.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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 . Compressing sequences... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16830.3453] [Ts/ts ratio ][ 4.329223] . ( 0 sec) [ -16829.2637] [ 3961] [depth= 1] . ( 1 sec) [ -16828.4962] [ 3964] [depth= 2] . ( 1 sec) [ -16826.8506] [ 3968] [depth= 2] . ( 1 sec) [ -16821.6884] [ 3962] [depth= 2] . ( 1 sec) [ -16818.1458] [ 3957] [depth= 1] . ( 1 sec) [ -16818.0222] [ 3958] [depth= 1] . ( 2 sec) [ -16807.5772] [ 3973] [depth= 1] . ( 2 sec) [ -16769.0734] [ 3958] [depth= 1] . ( 2 sec) [ -16757.1683] [ 3952] [depth= 1] . ( 2 sec) [ -16755.1537] [ 3957] [depth= 1] . ( 2 sec) [ -16744.0538] [ 3957] [depth= 1] . ( 2 sec) [ -16733.4736] [ 3957] [depth= 1] . ( 2 sec) [ -16726.4719] [ 3958] [depth= 1] . ( 2 sec) [ -16725.8551] [ 3959] [depth= 1] . ( 2 sec) [ -16725.3106] [ 3964] [depth= 1] . ( 3 sec) [ -16711.0954] [ 3960] [depth= 3] . ( 3 sec) [ -16708.9553] [ 3961] [depth= 2] . ( 3 sec) [ -16707.8704] [ 3966] [depth= 2] . ( 3 sec) [ -16689.7376] [ 3965] [depth= 1] . ( 3 sec) [ -16651.6411] [ 3966] [depth= 1] . ( 3 sec) [ -16634.8875] [ 3959] [depth= 2] . ( 3 sec) [ -16632.6953] [ 3959] [depth= 1] . ( 3 sec) [ -16626.3444] [ 3962] [depth= 2] . ( 3 sec) [ -16624.1693] [ 3967] [depth= 1] . ( 3 sec) [ -16619.7230] [ 3962] [depth= 2] . ( 4 sec) [ -16591.8799] [ 3966] [depth= 1] . ( 4 sec) [ -16588.3609] [ 3958] [depth= 2] . ( 4 sec) [ -16587.2347] [ 3961] [depth= 1] . ( 5 sec) [ -16584.0658] [ 3957] [depth= 1] . ( 5 sec) [ -16571.4420] [ 3961] [depth= 1] . ( 5 sec) [ -16571.2890] [ 3956] [depth= 2] . ( 5 sec) [ -16564.8742] [ 3955] [depth= 1] . ( 5 sec) [ -16549.3721] [ 3958] [depth= 1] . ( 6 sec) [ -16515.3600] [ 3954] [depth= 3] . ( 6 sec) [ -16514.7145] [ 3955] [depth= 1] . ( 6 sec) [ -16514.5823] [ 3954] [depth= 1] . ( 7 sec) [ -16512.8306] [ 3954] [depth= 1] . ( 7 sec) [ -16512.6753] [ 3954] [depth= 1] . ( 7 sec) [ -16512.3227] [ 3954] [depth= 1] . ( 9 sec) [ -16433.6378] [Branch lengths ] . ( 9 sec) [ -16408.2064] [Ts/ts ratio ][ 5.603125] . ( 9 sec) [ -16407.5346] [ 3954] [depth= 1] . ( 10 sec) [ -16405.6260] [ 3949] [depth= 1] . ( 12 sec) [ -16404.1186] [ 3948] [depth= 1] . ( 12 sec) [ -16403.7369] [ 3950] [depth= 1] . ( 12 sec) [ -16403.5484] [ 3953] [depth= 1] . ( 13 sec) [ -16394.9928] [ 3948] [depth= 1] . ( 13 sec) [ -16394.5688] [ 3946] [depth= 1] . ( 15 sec) [ -16394.5516] [ 3947] [depth= 1] . ( 16 sec) [ -16394.4974] [ 3947] [depth= 1] . ( 18 sec) [ -16371.8356] [Branch lengths ] . ( 18 sec) [ -16369.3614] [Ts/ts ratio ][ 6.080909] . ( 20 sec) [ -16367.7762] [ 3945] [depth= 1] . ( 26 sec) [ -16362.8539] [Branch lengths ] . ( 27 sec) [ -16362.3613] [Ts/ts ratio ][ 6.312034] . ( 35 sec) [ -16361.1720] [Branch lengths ] . ( 78 sec) [ -16361.0047] [Branch lengths ] . ( 78 sec) [ -16361.0047] [Topology ] . ( 79 sec) [ -16360.8241] [Topology ] . ( 81 sec) [ -16360.7295] [Topology ] . ( 82 sec) [ -16360.7143] [Topology ] . ( 83 sec) [ -16360.7097] [Topology ] . ( 85 sec) [ -16360.7079] [Topology ] . ( 86 sec) [ -16360.7071] [Topology ] . ( 86 sec) [ -16360.5025] [Ts/ts ratio ][ 6.466207] . ( 86 sec) [ -16360.5025] [Topology ] . ( 87 sec) [ -16360.4678] [Topology ] . ( 89 sec) [ -16360.4565] [Topology ] . ( 90 sec) [ -16360.4512] [Topology ] . ( 91 sec) [ -16360.4487] [Topology ] . ( 93 sec) [ -16360.4474] [Topology ] . ( 94 sec) [ -16360.4468] [Topology ] . ( 94 sec) [ -16360.4358] [Ts/ts ratio ][ 6.502813] . ( 94 sec) [ -16360.4358] [Topology ] . ( 95 sec) [ -16360.4325] [Topology ] . ( 97 sec) [ -16360.4312] [Topology ] . ( 98 sec) [ -16360.4305] [Topology ] . ( 98 sec) [ -16360.4298] [Ts/ts ratio ][ 6.512060] . ( 98 sec) [ -16360.4298] [Topology ] . ( 100 sec) [ -16360.4291] [Topology ] . ( 100 sec) [ -16360.4291] [Ts/ts ratio ][ 6.512060] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16360.429108. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 62.837891 0.994000 0.074245 69 5.882243 0.833000 0.050231 100 65.662047 1.000000 0.221055 47 0.634553 0.094000 0.048299 98 31.651461 0.975000 0.145123 100 125.935241 1.000000 0.302112 35 0.935200 0.508000 0.019546 93 20.808078 0.947000 0.078147 93 23.575973 0.936000 0.090043 90 28.424769 0.966000 0.150619 100 39.822634 0.994000 0.125180 100 64.567925 0.999000 0.159638 92 13.034377 0.923000 0.031275 71 4.892768 0.716000 0.070043 100 122.124215 1.000000 0.240337 74 2.642461 0.749000 0.003569 72 8.151591 0.823000 0.070869 100 64.558113 1.000000 0.188660 100 39.235786 0.988000 0.243081 100 133.974580 1.000000 0.253870 98 14.603990 0.933000 0.063218 88 10.512345 0.840000 0.058661 100 71.778821 1.000000 0.091116 98 19.646231 0.969000 0.049276 52 7.694969 0.883000 0.038441 95 47.689952 0.994000 0.071039 100 58.061510 0.999000 0.106362 35 5.037999 0.621000 0.029129 100 77.962993 1.000000 0.110722 100 78.240014 0.999000 0.113198 97 21.816528 0.972000 0.052300 100 54.930653 0.998000 0.071653 94 12.745821 0.937000 0.037301 53 3.358208 0.700000 0.015437 100 128.443021 1.000000 0.155974 76 22.103563 0.955000 0.070569 100 75.962468 0.998000 0.130095 100 81.709317 1.000000 0.152122 96 14.169239 0.916000 0.028434 59 4.341596 0.751000 0.002202 15 -1.000000 0.000000 0.000000 76 9.787463 0.874000 0.003018 91 15.533316 0.910000 0.029526 39 0.055889 0.000000 0.000441 71 10.548865 0.842000 0.003679 77 14.393963 0.885000 0.002298 29 -1.000000 0.000000 0.000000 57 13.528565 0.932000 0.081620 88 17.365846 0.916000 0.094342 50 2.160111 0.371000 0.021856 99 98.411443 1.000000 0.109144 . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 3h13m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo