.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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 . Compressing sequences... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -17550.8937] [GTR parameters ] . ( 1 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 1 sec) [ -17215.2965] [Topology ] . ( 2 sec) [ -16916.1845] [Topology ] . ( 4 sec) [ -16885.7882] [Topology ] . ( 5 sec) [ -16874.7992] [Topology ] . ( 7 sec) [ -16870.7493] [Topology ] . ( 8 sec) [ -16869.9252] [Topology ] . ( 9 sec) [ -16869.5950] [Topology ] . ( 11 sec) [ -16869.3884] [Topology ] . ( 12 sec) [ -16868.8474] [Topology ] . ( 13 sec) [ -16868.7091] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -16867.1125] [Topology ] . ( 30 sec) [ -16387.4659] [GTR parameters ] . ( 30 sec) [ -16321.3264] [Alpha ][ 0.313611] . ( 30 sec) [ -16321.3264] [Topology ] . ( 32 sec) [ -16296.0653] [Topology ] . ( 33 sec) [ -16291.6763] [Topology ] . ( 34 sec) [ -16289.9335] [Topology ] . ( 36 sec) [ -16289.0499] [Topology ] . ( 37 sec) [ -16288.5757] [Topology ] . ( 38 sec) [ -16288.3125] [Topology ] . ( 40 sec) [ -16288.1637] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -16267.6195] [GTR parameters ] . ( 56 sec) [ -16266.6873] [Alpha ][ 0.298004] . ( 56 sec) [ -16266.6873] [Topology ] . ( 57 sec) [ -16262.3457] [Topology ] . ( 58 sec) [ -16260.7450] [Topology ] . ( 60 sec) [ -16259.9619] [Topology ] . ( 61 sec) [ -16259.5615] [Topology ] . ( 62 sec) [ -16259.3516] [Topology ] . ( 64 sec) [ -16259.2400] [Topology ] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -16256.2006] [GTR parameters ] . ( 79 sec) [ -16256.1187] [Alpha ][ 0.293725] . ( 79 sec) [ -16256.1187] [Topology ] . ( 81 sec) [ -16255.1543] [Topology ] . ( 82 sec) [ -16254.7746] [Topology ] . ( 83 sec) [ -16254.5860] [Topology ] . ( 85 sec) [ -16254.4883] [Topology ] . ( 86 sec) [ -16254.4368] [Topology ] . ( 88 sec) [ -16254.4090] [Topology ] . Checking for NNIs, optimizing five branches... . ( 102 sec) [ -16253.8029] [GTR parameters ] . ( 102 sec) [ -16253.7748] [Alpha ][ 0.291349] . ( 102 sec) [ -16253.7748] [Topology ] . ( 103 sec) [ -16253.5624] [Topology ] . ( 104 sec) [ -16253.4790] [Topology ] . ( 106 sec) [ -16253.4367] [Topology ] . ( 107 sec) [ -16253.4143] [Topology ] . ( 108 sec) [ -16253.4022] [Topology ] . ( 110 sec) [ -16253.3957] [Topology ] . Checking for NNIs, optimizing five branches... . ( 126 sec) [ -16253.2584] [GTR parameters ] . ( 126 sec) [ -16253.2484] [Alpha ][ 0.289732] . ( 126 sec) [ -16253.2484] [Topology ] . ( 127 sec) [ -16253.1980] [Topology ] . ( 128 sec) [ -16253.1787] [Topology ] . ( 130 sec) [ -16253.1688] [Topology ] . ( 131 sec) [ -16253.1635] [Topology ] . ( 132 sec) [ -16253.1607] [Topology ] . ( 134 sec) [ -16253.1591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 148 sec) [ -16253.1248] [GTR parameters ] . ( 148 sec) [ -16253.1232] [Alpha ][ 0.289024] . ( 148 sec) [ -16253.1232] [Topology ] . ( 149 sec) [ -16253.1111] [Topology ] . ( 151 sec) [ -16253.1063] [Topology ] . ( 152 sec) [ -16253.1038] [Topology ] . ( 153 sec) [ -16253.1025] [Topology ] . ( 155 sec) [ -16253.1018] [Topology ] . Checking for NNIs, optimizing five branches... . ( 167 sec) [ -16253.0943] [GTR parameters ] . ( 167 sec) [ -16253.0940] [Alpha ][ 0.288675] . ( 167 sec) [ -16253.0940] [Topology ] . ( 169 sec) [ -16253.0908] [Topology ] . ( 170 sec) [ -16253.0895] [Topology ] . ( 171 sec) [ -16253.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -16253.0869] [GTR parameters ] . ( 185 sec) [ -16253.0869] [Alpha ][ 0.288675] . ( 185 sec) [ -16253.0869] [Topology ] . ( 187 sec) [ -16253.0856] [Topology ] . ( 188 sec) [ -16253.0850] [Topology ] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -16253.0850] [GTR parameters ] . ( 201 sec) [ -16253.0850] [Alpha ][ 0.288675] . ( 201 sec) [ -16253.0850] [Topology ] . ( 202 sec) [ -16253.0846] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084612. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h3m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 225.53user 0.00system 3:47.31elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps