.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data35.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... . 446 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=-10555.099857 . ( 1 sec) [ -10552.4569] [GTR parameters ] . ( 1 sec) [ -10551.5166] [Alpha ][ 0.903985] . ( 1 sec) [ -10551.5166] [Topology ] . ( 1 sec) [ -10484.8412] [Topology ] . ( 2 sec) [ -10473.4165] [Topology ] . ( 3 sec) [ -10469.6529] [Topology ] . ( 4 sec) [ -10468.0389] [Topology ] . ( 5 sec) [ -10467.2638] [Topology ] . ( 6 sec) [ -10466.8540] [Topology ] . ( 6 sec) [ -10466.6391] [Topology ] . ( 7 sec) [ -10466.5171] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.517115 . ( 14 sec) [ -10466.4575] [GTR parameters ] . ( 15 sec) [ -10466.4366] [Alpha ][ 0.917049] . ( 15 sec) [ -10466.4366] [Topology ] . ( 15 sec) [ -10466.3687] [Topology ] . ( 16 sec) [ -10466.3297] [Topology ] . ( 17 sec) [ -10466.3074] [Topology ] . ( 18 sec) [ -10466.2939] [Topology ] . ( 19 sec) [ -10466.2859] [Topology ] . ( 19 sec) [ -10466.2809] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.280895 . ( 26 sec) [ -10466.2807] [GTR parameters ] . ( 26 sec) [ -10466.2805] [Alpha ][ 0.918334] . ( 26 sec) [ -10466.2805] [Topology ] . ( 27 sec) [ -10466.2774] [Topology ] . ( 28 sec) [ -10466.2754] [Topology ] . ( 29 sec) [ -10466.2741] [Topology ] . ( 29 sec) [ -10466.2733] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10466.273300 . ( 36 sec) [ -10466.2733] [GTR parameters ] . ( 36 sec) [ -10466.2733] [Alpha ][ 0.918334] . ( 36 sec) [ -10466.2733] [Topology ] . ( 37 sec) [ -10466.2728] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10466.272790. . Printing the most likely tree in file 'data35.phy_phyml_tree.txt'... . Time used 0h0m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo