.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_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... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -29176.8561] [GTR parameters ] . ( 1 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 1 sec) [ -28718.2078] [Topology ] . ( 4 sec) [ -28358.1403] [Topology ] . ( 8 sec) [ -28287.7496] [Topology ] . ( 11 sec) [ -28272.6038] [Topology ] . ( 14 sec) [ -28264.6408] [Topology ] . ( 17 sec) [ -28262.2033] [Topology ] . ( 20 sec) [ -28260.6583] [Topology ] . ( 23 sec) [ -28260.9603] [Topology ] . Moving backward . ( 23 sec) [ -28257.1897] [Topology ] . ( 26 sec) [ -28256.3358] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -28255.2392] [Topology ] . ( 60 sec) [ -27042.7798] [GTR parameters ] . ( 60 sec) [ -26994.3318] [Alpha ][ 0.359977] . ( 60 sec) [ -26994.3318] [Topology ] . ( 64 sec) [ -26978.7021] [Topology ] . ( 67 sec) [ -26973.8576] [Topology ] . ( 70 sec) [ -26970.8549] [Topology ] . ( 73 sec) [ -26965.9230] [Topology ] . ( 76 sec) [ -26964.8842] [Topology ] . ( 80 sec) [ -26964.6376] [Topology ] . ( 83 sec) [ -26964.5529] [Topology ] . ( 86 sec) [ -26964.5265] [Topology ] . ( 89 sec) [ -26964.5174] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -26964.3230] [Topology ] . ( 122 sec) [ -26962.6025] [GTR parameters ] . ( 122 sec) [ -26958.2517] [Alpha ][ 0.325279] . ( 122 sec) [ -26958.2517] [Topology ] . ( 125 sec) [ -26956.9976] [Topology ] . ( 129 sec) [ -26956.5920] [Topology ] . ( 132 sec) [ -26956.4431] [Topology ] . ( 135 sec) [ -26956.3755] [Topology ] . ( 138 sec) [ -26955.4347] [Topology ] . ( 141 sec) [ -26955.3374] [Topology ] . ( 144 sec) [ -26955.3272] [Topology ] . ( 148 sec) [ -26955.3253] [Topology ] . ( 151 sec) [ -26955.3249] [Topology ] . Checking for NNIs, optimizing five branches... . ( 175 sec) [ -26955.2670] [Topology ] . ( 180 sec) [ -26955.1035] [GTR parameters ] . ( 181 sec) [ -26954.1330] [Alpha ][ 0.309800] . ( 181 sec) [ -26954.1330] [Topology ] . ( 184 sec) [ -26953.6506] [Topology ] . ( 187 sec) [ -26953.5250] [Topology ] . ( 190 sec) [ -26953.4835] [Topology ] . ( 193 sec) [ -26953.4690] [Topology ] . ( 196 sec) [ -26953.4637] [Topology ] . ( 200 sec) [ -26953.4617] [Topology ] . Checking for NNIs, optimizing five branches... . ( 228 sec) [ -26953.4424] [GTR parameters ] . ( 228 sec) [ -26953.1895] [Alpha ][ 0.302220] . ( 228 sec) [ -26953.1895] [Topology ] . ( 231 sec) [ -26953.0886] [Topology ] . ( 234 sec) [ -26953.0576] [Topology ] . ( 237 sec) [ -26953.0468] [Topology ] . ( 241 sec) [ -26953.0429] [Topology ] . ( 244 sec) [ -26953.0415] [Topology ] . ( 247 sec) [ -26953.0409] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -26953.0148] [Topology ] . ( 274 sec) [ -26953.0054] [GTR parameters ] . ( 274 sec) [ -26952.9089] [Alpha ][ 0.297401] . ( 274 sec) [ -26952.9089] [Topology ] . ( 277 sec) [ -26952.8427] [Topology ] . ( 280 sec) [ -26952.8242] [Topology ] . ( 283 sec) [ -26952.8180] [Topology ] . ( 286 sec) [ -26952.8158] [Topology ] . ( 290 sec) [ -26952.8150] [Topology ] . Checking for NNIs, optimizing five branches... . ( 317 sec) [ -26952.8136] [GTR parameters ] . ( 318 sec) [ -26952.7720] [Alpha ][ 0.294258] . ( 318 sec) [ -26952.7720] [Topology ] . ( 321 sec) [ -26952.7518] [Topology ] . ( 324 sec) [ -26952.7458] [Topology ] . ( 327 sec) [ -26952.7438] [Topology ] . ( 330 sec) [ -26952.7431] [Topology ] . Checking for NNIs, optimizing five branches... . ( 355 sec) [ -26952.7430] [GTR parameters ] . ( 355 sec) [ -26952.7312] [Alpha ][ 0.292591] . ( 355 sec) [ -26952.7312] [Topology ] . ( 359 sec) [ -26952.7242] [Topology ] . ( 362 sec) [ -26952.7221] [Topology ] . ( 365 sec) [ -26952.7214] [Topology ] . Checking for NNIs, optimizing five branches... . ( 393 sec) [ -26952.7198] [GTR parameters ] . ( 393 sec) [ -26952.7156] [Alpha ][ 0.291594] . ( 394 sec) [ -26952.7156] [Topology ] . ( 397 sec) [ -26952.7128] [Topology ] . ( 400 sec) [ -26952.7119] [Topology ] . Checking for NNIs, optimizing five branches... . ( 425 sec) [ -26952.7119] [GTR parameters ] . ( 425 sec) [ -26952.7109] [Alpha ][ 0.291108] . ( 425 sec) [ -26952.7109] [Topology ] . ( 428 sec) [ -26952.7096] [Topology ] . ( 431 sec) [ -26952.7092] [Topology ] . Checking for NNIs, optimizing five branches... . ( 456 sec) [ -26952.7091] [GTR parameters ] . ( 456 sec) [ -26952.7086] [Alpha ][ 0.290762] . ( 457 sec) [ -26952.7086] [Topology ] . ( 460 sec) [ -26952.7079] [Topology ] . Checking for NNIs, optimizing five branches... . ( 486 sec) [ -26952.7078] [GTR parameters ] . ( 486 sec) [ -26952.7078] [Alpha ][ 0.290471] . ( 486 sec) [ -26952.7078] [Topology ] . ( 489 sec) [ -26952.7072] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26952.707180. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 0h8m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 537.11user 0.00system 8:59.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps