.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2479_30x627_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 521 patterns found. (out of a total of 627 sites) . 123 sites without polymorphism (19.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 37Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -18178.5487] [Alpha ][ 0.611907] . ( 2 sec) [ -18178.5487] [Topology ] . ( 4 sec) [ -18078.2315] [Topology ] . ( 8 sec) [ -18069.5546] [Topology ] . ( 11 sec) [ -18067.9397] [Topology ] . ( 14 sec) [ -18067.8156] [Topology ] . ( 17 sec) [ -18067.4540] [Topology ] . ( 21 sec) [ -18067.6241] [Topology ] . Moving backward . ( 21 sec) [ -18066.7104] [Topology ] . ( 24 sec) [ -18066.3550] [Topology ] . ( 27 sec) [ -18066.3089] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -18061.5099] [Alpha ][ 0.723516] . ( 56 sec) [ -18061.5099] [Topology ] . ( 59 sec) [ -18060.8363] [Topology ] . ( 62 sec) [ -18060.5480] [Topology ] . ( 65 sec) [ -18060.4022] [Topology ] . ( 68 sec) [ -18060.3259] [Topology ] . ( 71 sec) [ -18060.2846] [Topology ] . ( 74 sec) [ -18060.2625] [Topology ] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -18060.0867] [Alpha ][ 0.746673] . ( 100 sec) [ -18060.0867] [Topology ] . ( 103 sec) [ -18060.0368] [Topology ] . ( 106 sec) [ -18060.0115] [Topology ] . ( 109 sec) [ -18059.9979] [Topology ] . ( 112 sec) [ -18059.9904] [Topology ] . ( 115 sec) [ -18059.9863] [Topology ] . ( 118 sec) [ -18059.9841] [Topology ] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -18059.9715] [Alpha ][ 0.753168] . ( 144 sec) [ -18059.9715] [Topology ] . ( 147 sec) [ -18059.9673] [Topology ] . ( 150 sec) [ -18059.9651] [Topology ] . ( 153 sec) [ -18059.9639] [Topology ] . ( 156 sec) [ -18059.9633] [Topology ] . Checking for NNIs, optimizing five branches... . ( 182 sec) [ -18059.9627] [Alpha ][ 0.754490] . ( 182 sec) [ -18059.9627] [Topology ] . ( 185 sec) [ -18059.9621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 210 sec) [ -18059.9621] [Alpha ][ 0.754490] . ( 211 sec) [ -18059.9621] [Topology ] . ( 214 sec) [ -18059.9617] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 264 sec) [ -18178.5487] [Alpha ][ 0.611907] . ( 266 sec) [ -18176.6899] [ 3274] [depth= 1] . ( 266 sec) [ -18176.2365] [ 3272] [depth= 1] . ( 267 sec) [ -18173.3351] [ 3274] [depth= 1] . ( 271 sec) [ -18169.5680] [ 3279] [depth= 1] . ( 273 sec) [ -18168.0103] [ 3274] [depth= 1] . ( 279 sec) [ -18163.4481] [ 3273] [depth= 1] . ( 279 sec) [ -18163.3021] [ 3273] [depth= 1] . ( 280 sec) [ -18161.4043] [ 3274] [depth= 1] . ( 280 sec) [ -18158.7458] [ 3273] [depth= 1] . ( 282 sec) [ -18151.5756] [ 3273] [depth= 2] . ( 284 sec) [ -18135.4753] [ 3269] [depth= 2] . ( 285 sec) [ -18133.6824] [ 3272] [depth= 1] . ( 286 sec) [ -18131.0336] [ 3267] [depth= 2] . ( 286 sec) [ -18125.8354] [ 3268] [depth= 1] . ( 287 sec) [ -18118.3604] [ 3263] [depth= 3] . ( 287 sec) [ -18113.1297] [ 3260] [depth= 1] . ( 291 sec) [ -18111.3813] [ 3264] [depth= 1] . ( 291 sec) [ -18105.5944] [ 3260] [depth= 3] . ( 292 sec) [ -18103.9480] [ 3260] [depth= 1] . ( 295 sec) [ -18102.8742] [ 3260] [depth= 1] . ( 297 sec) [ -18070.0648] [Branch lengths ] . ( 298 sec) [ -18066.2468] [Alpha ][ 0.711148] . ( 305 sec) [ -18063.1961] [ 3261] [depth= 2] . ( 311 sec) [ -18062.6789] [ 3262] [depth= 1] . ( 319 sec) [ -18061.8072] [ 3261] [depth= 1] . ( 331 sec) [ -18058.2511] [Branch lengths ] . ( 331 sec) [ -18058.0679] [Alpha ][ 0.734464] . ( 365 sec) [ -18057.3162] [Branch lengths ] . ( 365 sec) [ -18057.3162] [Topology ] . ( 368 sec) [ -18057.2145] [Topology ] . ( 371 sec) [ -18057.1762] [Topology ] . ( 375 sec) [ -18057.1555] [Topology ] . ( 378 sec) [ -18057.1440] [Topology ] . ( 381 sec) [ -18057.1376] [Topology ] . ( 384 sec) [ -18057.1339] [Topology ] . ( 384 sec) [ -18057.0207] [Alpha ][ 0.753094] . ( 384 sec) [ -18057.0207] [Topology ] . ( 388 sec) [ -18057.0029] [Topology ] . ( 391 sec) [ -18056.9939] [Topology ] . ( 394 sec) [ -18056.9889] [Topology ] . ( 397 sec) [ -18056.9861] [Topology ] . ( 400 sec) [ -18056.9845] [Topology ] . ( 403 sec) [ -18056.9836] [Topology ] . ( 403 sec) [ -18056.9790] [Alpha ][ 0.757039] . ( 404 sec) [ -18056.9790] [Topology ] . ( 407 sec) [ -18056.9774] [Topology ] . ( 410 sec) [ -18056.9765] [Topology ] . ( 410 sec) [ -18056.9765] [Alpha ][ 0.757796] . ( 410 sec) [ -18056.9765] [Topology ] . ( 413 sec) [ -18056.9758] [Topology ] . ( 414 sec) [ -18056.9758] [Alpha ][ 0.757796] . Checking for NNIs, optimizing five branches... . ( 440 sec) [ -18056.6146] [Topology ] . Checking for NNIs, optimizing five branches... . ( 466 sec) [ -18056.1621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 493 sec) [ -18056.0649] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -18059.961750 . Log likelihood obtained after SPR moves : -18056.064925 . Log likelihood of the current tree: -18056.064925. . Printing the most likely tree in file 'proteic_M2479_30x627_2005.phy_phyml_tree.txt'... . Time used 0h8m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 518.63user 0.00system 8:40.30elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps