.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2954_5x1006_2006.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 : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 85 patterns found. (out of a total of 1006 sites) . 959 sites without polymorphism (95.33%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 1Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4083.4228] [Alpha ][ 0.500960] . ( 0 sec) [ -3416.5001] [ 51] [depth= 1] . ( 0 sec) [ -3283.8366] [ 49] [depth= 1] . ( 0 sec) [ -3262.6863] [ 51] [depth= 1] . ( 0 sec) [ -3249.0687] [ 49] [depth= 1] . ( 0 sec) [ -3244.2751] [Branch lengths ] . ( 0 sec) [ -3244.2701] [Alpha ][ 0.436700] . ( 1 sec) [ -3243.7078] [Branch lengths ] . ( 1 sec) [ -3243.7078] [Topology ] . ( 1 sec) [ -3242.4457] [Topology ] . ( 1 sec) [ -3241.9136] [Topology ] . ( 1 sec) [ -3241.8892] [Topology ] . ( 1 sec) [ -3241.8870] [Topology ] . ( 1 sec) [ -3241.8867] [Topology ] . ( 1 sec) [ -3241.7474] [Alpha ][ 0.872112] . ( 1 sec) [ -3241.7474] [Topology ] . ( 1 sec) [ -3241.7458] [Topology ] . ( 1 sec) [ -3241.7457] [Topology ] . ( 1 sec) [ -3241.7402] [Alpha ][ 1.060967] . ( 1 sec) [ -3241.7402] [Topology ] . ( 1 sec) [ -3241.7401] [Topology ] . ( 1 sec) [ -3241.7401] [Alpha ][ 1.063787] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3241.740128. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4400.0658] [Alpha ][ 0.500960] . ( 1 sec) [ -3399.3412] [ 51] [depth= 2] . ( 1 sec) [ -3313.3825] [ 49] [depth= 1] . ( 1 sec) [ -3253.3789] [ 51] [depth= 1] . ( 1 sec) [ -3248.9337] [ 49] [depth= 1] . ( 1 sec) [ -3241.9035] [Branch lengths ] . ( 1 sec) [ -3241.8060] [Alpha ][ 0.999983] . ( 1 sec) [ -3241.7406] [Branch lengths ] . ( 1 sec) [ -3241.7406] [Topology ] . ( 1 sec) [ -3241.7406] [Topology ] . ( 1 sec) [ -3241.7401] [Alpha ][ 1.063736] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3241.740126. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3990.1167] [Alpha ][ 0.500960] . ( 1 sec) [ -3545.5996] [ 51] [depth= 1] . ( 1 sec) [ -3306.0793] [ 49] [depth= 1] . ( 1 sec) [ -3268.4486] [ 51] [depth= 1] . ( 1 sec) [ -3266.1276] [ 49] [depth= 1] . ( 1 sec) [ -3254.3611] [ 51] [depth= 1] . ( 1 sec) [ -3249.8252] [ 49] [depth= 1] . ( 1 sec) [ -3243.9141] [Branch lengths ] . ( 1 sec) [ -3243.9110] [Alpha ][ 0.562212] . ( 1 sec) [ -3242.5447] [Branch lengths ] . ( 1 sec) [ -3242.5447] [Topology ] . ( 1 sec) [ -3241.8363] [Topology ] . ( 1 sec) [ -3241.8115] [Topology ] . ( 2 sec) [ -3241.8094] [Topology ] . ( 2 sec) [ -3241.8092] [Topology ] . ( 2 sec) [ -3241.7413] [Alpha ][ 1.053864] . ( 2 sec) [ -3241.7413] [Topology ] . ( 2 sec) [ -3241.7402] [Topology ] . ( 2 sec) [ -3241.7401] [Topology ] . ( 2 sec) [ -3241.7401] [Alpha ][ 1.064264] . ( 2 sec) [ -3241.7401] [Topology ] . ( 2 sec) [ -3241.7401] [Topology ] . ( 2 sec) [ -3241.7401] [Alpha ][ 1.064264] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3241.740120. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3899.4917] [Alpha ][ 0.500960] . ( 0 sec) [ -3313.9816] [ 51] [depth= 1] . ( 0 sec) [ -3310.0673] [ 49] [depth= 1] . ( 0 sec) [ -3281.6715] [ 51] [depth= 1] . ( 0 sec) [ -3258.6581] [ 49] [depth= 1] . ( 0 sec) [ -3256.2579] [ 51] [depth= 1] . ( 0 sec) [ -3248.6235] [ 49] [depth= 1] . ( 0 sec) [ -3244.2666] [Branch lengths ] . ( 0 sec) [ -3244.2615] [Alpha ][ 0.436413] . ( 1 sec) [ -3243.6688] [Branch lengths ] . ( 1 sec) [ -3243.6688] [Topology ] . ( 1 sec) [ -3242.3936] [Topology ] . ( 1 sec) [ -3241.9131] [Topology ] . ( 1 sec) [ -3241.8894] [Topology ] . ( 1 sec) [ -3241.8872] [Topology ] . ( 1 sec) [ -3241.8870] [Topology ] . ( 1 sec) [ -3241.7475] [Alpha ][ 0.871543] . ( 1 sec) [ -3241.7475] [Topology ] . ( 1 sec) [ -3241.7459] [Topology ] . ( 1 sec) [ -3241.7458] [Topology ] . ( 1 sec) [ -3241.7402] [Alpha ][ 1.060955] . ( 1 sec) [ -3241.7402] [Topology ] . ( 1 sec) [ -3241.7401] [Topology ] . ( 1 sec) [ -3241.7401] [Alpha ][ 1.063785] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3241.740128. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -4139.8139] [Alpha ][ 0.500960] . ( 1 sec) [ -3315.2884] [ 51] [depth= 2] . ( 1 sec) [ -3289.4049] [ 49] [depth= 1] . ( 1 sec) [ -3278.5523] [ 51] [depth= 1] . ( 1 sec) [ -3263.9280] [ 49] [depth= 1] . ( 1 sec) [ -3254.8373] [ 51] [depth= 1] . ( 1 sec) [ -3247.7024] [Branch lengths ] . ( 1 sec) [ -3247.2365] [Alpha ][ 0.250961] . ( 1 sec) [ -3244.4834] [ 49] [depth= 1] . ( 1 sec) [ -3244.3368] [Branch lengths ] . ( 1 sec) [ -3244.2508] [Alpha ][ 0.435587] . ( 2 sec) [ -3243.6020] [Branch lengths ] . ( 2 sec) [ -3243.6020] [Topology ] . ( 2 sec) [ -3242.3112] [Topology ] . ( 2 sec) [ -3241.9096] [Topology ] . ( 2 sec) [ -3241.8894] [Topology ] . ( 2 sec) [ -3241.8878] [Topology ] . ( 2 sec) [ -3241.8877] [Topology ] . ( 2 sec) [ -3241.7476] [Alpha ][ 0.869900] . ( 2 sec) [ -3241.7476] [Topology ] . ( 2 sec) [ -3241.7460] [Topology ] . ( 2 sec) [ -3241.7459] [Topology ] . ( 2 sec) [ -3241.7402] [Alpha ][ 1.060929] . ( 2 sec) [ -3241.7402] [Topology ] . ( 2 sec) [ -3241.7401] [Topology ] . ( 2 sec) [ -3241.7401] [Alpha ][ 1.063781] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3241.740129. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3247.1494] [Alpha ][ 0.500960] . ( 0 sec) [ -3247.1494] [Topology ] . ( 0 sec) [ -3244.6107] [Topology ] . ( 1 sec) [ -3244.3861] [Topology ] . ( 1 sec) [ -3244.3677] [Topology ] . ( 1 sec) [ -3244.3658] [Topology ] . ( 1 sec) [ -3244.3619] [Topology ] . ( 1 sec) [ -3244.3327] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1 sec) [ -3244.3233] [Alpha ][ 0.417104] . ( 1 sec) [ -3244.3233] [Topology ] . ( 1 sec) [ -3244.1371] [Topology ] . ( 1 sec) [ -3243.3249] [Topology ] . ( 1 sec) [ -3242.0532] [Topology ] . ( 2 sec) [ -3241.9157] [Topology ] . ( 2 sec) [ -3241.9055] [Topology ] . ( 2 sec) [ -3241.9045] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2 sec) [ -3241.7508] [Alpha ][ 0.833146] . ( 2 sec) [ -3241.7508] [Topology ] . ( 2 sec) [ -3241.7489] [Topology ] . ( 2 sec) [ -3241.7488] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2 sec) [ -3241.7403] [Alpha ][ 1.060225] . ( 2 sec) [ -3241.7403] [Topology ] . ( 3 sec) [ -3241.7401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3 sec) [ -3241.7401] [Alpha ][ 1.063610] . ( 3 sec) [ -3241.7401] [Topology ] . ( 3 sec) [ -3241.7401] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -3247.1494] [Alpha ][ 0.500960] . ( 4 sec) [ -3244.3685] [Branch lengths ] . ( 4 sec) [ -3244.3685] [Topology ] . ( 4 sec) [ -3244.3664] [Topology ] . ( 4 sec) [ -3244.3661] [Topology ] . ( 4 sec) [ -3244.3539] [Alpha ][ 0.407044] . ( 4 sec) [ -3244.3539] [Topology ] . ( 4 sec) [ -3244.3529] [Topology ] . ( 4 sec) [ -3244.3462] [Topology ] . ( 4 sec) [ -3244.2963] [Topology ] . ( 4 sec) [ -3243.9790] [Topology ] . ( 4 sec) [ -3242.9133] [Topology ] . ( 5 sec) [ -3241.9597] [Topology ] . ( 5 sec) [ -3241.8010] [Alpha ][ 0.813092] . ( 5 sec) [ -3241.8010] [Topology ] . ( 5 sec) [ -3241.7558] [Topology ] . ( 5 sec) [ -3241.7512] [Topology ] . ( 5 sec) [ -3241.7507] [Topology ] . ( 5 sec) [ -3241.7404] [Alpha ][ 1.059983] . ( 5 sec) [ -3241.7404] [Topology ] . ( 5 sec) [ -3241.7401] [Topology ] . ( 5 sec) [ -3241.7401] [Alpha ][ 1.063443] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3241.740121 . Log likelihood obtained after SPR moves : -3241.740141 . Log likelihood of the current tree: -3241.740121. . Printing the most likely tree in file 'proteic_M2954_5x1006_2006.phy_phyml_tree.txt'... . Best log likelihood : -3241.740120 . Time used 0h0m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 13.43user 0.00system 0:18.14elapsed 74%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps