.......................... 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 : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : NNIs . 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 NNI moves)... . ( 1 sec) [ -36710.7724] [GTR parameters ] . ( 2 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 2 sec) [ -36466.0989] [Topology ] . ( 5 sec) [ -36209.2967] [Topology ] . ( 8 sec) [ -36187.4972] [Topology ] . ( 10 sec) [ -36183.6050] [Topology ] . ( 13 sec) [ -36182.2546] [Topology ] . ( 16 sec) [ -36181.6395] [Topology ] . ( 19 sec) [ -36181.3321] [Topology ] . ( 22 sec) [ -36181.1727] [Topology ] . ( 24 sec) [ -36181.0882] [Topology ] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -36180.6868] [Topology ] . ( 56 sec) [ -35322.5824] [GTR parameters ] . ( 56 sec) [ -35320.2697] [Alpha ][ 0.467463] . ( 56 sec) [ -35320.2697] [Topology ] . ( 59 sec) [ -35294.8290] [Topology ] . ( 62 sec) [ -35286.3497] [Topology ] . ( 64 sec) [ -35282.3406] [Topology ] . ( 67 sec) [ -35280.0868] [Topology ] . ( 70 sec) [ -35278.7376] [Topology ] . ( 73 sec) [ -35277.8949] [Topology ] . ( 76 sec) [ -35277.3529] [Topology ] . Checking for NNIs, optimizing five branches... . ( 104 sec) [ -35269.7035] [GTR parameters ] . ( 105 sec) [ -35268.4270] [Alpha ][ 0.491109] . ( 105 sec) [ -35268.4270] [Topology ] . ( 107 sec) [ -35265.7908] [Topology ] . ( 110 sec) [ -35264.1797] [Topology ] . ( 113 sec) [ -35263.1137] [Topology ] . ( 116 sec) [ -35262.3863] [Topology ] . ( 119 sec) [ -35261.8806] [Topology ] . ( 122 sec) [ -35261.5229] [Topology ] . Checking for NNIs, optimizing five branches... . ( 150 sec) [ -35260.9682] [GTR parameters ] . ( 150 sec) [ -35260.8456] [Alpha ][ 0.498712] . ( 150 sec) [ -35260.8456] [Topology ] . ( 153 sec) [ -35260.2677] [Topology ] . ( 156 sec) [ -35259.8627] [Topology ] . ( 159 sec) [ -35259.5713] [Topology ] . ( 162 sec) [ -35259.3594] [Topology ] . ( 164 sec) [ -35259.2041] [Topology ] . ( 167 sec) [ -35259.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -35258.9334] [GTR parameters ] . ( 195 sec) [ -35258.9280] [Alpha ][ 0.500271] . ( 195 sec) [ -35258.9280] [Topology ] . ( 198 sec) [ -35258.7614] [Topology ] . ( 201 sec) [ -35258.6406] [Topology ] . ( 204 sec) [ -35258.5508] [Topology ] . ( 207 sec) [ -35258.4836] [Topology ] . ( 210 sec) [ -35258.4333] [Topology ] . ( 212 sec) [ -35258.3953] [Topology ] . Checking for NNIs, optimizing five branches... . ( 238 sec) [ -35258.3366] [GTR parameters ] . ( 238 sec) [ -35258.3366] [Alpha ][ 0.500271] . ( 238 sec) [ -35258.3366] [Topology ] . ( 241 sec) [ -35258.2807] [Topology ] . ( 244 sec) [ -35258.2399] [Topology ] . ( 247 sec) [ -35258.2092] [Topology ] . ( 250 sec) [ -35258.1859] [Topology ] . ( 252 sec) [ -35258.1682] [Topology ] . ( 255 sec) [ -35258.1547] [Topology ] . Checking for NNIs, optimizing five branches... . ( 280 sec) [ -35258.1319] [GTR parameters ] . ( 280 sec) [ -35258.1319] [Alpha ][ 0.500271] . ( 280 sec) [ -35258.1319] [Topology ] . ( 283 sec) [ -35258.1114] [Topology ] . ( 286 sec) [ -35258.0963] [Topology ] . ( 289 sec) [ -35258.0849] [Topology ] . ( 292 sec) [ -35258.0762] [Topology ] . ( 294 sec) [ -35258.0695] [Topology ] . ( 297 sec) [ -35258.0644] [Topology ] . Checking for NNIs, optimizing five branches... . ( 321 sec) [ -35258.0563] [GTR parameters ] . ( 322 sec) [ -35258.0563] [Alpha ][ 0.500271] . ( 322 sec) [ -35258.0563] [Topology ] . ( 325 sec) [ -35258.0487] [Topology ] . ( 328 sec) [ -35258.0431] [Topology ] . ( 330 sec) [ -35258.0389] [Topology ] . ( 333 sec) [ -35258.0356] [Topology ] . ( 336 sec) [ -35258.0331] [Topology ] . ( 339 sec) [ -35258.0312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 363 sec) [ -35258.0280] [GTR parameters ] . ( 364 sec) [ -35258.0277] [Alpha ][ 0.499771] . ( 364 sec) [ -35258.0277] [Topology ] . ( 367 sec) [ -35258.0248] [Topology ] . ( 369 sec) [ -35258.0228] [Topology ] . ( 372 sec) [ -35258.0212] [Topology ] . ( 375 sec) [ -35258.0200] [Topology ] . ( 378 sec) [ -35258.0190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 404 sec) [ -35258.0177] [GTR parameters ] . ( 404 sec) [ -35258.0177] [Alpha ][ 0.499771] . ( 404 sec) [ -35258.0177] [Topology ] . ( 407 sec) [ -35258.0164] [Topology ] . ( 410 sec) [ -35258.0154] [Topology ] . Checking for NNIs, optimizing five branches... . ( 434 sec) [ -35258.0153] [GTR parameters ] . ( 434 sec) [ -35258.0153] [Alpha ][ 0.499771] . ( 434 sec) [ -35258.0153] [Topology ] . ( 437 sec) [ -35258.0145] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35258.014465. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 0h8m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 483.07user 0.00system 8:05.64elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps