.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2627_54x1915_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... . 1299 patterns found. (out of a total of 1915 sites) . 625 sites without polymorphism (32.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -35716.0992] [Ts/ts ratio ][ 4.272406] . ( 3 sec) [ -35714.7309] [ 8255] [depth= 1] . ( 3 sec) [ -35688.3994] [ 8246] [depth= 1] . ( 3 sec) [ -35687.8516] [ 8272] [depth= 1] . ( 4 sec) [ -35661.3575] [ 8246] [depth= 1] . ( 5 sec) [ -35648.4139] [ 8255] [depth= 1] . ( 5 sec) [ -35642.3948] [ 8252] [depth= 1] . ( 5 sec) [ -35638.7916] [ 8255] [depth= 1] . ( 5 sec) [ -35620.1401] [ 8276] [depth= 1] . ( 6 sec) [ -35596.4905] [ 8255] [depth= 1] . ( 6 sec) [ -35592.3827] [ 8259] [depth= 1] . ( 6 sec) [ -35557.9015] [ 8249] [depth= 1] . ( 6 sec) [ -35555.2379] [ 8254] [depth= 2] . ( 7 sec) [ -35554.6968] [ 8249] [depth= 2] . ( 7 sec) [ -35553.2512] [ 8252] [depth= 1] . ( 7 sec) [ -35552.2059] [ 8249] [depth= 1] . ( 8 sec) [ -35546.4967] [ 8254] [depth= 1] . ( 9 sec) [ -35544.2315] [ 8247] [depth= 1] . ( 9 sec) [ -35542.2497] [ 8250] [depth= 1] . ( 9 sec) [ -35538.4350] [ 8254] [depth= 1] . ( 9 sec) [ -35528.2171] [ 8251] [depth= 1] . ( 10 sec) [ -35516.3253] [ 8250] [depth= 1] . ( 14 sec) [ -35514.1705] [ 8249] [depth= 1] . ( 16 sec) [ -35370.6992] [Branch lengths ] . ( 16 sec) [ -35354.8469] [Ts/ts ratio ][ 4.915907] . ( 21 sec) [ -35354.0142] [ 8241] [depth= 1] . ( 21 sec) [ -35353.2509] [ 8245] [depth= 1] . ( 21 sec) [ -35349.1151] [ 8240] [depth= 1] . ( 22 sec) [ -35346.7261] [ 8233] [depth= 1] . ( 24 sec) [ -35344.8813] [ 8231] [depth= 1] . ( 30 sec) [ -35317.8624] [Branch lengths ] . ( 30 sec) [ -35316.9063] [Ts/ts ratio ][ 5.087328] . ( 44 sec) [ -35308.0526] [Branch lengths ] . ( 124 sec) [ -35305.0280] [Branch lengths ] . ( 125 sec) [ -35305.0280] [Topology ] . ( 127 sec) [ -35304.3746] [Topology ] . ( 130 sec) [ -35304.0527] [Topology ] . ( 133 sec) [ -35303.8320] [Topology ] . ( 136 sec) [ -35303.6756] [Topology ] . ( 139 sec) [ -35303.5629] [Topology ] . ( 142 sec) [ -35303.4816] [Topology ] . ( 142 sec) [ -35301.1819] [Ts/ts ratio ][ 5.376588] . ( 142 sec) [ -35301.1819] [Topology ] . ( 145 sec) [ -35300.7093] [Topology ] . ( 148 sec) [ -35300.4257] [Topology ] . ( 151 sec) [ -35300.2245] [Topology ] . ( 154 sec) [ -35300.0795] [Topology ] . ( 156 sec) [ -35299.9737] [Topology ] . ( 159 sec) [ -35299.8966] [Topology ] . ( 160 sec) [ -35299.7442] [Ts/ts ratio ][ 5.454466] . ( 160 sec) [ -35299.7442] [Topology ] . ( 163 sec) [ -35299.6263] [Topology ] . ( 165 sec) [ -35299.5441] [Topology ] . ( 168 sec) [ -35299.4844] [Topology ] . ( 171 sec) [ -35299.4409] [Topology ] . ( 174 sec) [ -35299.4089] [Topology ] . ( 177 sec) [ -35299.3854] [Topology ] . ( 177 sec) [ -35299.3474] [Ts/ts ratio ][ 5.493982] . ( 177 sec) [ -35299.3474] [Topology ] . ( 180 sec) [ -35299.3137] [Topology ] . ( 183 sec) [ -35299.2900] [Topology ] . ( 186 sec) [ -35299.2725] [Topology ] . ( 189 sec) [ -35299.2597] [Topology ] . ( 192 sec) [ -35299.2502] [Topology ] . ( 195 sec) [ -35299.2432] [Topology ] . ( 195 sec) [ -35299.2326] [Ts/ts ratio ][ 5.515101] . ( 195 sec) [ -35299.2326] [Topology ] . ( 198 sec) [ -35299.2228] [Topology ] . ( 201 sec) [ -35299.2158] [Topology ] . ( 204 sec) [ -35299.2107] [Topology ] . ( 206 sec) [ -35299.2069] [Topology ] . ( 209 sec) [ -35299.2041] [Topology ] . ( 212 sec) [ -35299.2021] [Topology ] . ( 213 sec) [ -35299.1991] [Ts/ts ratio ][ 5.526522] . ( 213 sec) [ -35299.1991] [Topology ] . ( 216 sec) [ -35299.1962] [Topology ] . ( 218 sec) [ -35299.1941] [Topology ] . ( 221 sec) [ -35299.1926] [Topology ] . ( 224 sec) [ -35299.1915] [Topology ] . ( 227 sec) [ -35299.1907] [Topology ] . ( 227 sec) [ -35299.1900] [Ts/ts ratio ][ 5.532048] . ( 228 sec) [ -35299.1900] [Topology ] . ( 230 sec) [ -35299.1890] [Topology ] . ( 233 sec) [ -35299.1883] [Topology ] . ( 234 sec) [ -35299.1883] [Ts/ts ratio ][ 5.532048] . ( 234 sec) [ -35299.1883] [Topology ] . ( 237 sec) [ -35299.1877] [Topology ] . ( 237 sec) [ -35299.1877] [Ts/ts ratio ][ 5.532048] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35299.187746. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 128.580423 1.000000 0.047984 100 67.664622 0.997000 0.036226 92 15.151225 0.950000 0.019025 100 53.909590 0.995000 0.049248 100 35.935744 0.989000 0.044447 100 102.875369 1.000000 0.091222 100 53.631920 0.995000 0.073653 96 14.114988 0.920000 0.051314 100 66.342348 0.999000 0.076254 48 4.848966 0.761000 0.012806 50 10.455232 0.821000 0.035078 64 14.014372 0.922000 0.031966 100 150.239468 1.000000 0.227042 100 86.640445 0.999000 0.090083 100 110.722412 1.000000 0.101173 100 96.085611 1.000000 0.097468 100 230.030106 1.000000 0.174762 97 18.077054 0.944000 0.047022 100 228.244181 1.000000 0.136245 100 58.801930 0.996000 0.051729 100 37.208693 0.985000 0.010887 100 119.732895 1.000000 0.100172 100 88.733752 1.000000 0.084216 100 48.032841 0.996000 0.039716 100 53.952194 0.999000 0.043295 63 3.205277 0.701000 0.008920 100 33.989117 0.984000 0.032704 100 230.045179 1.000000 0.078912 100 41.115356 0.986000 0.023883 97 23.569410 0.946000 0.018882 87 16.986420 0.922000 0.020704 100 276.575966 1.000000 0.111392 54 8.827408 0.817000 0.009670 99 173.336442 1.000000 0.027895 98 14.327616 0.899000 0.005623 81 26.957112 0.865000 0.005158 71 21.266557 0.937000 0.009461 43 9.670685 0.554000 0.006370 63 14.059737 0.899000 0.004751 91 52.648925 0.983000 0.009310 64 16.426780 0.909000 0.004040 32 3.377907 0.410000 0.001661 100 33.641299 0.965000 0.004082 57 34.307208 0.970000 0.004847 44 8.420636 0.884000 0.025024 100 282.596387 1.000000 0.211160 98 35.634120 0.994000 0.100828 99 27.160264 0.980000 0.085522 78 7.492036 0.769000 0.039120 100 112.846370 0.999000 0.157972 76 10.132621 0.754000 0.048256 . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 7h6m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo