1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2021/22

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion


CB:phylo

Z MBI
Revízia z 18:18, 15. november 2018; Brona (Diskusia | príspevky)

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IQ-TREE 1.5.5 built Jun 21 2017

Input file name: /data/dnb02/galaxy_db/files/007/835/dataset_7835838.dat Type of analysis: ModelFinder + tree reconstruction Random seed number: 89203

REFERENCES


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. http://dx.doi.org/10.1038/nmeth.4285

To cite IQ-TREE please use:

Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol, 32:268-274. http://dx.doi.org/10.1093/molbev/msu300

SEQUENCE ALIGNMENT


Input data: 14 sequences with 1353 nucleotide sites Number of constant sites: 819 (= 60.5322% of all sites) Number of invariant (constant or ambiguous constant) sites: 819 (= 60.5322% of all sites) Number of distinct site patterns: 402

ModelFinder


Best-fit model according to AIC: TPM3u+R3

List of models sorted by AIC scores:

Model LogL AIC w-AIC AICc w-AICc BIC w-BIC TPM3u+R3 -6484.1519 13036.3037 + 0.2041 13038.1095 + 0.2113 13213.4464 + 0.0188 TPM3+R3 -6484.1590 13036.3181 + 0.2026 13038.1238 + 0.2098 13213.4608 - 0.0186 TIM3+R3 -6483.5880 13037.1760 + 0.1319 13039.0894 + 0.1295 13219.5288 - 0.0009 GTR+R3 -6481.6202 13037.2404 + 0.1277 13039.3788 + 0.1120 13230.0134 - 0.0000 TVM+R3 -6482.7182 13037.4364 + 0.1158 13039.4607 + 0.1075 13224.9993 - 0.0001 TIM3e+R3 -6487.6518 13039.3036 + 0.0455 13040.9036 + 0.0523 13206.0262 + 0.7663 TVMe+R3 -6487.0604 13040.1209 + 0.0303 13041.8221 + 0.0330 13212.0535 + 0.0376 TPM3u+R4 -6484.1515 13040.3030 + 0.0276 13042.3273 + 0.0256 13227.8659 - 0.0000 TPM3+R4 -6484.1566 13040.3132 + 0.0275 13042.3375 + 0.0255 13227.8760 - 0.0000 SYM+R3 -6486.4088 13040.8176 + 0.0214 13042.6233 + 0.0221 13217.9603 - 0.0020 GTR+R4 -6481.5825 13041.1651 + 0.0180 13043.5413 + 0.0140 13244.3582 - 0.0000 TIM3+R4 -6483.5843 13041.1686 - 0.0179 13043.3070 + 0.0157 13233.9415 - 0.0000 TVM+R4 -6482.7050 13041.4100 - 0.0159 13043.6658 - 0.0131 13239.3931 - 0.0000 TIM3e+R4 -6487.6485 13043.2971 - 0.0062 13045.1028 - 0.0064 13220.4398 - 0.0006 TVMe+R4 -6487.0569 13044.1139 - 0.0041 13046.0273 - 0.0040 13226.4667 - 0.0000 SYM+R4 -6486.3833 13044.7666 - 0.0030 13046.7909 - 0.0028 13232.3294 - 0.0000 TPM3u+I+G4 -6493.7888 13051.5776 - 0.0001 13053.1776 - 0.0001 13218.3002 - 0.0017 TPM3+I+G4 -6493.7906 13051.5813 - 0.0001 13053.1813 - 0.0001 13218.3038 - 0.0017 TIM3+I+G4 -6492.7937 13051.5874 - 0.0001 13053.2886 - 0.0001 13223.5200 - 0.0001 TVM+I+G4 -6492.1091 13052.2182 - 0.0001 13054.0240 - 0.0001 13229.3609 - 0.0000 GTR+I+G4 -6491.1534 13052.3068 - 0.0001 13054.2203 - 0.0001 13234.6596 - 0.0000 TIM3e+I+G4 -6497.4051 13054.8102 - 0.0000 13056.2172 - 0.0000 13211.1126 + 0.0602 TVMe+I+G4 -6496.6163 13055.2326 - 0.0000 13056.7345 - 0.0000 13216.7451 - 0.0036 SYM+I+G4 -6495.7165 13055.4329 - 0.0000 13057.0329 - 0.0000 13222.1555 - 0.0002 TPM3+G4 -6497.1505 13056.3009 - 0.0000 13057.8028 - 0.0000 13217.8134 - 0.0021 TPM3u+G4 -6497.1509 13056.3017 - 0.0000 13057.8036 - 0.0000 13217.8142 - 0.0021 TIM3+G4 -6496.2755 13056.5509 - 0.0000 13058.1509 - 0.0000 13223.2735 - 0.0001 TVM+G4 -6495.5138 13057.0276 - 0.0000 13058.7289 - 0.0000 13228.9603 - 0.0000 TIM+R3 -6493.5296 13057.0592 - 0.0000 13058.9727 - 0.0000 13239.4120 - 0.0000 GTR+G4 -6494.6924 13057.3849 - 0.0000 13059.1906 - 0.0000 13234.5276 - 0.0000 K3Pu+R3 -6494.7049 13057.4099 - 0.0000 13059.2156 - 0.0000 13234.5526 - 0.0000 TN+R3 -6495.0069 13058.0138 - 0.0000 13059.8196 - 0.0000 13235.1565 - 0.0000 HKY+R3 -6496.1936 13058.3872 - 0.0000 13060.0885 - 0.0000 13230.3199 - 0.0000 TIM3e+G4 -6500.7507 13059.5015 - 0.0000 13060.8166 - 0.0000 13210.5938 + 0.0781 TVMe+G4 -6499.9635 13059.9271 - 0.0000 13061.3340 - 0.0000 13216.2295 - 0.0047 TIM2+R3 -6494.9827 13059.9654 - 0.0000 13061.8788 - 0.0000 13242.3182 - 0.0000 SYM+G4 -6499.0603 13060.1207 - 0.0000 13061.6226 - 0.0000 13221.6332 - 0.0003 TPM2u+R3 -6496.0747 13060.1494 - 0.0000 13061.9552 - 0.0000 13237.2921 - 0.0000 TPM2+R3 -6496.0752 13060.1504 - 0.0000 13061.9562 - 0.0000 13237.2931 - 0.0000 TIM+R4 -6493.5286 13061.0573 - 0.0000 13063.1957 - 0.0000 13253.8302 - 0.0000 K3Pu+R4 -6494.7074 13061.4148 - 0.0000 13063.4391 - 0.0000 13248.9777 - 0.0000 TN+R4 -6495.0077 13062.0154 - 0.0000 13064.0397 - 0.0000 13249.5783 - 0.0000 HKY+R4 -6496.1844 13062.3687 - 0.0000 13064.2822 - 0.0000 13244.7215 - 0.0000 TIM2+R4 -6494.9177 13063.8354 - 0.0000 13065.9738 - 0.0000 13256.6084 - 0.0000 TPM2+R4 -6496.0807 13064.1615 - 0.0000 13066.1858 - 0.0000 13251.7243 - 0.0000 TPM2u+R4 -6496.0835 13064.1670 - 0.0000 13066.1913 - 0.0000 13251.7299 - 0.0000 TIM3+R2 -6499.3464 13064.6928 - 0.0000 13066.3941 - 0.0000 13236.6254 - 0.0000 TPM3u+R2 -6500.3974 13064.7948 - 0.0000 13066.3948 - 0.0000 13231.5173 - 0.0000 TPM3+R2 -6500.4030 13064.8061 - 0.0000 13066.4061 - 0.0000 13231.5286 - 0.0000 GTR+R2 -6497.7012 13065.4023 - 0.0000 13067.3158 - 0.0000 13247.7551 - 0.0000 TVM+R2 -6498.7527 13065.5055 - 0.0000 13067.3112 - 0.0000 13242.6482 - 0.0000 K3P+R3 -6502.7802 13067.5605 - 0.0000 13069.0624 - 0.0000 13229.0730 - 0.0000 TIMe+R3 -6502.0586 13068.1171 - 0.0000 13069.7171 - 0.0000 13234.8397 - 0.0000 TIM3e+R2 -6504.1109 13068.2217 - 0.0000 13069.6287 - 0.0000 13224.5241 - 0.0001 TVMe+R2 -6503.3428 13068.6856 - 0.0000 13070.1875 - 0.0000 13230.1981 - 0.0000 SYM+R2 -6502.4447 13068.8894 - 0.0000 13070.4894 - 0.0000 13235.6120 - 0.0000 K2P+R3 -6504.5514 13069.1028 - 0.0000 13070.5098 - 0.0000 13225.4052 - 0.0000 TNe+R3 -6503.7947 13069.5893 - 0.0000 13071.0912 - 0.0000 13231.1018 - 0.0000 TIM+I+G4 -6501.8399 13069.6799 - 0.0000 13071.3812 - 0.0000 13241.6125 - 0.0000 K3Pu+I+G4 -6502.9512 13069.9024 - 0.0000 13071.5024 - 0.0000 13236.6250 - 0.0000 TN+I+G4 -6503.3820 13070.7640 - 0.0000 13072.3640 - 0.0000 13237.4865 - 0.0000 HKY+I+G4 -6504.5110 13071.0219 - 0.0000 13072.5238 - 0.0000 13232.5344 - 0.0000 TIM2e+R3 -6503.6774 13071.3548 - 0.0000 13072.9548 - 0.0000 13238.0774 - 0.0000 K3P+R4 -6502.7688 13071.5375 - 0.0000 13073.2388 - 0.0000 13243.4702 - 0.0000 TIMe+R4 -6502.0090 13072.0180 - 0.0000 13073.8238 - 0.0000 13249.1607 - 0.0000 TIM2+I+G4 -6503.2502 13072.5004 - 0.0000 13074.2017 - 0.0000 13244.4330 - 0.0000 TPM2u+I+G4 -6504.3466 13072.6933 - 0.0000 13074.2933 - 0.0000 13239.4158 - 0.0000 TPM2+I+G4 -6504.3766 13072.7532 - 0.0000 13074.3532 - 0.0000 13239.4757 - 0.0000 K2P+R4 -6504.5437 13073.0874 - 0.0000 13074.6874 - 0.0000 13239.8100 - 0.0000 TNe+R4 -6503.7942 13073.5884 - 0.0000 13075.2897 - 0.0000 13245.5210 - 0.0000 TIM+G4 -6504.9137 13073.8275 - 0.0000 13075.4275 - 0.0000 13240.5500 - 0.0000 K3Pu+G4 -6505.9833 13073.9666 - 0.0000 13075.4685 - 0.0000 13235.4791 - 0.0000 TN+G4 -6506.4436 13074.8872 - 0.0000 13076.3891 - 0.0000 13236.3997 - 0.0000 HKY+G4 -6507.5284 13075.0567 - 0.0000 13076.4637 - 0.0000 13231.3591 - 0.0000 TIM2e+R4 -6503.6646 13075.3293 - 0.0000 13077.1350 - 0.0000 13252.4720 - 0.0000 TIM2+G4 -6506.3760 13076.7519 - 0.0000 13078.3519 - 0.0000 13243.4745 - 0.0000 TPM2u+G4 -6507.4108 13076.8217 - 0.0000 13078.3235 - 0.0000 13238.3341 - 0.0000 TPM2+G4 -6507.4119 13076.8238 - 0.0000 13078.3257 - 0.0000 13238.3363 - 0.0000 K3P+I+G4 -6511.0072 13080.0144 - 0.0000 13081.3296 - 0.0000 13231.1067 - 0.0000 TIMe+I+G4 -6510.3392 13080.6783 - 0.0000 13082.0853 - 0.0000 13236.9807 - 0.0000 K2P+I+G4 -6512.9217 13081.8433 - 0.0000 13083.0699 - 0.0000 13227.7256 - 0.0000 TIM+R2 -6507.9441 13081.8883 - 0.0000 13083.5896 - 0.0000 13253.8209 - 0.0000 K3Pu+R2 -6508.9562 13081.9124 - 0.0000 13083.5124 - 0.0000 13248.6349 - 0.0000 TNe+I+G4 -6512.2152 13082.4305 - 0.0000 13083.7456 - 0.0000 13233.5228 - 0.0000 TN+R2 -6509.4793 13082.9586 - 0.0000 13084.5586 - 0.0000 13249.6811 - 0.0000 HKY+R2 -6510.4872 13082.9745 - 0.0000 13084.4764 - 0.0000 13244.4869 - 0.0000 TIM2e+I+G4 -6512.0111 13084.0222 - 0.0000 13085.4291 - 0.0000 13240.3246 - 0.0000 K3P+G4 -6514.0225 13084.0450 - 0.0000 13085.2716 - 0.0000 13229.9273 - 0.0000 TPM2+R2 -6510.3687 13084.7374 - 0.0000 13086.3374 - 0.0000 13251.4599 - 0.0000 TPM2u+R2 -6510.3726 13084.7453 - 0.0000 13086.3453 - 0.0000 13251.4678 - 0.0000 TIM2+R2 -6509.3749 13084.7498 - 0.0000 13086.4510 - 0.0000 13256.6824 - 0.0000 TIMe+G4 -6513.3858 13084.7716 - 0.0000 13086.0868 - 0.0000 13235.8639 - 0.0000 K2P+G4 -6515.9258 13085.8515 - 0.0000 13086.9927 - 0.0000 13226.5237 - 0.0000 TNe+G4 -6515.2438 13086.4876 - 0.0000 13087.7142 - 0.0000 13232.3699 - 0.0000 TIM2e+G4 -6515.0623 13088.1246 - 0.0000 13089.4398 - 0.0000 13239.2169 - 0.0000 K3P+R2 -6517.0776 13092.1551 - 0.0000 13093.4703 - 0.0000 13243.2474 - 0.0000 TIMe+R2 -6516.4439 13092.8877 - 0.0000 13094.2947 - 0.0000 13249.1901 - 0.0000 K2P+R2 -6518.9724 13093.9449 - 0.0000 13095.1715 - 0.0000 13239.8271 - 0.0000 TNe+R2 -6518.3028 13094.6056 - 0.0000 13095.9208 - 0.0000 13245.6979 - 0.0000 TPM3+I -6516.8740 13095.7480 - 0.0000 13097.2499 - 0.0000 13257.2605 - 0.0000 TPM3u+I -6516.8764 13095.7527 - 0.0000 13097.2546 - 0.0000 13257.2652 - 0.0000 TIM2e+R2 -6518.1101 13096.2201 - 0.0000 13097.6271 - 0.0000 13252.5225 - 0.0000 TIM3+I -6516.3933 13096.7866 - 0.0000 13098.3866 - 0.0000 13263.5092 - 0.0000 TVM+I -6515.4193 13096.8387 - 0.0000 13098.5400 - 0.0000 13268.7713 - 0.0000 GTR+I -6514.9781 13097.9563 - 0.0000 13099.7621 - 0.0000 13275.0990 - 0.0000 TVMe+I -6519.7647 13099.5293 - 0.0000 13100.9363 - 0.0000 13255.8317 - 0.0000 TIM3e+I -6521.3626 13100.7251 - 0.0000 13102.0403 - 0.0000 13251.8174 - 0.0000 SYM+I -6519.4790 13100.9579 - 0.0000 13102.4598 - 0.0000 13262.4704 - 0.0000 K3Pu+I -6524.1488 13110.2975 - 0.0000 13111.7994 - 0.0000 13271.8100 - 0.0000 TIM+I -6523.5987 13111.1973 - 0.0000 13112.7973 - 0.0000 13277.9198 - 0.0000 HKY+I -6525.7809 13111.5617 - 0.0000 13112.9687 - 0.0000 13267.8641 - 0.0000 TN+I -6525.2349 13112.4698 - 0.0000 13113.9717 - 0.0000 13273.9822 - 0.0000 TPM2u+I -6525.7736 13113.5472 - 0.0000 13115.0491 - 0.0000 13275.0597 - 0.0000 TPM2+I -6525.7755 13113.5510 - 0.0000 13115.0529 - 0.0000 13275.0634 - 0.0000 TIM2+I -6525.2400 13114.4800 - 0.0000 13116.0800 - 0.0000 13281.2025 - 0.0000 K3P+I -6532.0606 13120.1213 - 0.0000 13121.3479 - 0.0000 13266.0035 - 0.0000 TIMe+I -6531.7865 13121.5729 - 0.0000 13122.8881 - 0.0000 13272.6652 - 0.0000 K2P+I -6533.9918 13121.9835 - 0.0000 13123.1246 - 0.0000 13262.6557 - 0.0000 TNe+I -6533.7370 13123.4740 - 0.0000 13124.7006 - 0.0000 13269.3562 - 0.0000 TIM2e+I -6533.3935 13124.7870 - 0.0000 13126.1022 - 0.0000 13275.8793 - 0.0000 TIM3 -6726.4247 13514.8494 - 0.0000 13516.3513 - 0.0000 13676.3619 - 0.0000 TIM3e -6729.4731 13514.9461 - 0.0000 13516.1727 - 0.0000 13660.8284 - 0.0000 SYM -6727.5502 13515.1004 - 0.0000 13516.5074 - 0.0000 13671.4028 - 0.0000 GTR -6724.9044 13515.8089 - 0.0000 13517.5102 - 0.0000 13687.7415 - 0.0000 TVMe -6728.9701 13515.9403 - 0.0000 13517.2555 - 0.0000 13667.0326 - 0.0000 TPM3 -6728.2147 13516.4294 - 0.0000 13517.8363 - 0.0000 13672.7318 - 0.0000 TPM3u -6728.2414 13516.4827 - 0.0000 13517.8897 - 0.0000 13672.7851 - 0.0000 TVM -6726.6869 13517.3738 - 0.0000 13518.9738 - 0.0000 13684.0964 - 0.0000 TIM -6738.0914 13538.1828 - 0.0000 13539.6847 - 0.0000 13699.6953 - 0.0000 K3Pu -6739.7929 13539.5859 - 0.0000 13540.9928 - 0.0000 13695.8882 - 0.0000 TN -6740.0581 13540.1161 - 0.0000 13541.5231 - 0.0000 13696.4185 - 0.0000 HKY -6741.7189 13541.4378 - 0.0000 13542.7530 - 0.0000 13692.5301 - 0.0000 TIM2 -6739.8706 13541.7413 - 0.0000 13543.2432 - 0.0000 13703.2538 - 0.0000 TIMe -6742.9053 13541.8105 - 0.0000 13543.0371 - 0.0000 13687.6927 - 0.0000 K3P -6744.2238 13542.4475 - 0.0000 13543.5886 - 0.0000 13683.1197 - 0.0000 TPM2u -6741.5518 13543.1037 - 0.0000 13544.5106 - 0.0000 13699.4060 - 0.0000 TPM2 -6741.5605 13543.1209 - 0.0000 13544.5279 - 0.0000 13699.4233 - 0.0000 TNe -6744.9280 13543.8560 - 0.0000 13544.9972 - 0.0000 13684.5282 - 0.0000 TIM2e -6744.2462 13544.4924 - 0.0000 13545.7190 - 0.0000 13690.3746 - 0.0000 K2P -6746.2724 13544.5449 - 0.0000 13545.6037 - 0.0000 13680.0069 - 0.0000 F81+R3 -6765.1604 13594.3209 - 0.0000 13595.9209 - 0.0000 13761.0434 - 0.0000 JC+R3 -6769.9522 13597.9045 - 0.0000 13599.2196 - 0.0000 13748.9968 - 0.0000 F81+R4 -6765.1441 13598.2882 - 0.0000 13600.0939 - 0.0000 13775.4309 - 0.0000 JC+R4 -6769.9356 13601.8712 - 0.0000 13603.3731 - 0.0000 13763.3836 - 0.0000 F81+I+G4 -6770.9751 13601.9503 - 0.0000 13603.3572 - 0.0000 13758.2526 - 0.0000 F81+G4 -6773.3335 13604.6669 - 0.0000 13605.9821 - 0.0000 13755.7592 - 0.0000 JC+I+G4 -6775.6599 13605.3197 - 0.0000 13606.4608 - 0.0000 13745.9919 - 0.0000 JC+G4 -6778.0076 13608.0153 - 0.0000 13609.0741 - 0.0000 13743.4773 - 0.0000 F81+R2 -6776.0795 13612.1589 - 0.0000 13613.5659 - 0.0000 13768.4613 - 0.0000 JC+R2 -6780.8140 13615.6280 - 0.0000 13616.7691 - 0.0000 13756.3002 - 0.0000 F81+I -6787.1972 13632.3944 - 0.0000 13633.7096 - 0.0000 13783.4867 - 0.0000 JC+I -6791.8718 13635.7436 - 0.0000 13636.8024 - 0.0000 13771.2056 - 0.0000 F81 -6988.8857 14033.7714 - 0.0000 14034.9980 - 0.0000 14179.6536 - 0.0000 JC -6992.3848 14034.7697 - 0.0000 14035.7493 - 0.0000 14165.0217 - 0.0000

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: TPM3u+F+R3

Rate parameter R:

 A-C: 2.2434
 A-G: 9.0753
 A-T: 1.0000
 C-G: 2.2434
 C-T: 9.0753
 G-T: 1.0000

State frequencies: (empirical counts from alignment)

 pi(A) = 0.2796
 pi(C) = 0.2485
 pi(G) = 0.2405
 pi(T) = 0.2313

Rate matrix Q:

 A   -0.9633    0.1807    0.7076     0.075
 C    0.2034    -1.059    0.1749    0.6806
 G    0.8227    0.1807    -1.078     0.075
 T   0.09065     0.731   0.07797   -0.8996

Model of rate heterogeneity: FreeRate with 3 categories Site proportion and rates: (0.4882,0.01167) (0.4523,1.312) (0.05954,6.733)

Category  Relative_rate  Proportion
 1         0.01167        0.4882
 2         1.312          0.4523
 3         6.733          0.05954

MAXIMUM LIKELIHOOD TREE


Log-likelihood of the tree: -6484.7034 (s.e. 159.9164) Unconstrained log-likelihood (without tree): -5359.1653 Number of free parameters (#branches + #model parameters): 34 Akaike information criterion (AIC) score: 13037.4069 Corrected Akaike information criterion (AICc) score: 13039.2126 Bayesian information criterion (BIC) score: 13214.5496

Total tree length (sum of branch lengths): 1.0523 Sum of internal branch lengths: 0.2691 (25.5745% of tree length)

NOTE: Tree is UNROOTED although outgroup taxon 'human' is drawn at root

+--human | +--chimp | | +--rhesus +--|

  |      +-------bushbaby
  |   +--|
  |   |  |  +-------rabbit
  |   |  +--|
  |   |     +------elephant
  +---|
      |                 +--mouse
      |     +-----------|
      |     |           +----rat
      |  +--|
      |  |  |         +---------------------------------opossum
      |  |  +---------|
      |  |            |      +-----------platypus
      |  |            +------|
      |  |                   +--------------------------------chicken
      +--|
         |     +--pig
         |  +--|
         |  |  +---cow
         +--|
            +------dog

Tree in newick format:

(human:0.0030783239,chimp:0.0021697421,(rhesus:0.0101007881,((bushbaby:0.0516935606,(rabbit:0.0504519320,elephant:0.0417636379):0.008816):0.007604,(((mouse:0.0218412291,rat:0.0338195871):0.072583,(opossum:0.2034752433,(platypus:0.0761360840,chicken:0.1963884954):0.041933):0.062421):0.017824,((pig:0.0224889495,cow:0.0253462151):0.015545,dog:0.0444600788):0.006520):0.003059):0.023932):0.008895);

TIME STAMP


Date and time: Thu Nov 15 12:42:17 2018 Total CPU time used: 81.8009 seconds (0h:1m:21s) Total wall-clock time used: 7.03197 seconds (0h:0m:7s)