1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2022/23

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CB:phylo

Z MBI
Revízia z 17:18, 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)