.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1991_32x129_2004.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 . 9 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 113 patterns found. (out of a total of 129 sites) . 25 sites without polymorphism (19.38%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 0 sec) [ -2496.1543] [Topology ] . ( 1 sec) [ -2426.2101] [Topology ] . ( 2 sec) [ -2408.7866] [Topology ] . ( 3 sec) [ -2399.9867] [Topology ] . ( 5 sec) [ -2397.8601] [Topology ] . ( 6 sec) [ -2397.4479] [Topology ] . ( 7 sec) [ -2397.3036] [Topology ] . ( 8 sec) [ -2397.2430] [Topology ] . ( 9 sec) [ -2397.2138] [Topology ] . ( 10 sec) [ -2397.1983] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -2395.8503] [Topology ] . ( 18 sec) [ -2394.5012] [Alpha ][ 1.313066] . ( 18 sec) [ -2394.5012] [Topology ] . ( 19 sec) [ -2394.4118] [Topology ] . ( 21 sec) [ -2394.3864] [Topology ] . ( 22 sec) [ -2394.3757] [Topology ] . ( 23 sec) [ -2394.3709] [Topology ] . ( 24 sec) [ -2394.3686] [Topology ] . ( 25 sec) [ -2394.3674] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -2394.1201] [Topology ] . ( 34 sec) [ -2394.1162] [Alpha ][ 1.291508] . ( 34 sec) [ -2394.1162] [Topology ] . ( 35 sec) [ -2394.1143] [Topology ] . ( 36 sec) [ -2394.1136] [Topology ] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -2394.1136] [Alpha ][ 1.289494] . ( 43 sec) [ -2394.1136] [Topology ] . ( 44 sec) [ -2394.1132] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2394.113150. . Printing the most likely tree in file 'proteic_M1991_32x129_2004.phy_phyml_tree.txt'... . Time used 0h0m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 53.34user 0.00system 0:59.59elapsed 89%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps