.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data61.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... . 443 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10669.048113 . ( 1 sec) [ -10666.4815] [GTR parameters ] . ( 1 sec) [ -10666.1551] [Alpha ][ 0.942575] . ( 1 sec) [ -10666.1551] [Topology ] . ( 2 sec) [ -10601.6847] [Topology ] . ( 3 sec) [ -10591.0335] [Topology ] . ( 4 sec) [ -10588.0682] [Topology ] . ( 5 sec) [ -10586.8013] [Topology ] . ( 6 sec) [ -10586.1775] [Topology ] . ( 7 sec) [ -10585.8506] [Topology ] . ( 8 sec) [ -10585.6740] [Topology ] . ( 8 sec) [ -10585.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.576851 . ( 15 sec) [ -10585.4824] [GTR parameters ] . ( 15 sec) [ -10585.3893] [Alpha ][ 0.970827] . ( 15 sec) [ -10585.3893] [Topology ] . ( 16 sec) [ -10585.3253] [Topology ] . ( 17 sec) [ -10585.2917] [Topology ] . ( 19 sec) [ -10585.2731] [Topology ] . ( 20 sec) [ -10585.2627] [Topology ] . ( 21 sec) [ -10585.2568] [Topology ] . ( 23 sec) [ -10585.2535] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.253512 . ( 34 sec) [ -10585.2534] [GTR parameters ] . ( 34 sec) [ -10585.2530] [Alpha ][ 0.972592] . ( 34 sec) [ -10585.2530] [Topology ] . ( 36 sec) [ -10585.2511] [Topology ] . ( 37 sec) [ -10585.2501] [Topology ] . ( 39 sec) [ -10585.2495] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.249466 . ( 48 sec) [ -10585.2495] [GTR parameters ] . ( 48 sec) [ -10585.2495] [Alpha ][ 0.972592] . ( 48 sec) [ -10585.2495] [Topology ] . ( 49 sec) [ -10585.2491] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.249115. . Printing the most likely tree in file 'data61.phy_phyml_tree.txt'... . Time used 0h1m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo