.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2302_24x365_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 . 19 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 261 patterns found. (out of a total of 365 sites) . 103 sites without polymorphism (28.22%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 15Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -4218.6216] [Alpha ][ 1.394511] . ( 0 sec) [ -4218.6216] [Topology ] . ( 2 sec) [ -4207.3938] [Topology ] . ( 4 sec) [ -4205.0043] [Topology ] . ( 5 sec) [ -4204.6545] [Topology ] . ( 7 sec) [ -4204.5667] [Topology ] . ( 8 sec) [ -4204.5412] [Topology ] . ( 10 sec) [ -4204.5337] [Topology ] . ( 11 sec) [ -4204.5316] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -4204.5258] [Alpha ][ 1.370680] . ( 20 sec) [ -4204.5258] [Topology ] . ( 22 sec) [ -4204.5250] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -4204.5250] [Alpha ][ 1.370680] . ( 31 sec) [ -4204.5250] [Topology ] . ( 32 sec) [ -4204.5248] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -4218.6216] [Alpha ][ 1.394511] . ( 52 sec) [ -4216.6126] [ 592] [depth= 1] . ( 56 sec) [ -4216.4084] [ 592] [depth= 1] . ( 56 sec) [ -4216.3831] [ 592] [depth= 1] . ( 57 sec) [ -4216.2531] [ 592] [depth= 1] . ( 57 sec) [ -4216.2399] [ 592] [depth= 2] . ( 57 sec) [ -4216.2290] [ 592] [depth= 2] . ( 71 sec) [ -4215.8317] [ 592] [depth= 1] . ( 71 sec) [ -4215.7582] [ 592] [depth= 3] . ( 72 sec) [ -4215.6970] [ 592] [depth= 1] . ( 72 sec) [ -4215.5894] [ 592] [depth= 3] . ( 73 sec) [ -4215.5269] [ 592] [depth= 3] . ( 73 sec) [ -4215.3859] [ 592] [depth= 1] . ( 74 sec) [ -4215.3518] [ 592] [depth= 4] . ( 76 sec) [ -4215.3341] [ 592] [depth= 4] . ( 81 sec) [ -4204.6858] [Branch lengths ] . ( 81 sec) [ -4204.6845] [Alpha ][ 1.383700] . ( 132 sec) [ -4204.5317] [Branch lengths ] . ( 132 sec) [ -4204.5317] [Topology ] . ( 133 sec) [ -4204.5276] [Topology ] . ( 135 sec) [ -4204.5269] [Topology ] . ( 135 sec) [ -4204.5251] [Alpha ][ 1.370749] . ( 135 sec) [ -4204.5251] [Topology ] . ( 136 sec) [ -4204.5248] [Topology ] . ( 137 sec) [ -4204.5248] [Alpha ][ 1.369378] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4204.524817 . Log likelihood obtained after SPR moves : -4204.524808 . Log likelihood of the current tree: -4204.524808. . Printing the most likely tree in file 'proteic_M2302_24x365_2005.phy_phyml_tree.txt'... . Time used 0h2m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 144.63user 0.00system 2:25.52elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps