.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data71.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... . 455 patterns found. (out of a total of 500 sites) . 44 sites without polymorphism (8.80%). . 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=-11033.487122 . ( 0 sec) [ -11032.9128] [GTR parameters ] . ( 0 sec) [ -11030.8409] [Alpha ][ 1.162653] . ( 0 sec) [ -11030.8409] [Topology ] . ( 2 sec) [ -10949.5341] [Topology ] . ( 3 sec) [ -10930.4633] [Topology ] . ( 4 sec) [ -10926.6486] [Topology ] . ( 5 sec) [ -10925.5193] [Topology ] . ( 6 sec) [ -10925.0495] [Topology ] . ( 6 sec) [ -10924.8277] [Topology ] . ( 7 sec) [ -10924.7164] [Topology ] . ( 8 sec) [ -10924.6577] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.657736 . ( 17 sec) [ -10924.5882] [GTR parameters ] . ( 17 sec) [ -10924.3961] [Alpha ][ 1.113397] . ( 17 sec) [ -10924.3961] [Topology ] . ( 19 sec) [ -10924.3525] [Topology ] . ( 20 sec) [ -10924.3339] [Topology ] . ( 22 sec) [ -10924.3239] [Topology ] . ( 23 sec) [ -10924.3183] [Topology ] . ( 25 sec) [ -10924.3151] [Topology ] . ( 26 sec) [ -10924.3133] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.313310 . ( 39 sec) [ -10924.3131] [GTR parameters ] . ( 39 sec) [ -10924.3124] [Alpha ][ 1.110450] . ( 39 sec) [ -10924.3124] [Topology ] . ( 41 sec) [ -10924.3113] [Topology ] . ( 42 sec) [ -10924.3107] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.310696 . ( 54 sec) [ -10924.3107] [GTR parameters ] . ( 54 sec) [ -10924.3107] [Alpha ][ 1.110450] . ( 54 sec) [ -10924.3107] [Topology ] . ( 56 sec) [ -10924.3103] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10924.310330. . Printing the most likely tree in file 'data71.phy_phyml_tree.txt'... . Time used 0h1m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo