.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1372_23x394_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 246 patterns found. (out of a total of 394 sites) . 162 sites without polymorphism (41.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 1 sec) [ -4512.1912] [Topology ] . ( 3 sec) [ -4483.0594] [Topology ] . ( 4 sec) [ -4477.9104] [Topology ] . ( 6 sec) [ -4476.3403] [Topology ] . ( 7 sec) [ -4475.2627] [Topology ] . ( 9 sec) [ -4474.9882] [Topology ] . ( 10 sec) [ -4474.9096] [Topology ] . ( 12 sec) [ -4474.8846] [Topology ] . ( 14 sec) [ -4474.8756] [Topology ] . ( 15 sec) [ -4474.8722] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -4474.5121] [Alpha ][ 0.655762] . ( 24 sec) [ -4474.5121] [Topology ] . ( 25 sec) [ -4474.4958] [Topology ] . ( 27 sec) [ -4474.4919] [Topology ] . ( 28 sec) [ -4474.4903] [Topology ] . ( 29 sec) [ -4474.4896] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -4474.4890] [Alpha ][ 0.658482] . ( 38 sec) [ -4474.4890] [Topology ] . ( 40 sec) [ -4474.4886] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -4474.4886] [Alpha ][ 0.658482] . ( 49 sec) [ -4474.4886] [Topology ] . ( 50 sec) [ -4474.4884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4474.488419. . Printing the most likely tree in file 'proteic_M1372_23x394_2003.phy_phyml_tree.txt'... . Time used 0h1m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 66.17user 0.00system 1:14.46elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps