.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2974_56x827_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... . 330 patterns found. (out of a total of 827 sites) . 592 sites without polymorphism (71.58%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5680.5297] [Ts/ts ratio ][ 4.135362] . ( 0 sec) [ -5676.4055] [ 870] [depth= 1] . ( 1 sec) [ -5675.0489] [ 873] [depth= 1] . ( 1 sec) [ -5673.9623] [ 873] [depth= 1] . ( 2 sec) [ -5673.6150] [ 873] [depth= 1] . ( 2 sec) [ -5673.5883] [ 873] [depth= 1] . ( 2 sec) [ -5670.4294] [ 873] [depth= 1] . ( 2 sec) [ -5666.4391] [ 873] [depth= 1] . ( 2 sec) [ -5658.3536] [ 872] [depth= 1] . ( 2 sec) [ -5655.6043] [ 873] [depth= 1] . ( 2 sec) [ -5647.7557] [ 870] [depth= 1] . ( 2 sec) [ -5643.6002] [ 873] [depth= 3] . ( 2 sec) [ -5642.4479] [ 874] [depth= 1] . ( 2 sec) [ -5634.5238] [ 873] [depth= 1] . ( 3 sec) [ -5629.4338] [ 873] [depth= 2] . ( 3 sec) [ -5627.8739] [ 870] [depth= 1] . ( 3 sec) [ -5619.9914] [ 867] [depth= 1] . ( 3 sec) [ -5619.9244] [ 871] [depth= 1] . ( 4 sec) [ -5611.7731] [ 867] [depth= 1] . ( 4 sec) [ -5608.5362] [ 866] [depth= 2] . ( 4 sec) [ -5607.8904] [ 866] [depth= 1] . ( 4 sec) [ -5606.0173] [ 866] [depth= 1] . ( 4 sec) [ -5605.2876] [ 866] [depth= 1] . ( 4 sec) [ -5605.2606] [ 866] [depth= 1] . ( 4 sec) [ -5601.1965] [ 866] [depth= 1] . ( 5 sec) [ -5598.9579] [ 867] [depth= 1] . ( 5 sec) [ -5598.5424] [ 866] [depth= 1] . ( 7 sec) [ -5598.4386] [ 866] [depth= 1] . ( 7 sec) [ -5598.4257] [ 866] [depth= 2] . ( 8 sec) [ -5553.6443] [Branch lengths ] . ( 8 sec) [ -5553.0504] [Ts/ts ratio ][ 4.482749] . ( 9 sec) [ -5549.8449] [ 863] [depth= 1] . ( 10 sec) [ -5549.8246] [ 863] [depth= 1] . ( 11 sec) [ -5548.6571] [ 868] [depth= 9] . ( 11 sec) [ -5548.1208] [ 868] [depth= 1] . ( 11 sec) [ -5547.9359] [ 871] [depth= 1] . ( 17 sec) [ -5544.7974] [Branch lengths ] . ( 17 sec) [ -5544.7932] [Ts/ts ratio ][ 4.512874] . ( 19 sec) [ -5543.6941] [ 868] [depth= 1] . ( 26 sec) [ -5543.3417] [Branch lengths ] . ( 26 sec) [ -5543.3417] [Ts/ts ratio ][ 4.512874] . ( 35 sec) [ -5543.3201] [Branch lengths ] . ( 67 sec) [ -5543.3191] [Branch lengths ] . ( 67 sec) [ -5543.3191] [Topology ] . ( 68 sec) [ -5543.3191] [Topology ] . ( 68 sec) [ -5543.3191] [Ts/ts ratio ][ 4.512874] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5543.319113. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 181.412597 1.000000 0.088664 16 3.371986 0.507000 0.012614 59 19.046253 0.951000 0.023778 43 3.007848 0.742000 0.010795 100 51.044592 0.990000 0.041638 95 21.694987 0.953000 0.024412 5 4.841327 0.558000 0.014550 35 6.020047 0.848000 0.010341 100 78.968324 1.000000 0.062448 100 21.546757 0.966000 0.028013 38 1.641319 0.312000 0.007553 80 13.733670 0.887000 0.018830 87 17.921362 0.907000 0.014691 4 13.358286 0.919000 0.015118 24 11.733725 0.921000 0.016424 27 24.177996 0.973000 0.022928 17 1.426823 0.365000 0.002231 87 74.634844 0.999000 0.025689 39 5.187164 0.721000 0.003943 49 6.499410 0.829000 0.006897 28 -1.000000 0.000000 0.000000 14 2.009961 0.393000 0.004263 71 19.316887 0.920000 0.015183 100 31.666074 0.980000 0.020259 33 -1.000000 0.000000 0.000000 98 53.402641 0.998000 0.028602 85 7.515273 0.813000 0.004147 14 -1.000000 0.000000 0.000000 26 1.293150 0.327000 0.003533 100 59.110158 0.999000 0.027544 6 3.654215 0.677000 0.003916 16 13.218498 0.882000 0.009750 18 4.667977 0.799000 0.008815 58 16.793259 0.899000 0.008645 84 29.640441 0.968000 0.016868 98 38.570256 0.978000 0.013645 10 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 17 -1.000000 0.000000 0.000000 39 -1.000000 0.000000 0.000000 52 2.874233 0.689000 0.013332 88 8.247581 0.899000 0.021667 100 94.561498 1.000000 0.065742 89 11.655390 0.854000 0.010169 99 65.442037 0.996000 0.044506 100 30.270233 0.960000 0.024815 81 10.770162 0.863000 0.008582 78 9.744681 0.778000 0.010453 94 13.480004 0.914000 0.010823 85 6.393264 0.862000 0.010739 100 74.703588 0.998000 0.037899 90 17.071631 0.933000 0.014783 68 4.715868 0.749000 0.001941 . Printing the most likely tree in file 'nucleic_M2974_56x827_2006.phy_phyml_tree.txt'... . Time used 1h41m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo