.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1377_19x1566_2003.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... . 921 patterns found. (out of a total of 1566 sites) . 698 sites without polymorphism (44.57%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -17793.6885] [Alpha ][ 0.500960] . ( 1 sec) [ -17793.6885] [Topology ] . ( 5 sec) [ -17680.2591] [Topology ] . ( 8 sec) [ -17661.7294] [Topology ] . ( 12 sec) [ -17656.0697] [Topology ] . ( 15 sec) [ -17648.2077] [Topology ] . ( 18 sec) [ -17643.9261] [Topology ] . ( 22 sec) [ -17643.0631] [Topology ] . ( 25 sec) [ -17633.7399] [Topology ] . ( 28 sec) [ -17629.7436] [Topology ] . ( 32 sec) [ -17620.8479] [Topology ] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -17609.7171] [Topology ] . ( 65 sec) [ -17609.2110] [Alpha ][ 0.528546] . ( 65 sec) [ -17609.2110] [Topology ] . ( 68 sec) [ -17605.1469] [Topology ] . ( 72 sec) [ -17601.1654] [Topology ] . ( 75 sec) [ -17600.4781] [Topology ] . ( 78 sec) [ -17600.3854] [Topology ] . ( 82 sec) [ -17600.3683] [Topology ] . ( 85 sec) [ -17600.3645] [Topology ] . ( 88 sec) [ -17600.3635] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -17600.0824] [Topology ] . ( 117 sec) [ -17600.0748] [Alpha ][ 0.532088] . ( 118 sec) [ -17600.0748] [Topology ] . ( 121 sec) [ -17594.8402] [Topology ] . ( 124 sec) [ -17592.2125] [Topology ] . ( 128 sec) [ -17590.8005] [Topology ] . ( 131 sec) [ -17588.6849] [Topology ] . ( 135 sec) [ -17581.0510] [Topology ] . ( 138 sec) [ -17576.6491] [Topology ] . ( 141 sec) [ -17576.1519] [Topology ] . ( 145 sec) [ -17576.1165] [Topology ] . ( 148 sec) [ -17576.1127] [Topology ] . Checking for NNIs, optimizing five branches... . ( 179 sec) [ -17576.0929] [Alpha ][ 0.537844] . ( 179 sec) [ -17576.0929] [Topology ] . ( 182 sec) [ -17576.0925] [Topology ] . Checking for NNIs, optimizing five branches... . ( 210 sec) [ -17576.0925] [Alpha ][ 0.537844] . ( 210 sec) [ -17576.0925] [Topology ] . ( 214 sec) [ -17576.0925] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 270 sec) [ -17793.6885] [Alpha ][ 0.500960] . ( 272 sec) [ -17790.9930] [ 2484] [depth= 1] . ( 273 sec) [ -17789.5885] [ 2486] [depth= 1] . ( 275 sec) [ -17780.0007] [ 2470] [depth= 1] . ( 276 sec) [ -17748.4106] [ 2467] [depth= 4] . ( 278 sec) [ -17692.7793] [ 2457] [depth= 4] . ( 279 sec) [ -17683.5541] [ 2454] [depth= 3] . ( 281 sec) [ -17669.3304] [ 2456] [depth= 3] . ( 282 sec) [ -17666.8827] [ 2457] [depth= 1] . ( 283 sec) [ -17639.5784] [ 2450] [depth= 4] . ( 284 sec) [ -17637.8291] [ 2448] [depth= 1] . ( 284 sec) [ -17635.0257] [ 2451] [depth= 3] . ( 285 sec) [ -17630.9459] [ 2460] [depth= 1] . ( 289 sec) [ -17627.8661] [ 2457] [depth= 1] . ( 290 sec) [ -17626.4651] [ 2459] [depth= 1] . ( 303 sec) [ -17621.7974] [ 2460] [depth= 1] . ( 308 sec) [ -17593.2880] [Branch lengths ] . ( 308 sec) [ -17593.0826] [Alpha ][ 0.518577] . ( 311 sec) [ -17568.7357] [ 2451] [depth= 1] . ( 320 sec) [ -17568.0733] [ 2445] [depth= 3] . ( 322 sec) [ -17566.2837] [ 2446] [depth= 4] . ( 326 sec) [ -17563.1045] [ 2444] [depth= 1] . ( 347 sec) [ -17553.9193] [Branch lengths ] . ( 348 sec) [ -17553.8091] [Alpha ][ 0.531665] . ( 397 sec) [ -17553.2150] [Branch lengths ] . ( 397 sec) [ -17553.2150] [Topology ] . ( 400 sec) [ -17553.1839] [Topology ] . ( 404 sec) [ -17553.1753] [Topology ] . ( 407 sec) [ -17553.1719] [Topology ] . ( 410 sec) [ -17553.1703] [Topology ] . ( 414 sec) [ -17553.1696] [Topology ] . ( 414 sec) [ -17553.1685] [Alpha ][ 0.533014] . ( 415 sec) [ -17553.1685] [Topology ] . ( 418 sec) [ -17553.1681] [Topology ] . ( 419 sec) [ -17553.1681] [Alpha ][ 0.533014] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -17576.092483 . Log likelihood obtained after SPR moves : -17553.168074 . Log likelihood of the current tree: -17553.168074. . Printing the most likely tree in file 'proteic_M1377_19x1566_2003.phy_phyml_tree.txt'... . Time used 0h7m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 444.82user 0.00system 7:28.41elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps