.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2916_143x897_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 73 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 303 patterns found. (out of a total of 897 sites) . 620 sites without polymorphism (69.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3630.3720] [Ts/ts ratio ][ 2.065211] . ( 1 sec) [ -3630.2095] [ 352] [depth= 1] . ( 1 sec) [ -3629.4756] [ 352] [depth= 1] . ( 1 sec) [ -3629.3240] [ 352] [depth= 1] . ( 1 sec) [ -3628.8017] [ 352] [depth= 1] . ( 1 sec) [ -3628.7426] [ 352] [depth= 1] . ( 2 sec) [ -3628.7313] [ 352] [depth= 2] . ( 2 sec) [ -3628.4519] [ 352] [depth= 1] . ( 2 sec) [ -3627.7108] [ 352] [depth= 1] . ( 2 sec) [ -3627.5369] [ 352] [depth= 4] . ( 2 sec) [ -3627.5124] [ 352] [depth= 3] . ( 2 sec) [ -3627.3237] [ 352] [depth= 2] . ( 2 sec) [ -3626.5606] [ 352] [depth= 1] . ( 2 sec) [ -3626.2684] [ 352] [depth= 1] . ( 3 sec) [ -3626.1409] [ 352] [depth= 5] . ( 3 sec) [ -3625.9061] [ 352] [depth= 4] . ( 3 sec) [ -3625.4162] [ 352] [depth= 1] . ( 3 sec) [ -3624.7800] [ 352] [depth= 7] . ( 3 sec) [ -3624.7273] [ 352] [depth= 1] . ( 3 sec) [ -3624.0440] [ 352] [depth= 1] . ( 3 sec) [ -3623.6773] [ 352] [depth= 1] . ( 5 sec) [ -3623.6655] [ 352] [depth= 1] . ( 6 sec) [ -3623.6372] [ 352] [depth= 1] . ( 6 sec) [ -3620.3323] [ 352] [depth= 1] . ( 6 sec) [ -3619.3138] [ 352] [depth= 1] . ( 6 sec) [ -3619.2868] [ 352] [depth= 2] . ( 7 sec) [ -3619.2668] [ 352] [depth= 2] . ( 7 sec) [ -3619.2444] [ 352] [depth= 2] . ( 7 sec) [ -3619.2316] [ 352] [depth= 1] . ( 10 sec) [ -3618.6672] [ 352] [depth= 1] . ( 10 sec) [ -3618.4694] [ 352] [depth= 1] . ( 12 sec) [ -3618.4059] [ 352] [depth= 1] . ( 12 sec) [ -3617.4856] [ 352] [depth= 1] . ( 13 sec) [ -3617.4720] [ 352] [depth= 1] . ( 15 sec) [ -3617.4446] [ 352] [depth= 1] . ( 15 sec) [ -3617.4158] [ 352] [depth= 1] . ( 17 sec) [ -3617.3909] [ 352] [depth= 2] . ( 19 sec) [ -3617.1403] [ 351] [depth= 6] . ( 19 sec) [ -3615.8913] [ 351] [depth= 1] . ( 19 sec) [ -3615.7953] [ 351] [depth= 1] . ( 19 sec) [ -3615.7604] [ 351] [depth= 2] . ( 21 sec) [ -3615.5573] [ 351] [depth= 2] . ( 21 sec) [ -3614.4870] [ 351] [depth= 2] . ( 21 sec) [ -3614.2441] [ 351] [depth= 2] . ( 21 sec) [ -3614.2268] [ 351] [depth= 3] . ( 22 sec) [ -3614.1821] [ 351] [depth= 2] . ( 22 sec) [ -3614.1253] [ 351] [depth= 1] . ( 22 sec) [ -3613.8340] [ 351] [depth= 1] . ( 22 sec) [ -3613.7680] [ 351] [depth= 1] . ( 22 sec) [ -3613.0446] [ 350] [depth= 4] . ( 22 sec) [ -3613.0241] [ 350] [depth= 2] . ( 23 sec) [ -3611.5864] [ 350] [depth= 2] . ( 23 sec) [ -3608.1074] [ 350] [depth= 3] . ( 23 sec) [ -3607.9180] [ 350] [depth= 3] . ( 23 sec) [ -3607.7186] [ 350] [depth= 1] . ( 23 sec) [ -3601.6315] [ 349] [depth= 1] . ( 23 sec) [ -3601.6082] [ 349] [depth= 6] . ( 23 sec) [ -3601.5975] [ 349] [depth= 1] . ( 23 sec) [ -3600.6645] [ 349] [depth= 4] . ( 24 sec) [ -3600.6083] [ 349] [depth= 3] . ( 24 sec) [ -3600.5981] [ 349] [depth= 2] . ( 28 sec) [ -3600.3060] [ 349] [depth= 1] . ( 28 sec) [ -3599.8783] [ 349] [depth= 2] . ( 28 sec) [ -3597.9174] [ 349] [depth= 1] . ( 35 sec) [ -3597.7091] [ 349] [depth= 2] . ( 35 sec) [ -3597.0181] [ 349] [depth= 1] . ( 36 sec) [ -3596.9990] [ 349] [depth= 2] . ( 37 sec) [ -3596.9868] [ 349] [depth= 1] . ( 40 sec) [ -3596.9268] [ 349] [depth= 3] . ( 42 sec) [ -3596.8645] [ 349] [depth= 7] . ( 43 sec) [ -3596.3138] [ 349] [depth= 1] . ( 43 sec) [ -3596.0254] [ 349] [depth= 1] . ( 44 sec) [ -3592.4781] [ 349] [depth= 3] . ( 44 sec) [ -3592.4553] [ 349] [depth= 1] . ( 44 sec) [ -3592.2695] [ 349] [depth= 1] . ( 44 sec) [ -3591.4437] [ 349] [depth= 1] . ( 47 sec) [ -3591.1298] [ 349] [depth= 1] . ( 48 sec) [ -3591.0480] [ 349] [depth= 1] . ( 48 sec) [ -3591.0253] [ 349] [depth= 1] . ( 48 sec) [ -3590.9870] [ 349] [depth= 3] . ( 48 sec) [ -3590.9415] [ 349] [depth= 3] . ( 48 sec) [ -3590.7797] [ 349] [depth= 1] . ( 48 sec) [ -3590.7507] [ 349] [depth= 2] . ( 48 sec) [ -3590.6780] [ 349] [depth= 3] . ( 50 sec) [ -3590.5424] [ 349] [depth= 6] . ( 50 sec) [ -3590.4696] [ 349] [depth= 2] . ( 50 sec) [ -3590.4564] [ 349] [depth= 2] . ( 50 sec) [ -3589.9665] [ 349] [depth= 1] . ( 51 sec) [ -3589.8333] [ 349] [depth= 1] . ( 51 sec) [ -3583.4961] [ 348] [depth= 6] . ( 51 sec) [ -3583.3768] [ 348] [depth= 7] . ( 52 sec) [ -3583.3124] [ 348] [depth= 2] . ( 52 sec) [ -3583.2547] [ 348] [depth= 2] . ( 52 sec) [ -3583.1565] [ 348] [depth= 6] . ( 52 sec) [ -3583.1454] [ 348] [depth= 1] . ( 53 sec) [ -3583.1145] [ 348] [depth= 3] . ( 53 sec) [ -3582.8743] [ 348] [depth= 5] . ( 53 sec) [ -3582.2101] [ 348] [depth= 4] . ( 53 sec) [ -3582.1614] [ 348] [depth= 2] . ( 54 sec) [ -3581.9670] [ 348] [depth= 3] . ( 54 sec) [ -3581.3895] [ 348] [depth= 2] . ( 54 sec) [ -3581.3739] [ 348] [depth= 7] . ( 54 sec) [ -3581.3596] [ 348] [depth= 8] . ( 54 sec) [ -3581.0148] [ 348] [depth= 1] . ( 54 sec) [ -3581.0044] [ 348] [depth= 2] . ( 54 sec) [ -3580.8534] [ 348] [depth= 8] . ( 55 sec) [ -3580.7937] [ 348] [depth= 1] . ( 56 sec) [ -3580.7679] [ 348] [depth= 7] . ( 57 sec) [ -3580.5917] [ 348] [depth= 7] . ( 57 sec) [ -3575.6464] [ 347] [depth= 5] . ( 57 sec) [ -3575.6288] [ 347] [depth= 2] . ( 57 sec) [ -3575.4585] [ 347] [depth= 6] . ( 58 sec) [ -3575.3429] [ 347] [depth= 2] . ( 66 sec) [ -3575.2056] [ 347] [depth= 1] . ( 66 sec) [ -3574.9812] [ 347] [depth= 2] . ( 66 sec) [ -3574.9164] [ 347] [depth= 2] . ( 66 sec) [ -3574.4184] [ 347] [depth= 1] . ( 66 sec) [ -3574.2795] [ 347] [depth= 2] . ( 68 sec) [ -3574.1813] [ 347] [depth= 1] . ( 69 sec) [ -3565.2719] [ 346] [depth= 17] . ( 69 sec) [ -3565.1794] [ 346] [depth= 1] . ( 69 sec) [ -3565.1472] [ 346] [depth= 1] . ( 86 sec) [ -3564.9809] [ 346] [depth= 2] . ( 86 sec) [ -3564.9605] [ 346] [depth= 2] . ( 87 sec) [ -3564.9444] [ 346] [depth= 1] . ( 88 sec) [ -3564.8805] [ 346] [depth= 2] . ( 88 sec) [ -3564.8157] [ 346] [depth= 1] . ( 90 sec) [ -3564.7808] [ 346] [depth= 4] . ( 91 sec) [ -3564.5396] [ 346] [depth= 1] . ( 92 sec) [ -3564.3923] [ 346] [depth= 3] . ( 92 sec) [ -3564.2852] [ 346] [depth= 2] . ( 92 sec) [ -3564.2254] [ 346] [depth= 7] . ( 93 sec) [ -3564.1749] [ 346] [depth= 5] . ( 93 sec) [ -3563.6279] [ 346] [depth= 4] . ( 93 sec) [ -3563.6125] [ 346] [depth= 3] . ( 94 sec) [ -3563.5008] [ 346] [depth= 2] . ( 94 sec) [ -3563.2784] [ 346] [depth= 6] . ( 94 sec) [ -3556.6126] [ 345] [depth= 3] . ( 94 sec) [ -3554.4076] [ 345] [depth= 8] . ( 94 sec) [ -3554.3951] [ 345] [depth= 1] . ( 94 sec) [ -3554.2407] [ 345] [depth= 1] . ( 96 sec) [ -3554.1923] [ 345] [depth= 10] . ( 97 sec) [ -3553.9580] [ 345] [depth= 3] . ( 97 sec) [ -3553.7003] [ 345] [depth= 1] . ( 98 sec) [ -3553.5419] [ 345] [depth= 1] . ( 98 sec) [ -3553.2262] [ 345] [depth= 1] . ( 98 sec) [ -3553.2004] [ 345] [depth= 2] . ( 98 sec) [ -3553.1613] [ 345] [depth= 2] . ( 98 sec) [ -3553.1355] [ 345] [depth= 7] . ( 100 sec) [ -3553.1083] [ 345] [depth= 5] . ( 101 sec) [ -3553.0226] [ 345] [depth= 1] . ( 101 sec) [ -3553.0121] [ 345] [depth= 1] . ( 101 sec) [ -3552.8849] [ 345] [depth= 2] . ( 101 sec) [ -3552.8737] [ 345] [depth= 3] . ( 102 sec) [ -3552.8127] [ 345] [depth= 2] . ( 102 sec) [ -3552.4186] [ 345] [depth= 1] . ( 102 sec) [ -3552.3701] [ 345] [depth= 3] . ( 102 sec) [ -3552.3412] [ 345] [depth= 2] . ( 102 sec) [ -3552.1853] [ 345] [depth= 3] . ( 102 sec) [ -3552.1478] [ 345] [depth= 4] . ( 102 sec) [ -3552.0808] [ 345] [depth= 3] . ( 103 sec) [ -3552.0142] [ 345] [depth= 4] . ( 103 sec) [ -3552.0034] [ 345] [depth= 2] . ( 103 sec) [ -3551.9819] [ 345] [depth= 2] . ( 104 sec) [ -3551.9357] [ 345] [depth= 3] . ( 104 sec) [ -3551.9209] [ 345] [depth= 4] . ( 115 sec) [ -3544.1708] [Branch lengths ] . ( 115 sec) [ -3544.1693] [Ts/ts ratio ][ 2.077490] . ( 171 sec) [ -3543.9709] [ 345] [depth= 10] . ( 192 sec) [ -3542.8895] [ 345] [depth= 6] . ( 193 sec) [ -3542.7690] [ 345] [depth= 1] . ( 198 sec) [ -3538.7891] [ 344] [depth= 1] . ( 208 sec) [ -3538.7341] [ 344] [depth= 1] . ( 212 sec) [ -3538.4663] [ 344] [depth= 8] . ( 212 sec) [ -3538.3177] [ 344] [depth= 1] . ( 270 sec) [ -3537.3088] [ 344] [depth= 6] . ( 277 sec) [ -3536.9604] [ 344] [depth= 3] . ( 311 sec) [ -3535.9944] [Branch lengths ] . ( 312 sec) [ -3535.8653] [Ts/ts ratio ][ 2.198658] . ( 514 sec) [ -3535.8540] [Branch lengths ] . ( 578 sec) [ -3535.8143] [ 343] [depth= 6] . ( 606 sec) [ -3535.7639] [Branch lengths ] . ( 606 sec) [ -3535.7583] [Ts/ts ratio ][ 2.224991] . ( 606 sec) [ -3535.7583] [Topology ] . ( 608 sec) [ -3535.7582] [Topology ] . ( 608 sec) [ -3535.7582] [Ts/ts ratio ][ 2.224991] . Checking for NNIs, optimizing five branches... . ( 619 sec) [ -3535.7567] [Topology ] . Checking for NNIs, optimizing five branches... . ( 630 sec) [ -3535.7566] [Topology ] . Checking for NNIs, optimizing five branches... . ( 641 sec) [ -3535.7565] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3535.756527. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 28 -1.000000 0.000000 0.000000 91 43.488240 0.964000 0.005623 2 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 34 10.701421 0.832000 0.001688 6 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 94 21.691948 0.930000 0.008823 88 19.539729 0.925000 0.010359 97 27.581312 0.974000 0.015520 40 14.011398 0.918000 0.008521 26 4.668827 0.759000 0.002214 57 27.574196 0.945000 0.004108 10 -1.000000 0.000000 0.000000 58 12.302683 0.843000 0.001357 25 -1.000000 0.000000 0.000000 64 7.109558 0.767000 0.001352 61 9.465751 0.759000 0.001364 12 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 30 7.164571 0.759000 0.001356 49 8.096873 0.774000 0.001369 12 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 33 12.129205 0.841000 0.001367 64 10.544222 0.859000 0.001364 6 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 13 -1.000000 0.000000 0.000000 22 12.184945 0.864000 0.004809 75 13.863831 0.832000 0.006909 11 5.066463 0.741000 0.001383 84 26.370930 0.914000 0.004109 6 6.161927 0.768000 0.001379 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 29 4.014994 0.740000 0.001354 27 29.105617 0.912000 0.005500 96 36.716270 0.965000 0.005524 8 5.732956 0.749000 0.001344 9 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 54 8.056657 0.748000 0.001361 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 46 17.177478 0.883000 0.002733 42 6.534571 0.788000 0.001348 7 -1.000000 0.000000 0.000000 63 13.518933 0.866000 0.001354 8 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 7 19.357428 0.893000 0.002722 5 18.148153 0.878000 0.002745 24 3.939471 0.765000 0.001311 3 7.501006 0.722000 0.001352 14 22.887965 0.867000 0.004075 18 23.597156 0.942000 0.004071 90 21.162340 0.908000 0.002723 3 -1.000000 0.000000 0.000000 89 41.951486 0.967000 0.004124 11 -1.000000 0.000000 0.000000 15 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 55 28.046727 0.944000 0.004104 24 -1.000000 0.000000 0.000000 88 45.492729 0.971000 0.006844 0 0.000218 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 0.001456 0.000000 0.001386 34 13.816126 0.888000 0.002707 53 16.793953 0.872000 0.003651 0 -1.000000 0.000000 0.000000 31 17.176360 0.882000 0.002798 37 15.483048 0.850000 0.002796 37 8.323296 0.769000 0.001399 39 8.893256 0.782000 0.001351 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 33 15.580531 0.925000 0.001355 65 8.736173 0.747000 0.001357 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 26 15.097775 0.848000 0.001354 10 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 97 45.239601 0.958000 0.005463 11 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 64 14.184566 0.911000 0.001357 40 11.388338 0.826000 0.001443 5 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 52 10.268239 0.817000 0.001449 15 13.909343 0.927000 0.001353 12 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 0 0.000216 0.000000 0.000012 4 -1.000000 0.000000 0.000000 0 0.006207 0.000000 0.001191 0 -1.000000 0.000000 0.000001 1 0.004011 0.000000 0.000410 1 5.729357 0.435000 0.003256 5 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 0 4.569673 0.799000 0.001620 73 18.147730 0.885000 0.002716 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 35 12.404315 0.838000 0.001354 38 14.073291 0.869000 0.002712 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 46 10.941961 0.811000 0.001622 1 -1.000000 0.000000 0.000000 25 10.833911 0.838000 0.001352 7 -1.000000 0.000000 0.000000 86 27.882106 0.955000 0.002708 21 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2916_143x897_2006.phy_phyml_tree.txt'... . Time used 16h44m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo