.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2655_50x872_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 374 patterns found. (out of a total of 872 sites) . 550 sites without polymorphism (63.07%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -6841.6794] [GTR parameters ] . ( 2 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 2 sec) [ -6721.7547] [Topology ] . ( 3 sec) [ -6612.7666] [Topology ] . ( 3 sec) [ -6594.7043] [Topology ] . ( 4 sec) [ -6588.9103] [Topology ] . ( 5 sec) [ -6587.3875] [Topology ] . ( 6 sec) [ -6586.8383] [Topology ] . ( 7 sec) [ -6586.3648] [Topology ] . ( 8 sec) [ -6586.2689] [Topology ] . ( 8 sec) [ -6586.2243] [Topology ] . ( 9 sec) [ -6586.1240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -6584.3212] [Topology ] . ( 17 sec) [ -6582.0995] [GTR parameters ] . ( 17 sec) [ -6525.0173] [Alpha ][ 0.250961] . ( 17 sec) [ -6525.0173] [Topology ] . ( 18 sec) [ -6522.2195] [Topology ] . ( 19 sec) [ -6520.3490] [Topology ] . ( 20 sec) [ -6519.9884] [Topology ] . ( 21 sec) [ -6519.8839] [Topology ] . ( 22 sec) [ -6519.8444] [Topology ] . ( 23 sec) [ -6519.8279] [Topology ] . ( 24 sec) [ -6519.8204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -6518.8123] [GTR parameters ] . ( 31 sec) [ -6518.2445] [Alpha ][ 0.234545] . ( 31 sec) [ -6518.2445] [Topology ] . ( 32 sec) [ -6518.2141] [Topology ] . ( 33 sec) [ -6518.2079] [Topology ] . ( 33 sec) [ -6518.2054] [Topology ] . ( 34 sec) [ -6518.2043] [Topology ] . ( 35 sec) [ -6518.2038] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -6518.1914] [GTR parameters ] . ( 42 sec) [ -6518.1893] [Alpha ][ 0.233524] . ( 42 sec) [ -6518.1893] [Topology ] . ( 43 sec) [ -6518.1887] [Topology ] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -6518.1886] [GTR parameters ] . ( 50 sec) [ -6518.1886] [Alpha ][ 0.233524] . ( 50 sec) [ -6518.1886] [Topology ] . ( 51 sec) [ -6518.1884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6518.188398. . Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'... . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 64.09user 0.00system 1:05.59elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps