.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1990_35x153_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 . 5 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 104 patterns found. (out of a total of 153 sites) . 83 sites without polymorphism (54.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1475.6886] [Alpha ][ 0.500960] . ( 1 sec) [ -1475.6886] [Topology ] . ( 2 sec) [ -1458.9478] [Topology ] . ( 3 sec) [ -1456.3850] [Topology ] . ( 5 sec) [ -1455.6479] [Topology ] . ( 6 sec) [ -1455.3351] [Topology ] . ( 7 sec) [ -1455.1478] [Topology ] . ( 8 sec) [ -1455.0229] [Topology ] . ( 9 sec) [ -1454.9621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -1454.8907] [Topology ] . ( 17 sec) [ -1454.4162] [Alpha ][ 0.419100] . ( 17 sec) [ -1454.4162] [Topology ] . ( 18 sec) [ -1454.3127] [Topology ] . ( 19 sec) [ -1454.2962] [Topology ] . ( 20 sec) [ -1454.2898] [Topology ] . ( 21 sec) [ -1454.2869] [Topology ] . ( 22 sec) [ -1454.2855] [Topology ] . ( 23 sec) [ -1454.2845] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -1454.2697] [Alpha ][ 0.406420] . ( 30 sec) [ -1454.2697] [Topology ] . ( 31 sec) [ -1454.2659] [Topology ] . ( 32 sec) [ -1454.2653] [Topology ] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -1454.2647] [Alpha ][ 0.403661] . ( 41 sec) [ -1454.2647] [Topology ] . ( 42 sec) [ -1454.2640] [Topology ] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -1454.2639] [Alpha ][ 0.403166] . ( 51 sec) [ -1454.2639] [Topology ] . ( 52 sec) [ -1454.2635] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1454.263454. . Printing the most likely tree in file 'proteic_M1990_35x153_2004.phy_phyml_tree.txt'... . Time used 0h1m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 62.92user 0.00system 1:11.38elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps