.560 - 1.1e-91 43015.363 - 1.25e-90 TN+F+I+G4 -21360.513 42797.025 - 9.37e-92 42798.538 - 1.11e-91 43009.821 - 1.99e-89 TIM+F+R4 -21355.513 42797.026 - 9.36e-92 42798.963 - 8.97e-92 43037.822 - 1.65e-95 TIM+F+R3 -21357.556 42797.112 - 8.97e-92 42798.872 - 9.38e-92 43026.708 - 4.28e-93 TIM+F+I+G4 -21360.243 42798.486 - 4.51e-92 42800.080 - 5.13e-92 43016.883 - 5.83e-91 TVMe+R4 -21399.174 42880.347 - 7.56e-110 42882.108 - 7.9e-110 43109.943 - 3.61e-111 TVMe+R3 -21401.314 42880.629 - 6.57e-110 42882.222 - 7.46e-110 43099.025 - 8.48e-109 TVMe+I+G4 -21407.599 42889.197 - 9.05e-112 42890.632 - 1.11e-111 43096.393 - 3.16e-108 TPM3+F+R4 -21454.450 42992.899 - 2.74e-134 42994.747 - 2.75e-134 43228.095 - 7.97e-137 TPM3u+F+R4 -21454.450 42992.900 - 2.74e-134 42994.747 - 2.74e-134 43228.096 - 7.96e-137 HKY+F+R4 -21455.722 42993.443 - 2.09e-134 42995.204 - 2.18e-134 43223.039 - 9.98e-136 K3Pu+F+R4 -21455.631 42995.261 - 8.42e-135 42997.109 - 8.43e-135 43230.457 - 2.44e-137 HKY+F+R3 -21463.042 43004.085 - 1.02e-136 43005.678 - 1.16e-136 43222.481 - 1.32e-135 TPM3u+F+R3 -21462.230 43004.460 - 8.47e-137 43006.136 - 9.24e-137 43228.456 - 6.65e-137 TPM3+F+R3 -21462.230 43004.460 - 8.47e-137 43006.136 - 9.24e-137 43228.456 - 6.65e-137 K3Pu+F+R3 -21462.810 43005.619 - 4.74e-137 43007.296 - 5.17e-137 43229.616 - 3.72e-137 HKY+F+I+G4 -21475.774 43025.549 - 2.23e-141 43026.983 - 2.74e-141 43232.745 - 7.79e-138 TPM3+F+I+G4 -21474.941 43025.882 - 1.89e-141 43027.395 - 2.23e-141 43238.678 - 4.01e-139 TPM3u+F+I+G4 -21474.941 43025.882 - 1.89e-141 43027.395 - 2.23e-141 43238.678 - 4.01e-139 K3Pu+F+I+G4 -21475.438 43026.876 - 1.15e-141 43028.389 - 1.36e-141 43239.673 - 2.44e-139 GTR+F+I -21615.548 43311.095 - 2.2e-203 43312.772 - 2.4e-203 43535.092 - 1.73e-203 TNe+R3 -21704.582 43483.163 - 9.52e-241 43484.598 - 1.17e-240 43690.359 - 3.32e-237 TIM3e+R3 -21704.085 43484.170 - 5.75e-241 43485.683 - 6.81e-241 43696.966 - 1.22e-238 TIMe+R3 -21704.505 43485.010 - 3.78e-241 43486.523 - 4.47e-241 43697.807 - 8.03e-239 TNe+R4 -21704.150 43486.301 - 1.98e-241 43487.894 - 2.25e-241 43704.697 - 2.56e-240 TIM3e+R4 -21703.604 43487.208 - 1.26e-241 43488.884 - 1.37e-241 43711.204 - 9.9e-242 TIMe+R4 -21704.086 43488.173 - 7.78e-242 43489.849 - 8.48e-242 43712.169 - 6.11e-242 TNe+I+G4 -21709.284 43488.568 - 6.38e-242 43489.853 - 8.47e-242 43684.565 - 6.03e-236 TIM3e+I+G4 -21708.558 43489.116 - 4.85e-242 43490.475 - 6.2e-242 43690.713 - 2.79e-237 TIMe+I+G4 -21709.224 43490.448 - 2.49e-242 43491.806 - 3.19e-242 43692.044 - 1.43e-237 K2P+R3 -21823.500 43718.999 - 5.85e-292 43720.358 - 7.49e-292 43920.596 - 3.36e-287 K3P+R3 -21823.376 43720.751 - 2.44e-292 43722.186 - 3e-292 43927.948 - 8.51e-289 K2P+R4 -21823.167 43722.335 - 1.1e-292 43723.848 - 1.31e-292 43935.131 - 2.35e-290 K3P+R4 -21823.083 43724.166 - 4.42e-293 43725.759 - 5.03e-293 43942.562 - 5.71e-292 K2P+I+G4 -21833.956 43735.912 - 1.24e-295 43737.125 - 1.71e-295 43926.309 - 1.93e-288 K3P+I+G4 -21833.805 43737.610 - 5.32e-296 43738.895 - 7.06e-296 43933.607 - 5.03e-290 F81+F+R3 -22009.843 44095.685 - 0 44097.198 - 0 44308.482 - 0 F81+F+R4 -22009.976 44099.953 - 0 44101.629 - 0 44323.949 - 0 F81+F+I+G4 -22019.498 44110.995 - 0 44112.354 - 0 44312.592 - 0 JC+R3 -22234.620 44539.239 - 0 44540.524 - 0 44735.236 - 0 JC+R4 -22234.619 44543.237 - 0 44544.672 - 0 44750.434 - 0 JC+I+G4 -22245.563 44557.127 - 0 44558.269 - 0 44741.923 - 0 GTR+F -22701.469 45480.938 - 0 45482.531 - 0 45699.334 - 0 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: GTR+F+I+G4 Rate parameter R: A-C: 4.1054 A-G: 5.7074 A-T: 4.2469 C-G: 0.4663 C-T: 16.9411 G-T: 1.0000 State frequencies: (empirical counts from alignment) pi(A) = 0.3547 pi(C) = 0.2282 pi(G) = 0.1919 pi(T) = 0.2252 Rate matrix Q: A -0.7493 0.2349 0.2746 0.2398 C 0.3651 -1.344 0.02244 0.9564 G 0.5075 0.02668 -0.5907 0.05645 T 0.3776 0.9694 0.04812 -1.395 Model of rate heterogeneity: Invar+Gamma with 4 categories Proportion of invariable sites: 0.1542 Gamma shape alpha: 0.7289 Category Relative_rate Proportion 0 0 0.1542 1 0.09503 0.2115 2 0.4456 0.2115 3 1.106 0.2115 4 3.083 0.2115 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -21148.8588 (s.e. 336.2542) Unconstrained log-likelihood (without tree): -11402.5956 Number of free parameters (#branches + #model parameters): 41 Akaike information criterion (AIC) score: 42379.7177 Corrected Akaike information criterion (AICc) score: 42381.4784 Bayesian information criterion (BIC) score: 42609.3137 Total tree length (sum of branch lengths): 4.2205 Sum of internal branch lengths: 0.9915 (23.4917% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root +-------------LngfishAu | | +--------------LngfishSA +-------| | +------------LngfishAf | | +--------------------Frog +------| | +-----------------Turtle | +--| | | | +------------------------Crocodile | | +----| | | +------------------Bird | +--| | | +---------------------------Sphenodon | +-----| | | +-------------------------------Lizard +---------| | +--------------Human | +--| | | | +------Seal | | +--| | | | +-----Cow | | +--| | | +-------Whale | +---| | | | +---Mouse | | +---------| | | +------Rat +-----------| | +--------------Platypus +--| +-----------Opossum Tree in newick format: (LngfishAu:0.1714304303,(LngfishSA:0.1874078130,LngfishAf:0.1655666101):0.1066468995,(Frog:0.2562616096,((((Turtle:0.2217445831,(Crocodile:0.3074458518,Bird:0.2322075335):0.0655121225):0.0363678967,Sphenodon:0.3447364168):0.0200637473,Lizard:0.3880194791):0.0738122103,(((Human:0.1853213365,(Seal:0.0949642456,(Cow:0.0821719001,Whale:0.1015204922):0.0403901129):0.0251384618):0.0338485083,(Mouse:0.0584938935,Rat:0.0904123219):0.1211393562):0.0601841444,(Platypus:0.1908357781,Opossum:0.1505286126):0.0379889873):0.1491927499):0.1277062294):0.0934890057); TIME STAMP ---------- Date and time: Fri Mar 15 19:48:02 2024 Total CPU time used: 35.1658 seconds (0h:0m:35s) Total wall-clock time used: 3.8806 seconds (0h:0m:3s)