.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_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... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -15011.6040] [GTR parameters ] . ( 2 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 2 sec) [ -14780.7799] [Topology ] . ( 4 sec) [ -14624.4043] [Topology ] . ( 6 sec) [ -14602.8474] [Topology ] . ( 8 sec) [ -14597.0947] [Topology ] . ( 9 sec) [ -14595.2996] [Topology ] . ( 11 sec) [ -14594.6333] [Topology ] . ( 13 sec) [ -14594.3799] [Topology ] . ( 15 sec) [ -14594.2815] [Topology ] . ( 17 sec) [ -14594.2428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -14114.5883] [GTR parameters ] . ( 37 sec) [ -14006.0829] [Alpha ][ 0.250961] . ( 37 sec) [ -14006.0829] [Topology ] . ( 39 sec) [ -14001.9646] [Topology ] . ( 41 sec) [ -14000.6200] [Topology ] . ( 43 sec) [ -14000.2713] [Topology ] . ( 45 sec) [ -14000.1289] [Topology ] . ( 47 sec) [ -14000.0645] [Topology ] . ( 49 sec) [ -14000.0344] [Topology ] . ( 51 sec) [ -14000.0201] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -13998.9233] [GTR parameters ] . ( 71 sec) [ -13998.9208] [Alpha ][ 0.250133] . ( 71 sec) [ -13998.9208] [Topology ] . ( 73 sec) [ -13998.8831] [Topology ] . ( 75 sec) [ -13998.8674] [Topology ] . ( 76 sec) [ -13998.8600] [Topology ] . ( 78 sec) [ -13998.8564] [Topology ] . ( 80 sec) [ -13998.8547] [Topology ] . ( 82 sec) [ -13998.8539] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -13998.8521] [GTR parameters ] . ( 99 sec) [ -13998.8503] [Alpha ][ 0.250757] . ( 99 sec) [ -13998.8503] [Topology ] . ( 101 sec) [ -13998.8493] [Topology ] . Checking for NNIs, optimizing five branches... . ( 116 sec) [ -13998.8493] [GTR parameters ] . ( 116 sec) [ -13998.8493] [Alpha ][ 0.250757] . ( 117 sec) [ -13998.8493] [Topology ] . ( 118 sec) [ -13998.8488] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13998.848836. . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Time used 0h2m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 148.15user 0.00system 2:30.57elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps