.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data43.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... . 428 patterns found. (out of a total of 500 sites) . 67 sites without polymorphism (13.40%). . 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=-10318.994783 . ( 1 sec) [ -10312.0688] [GTR parameters ] . ( 1 sec) [ -10311.6492] [Alpha ][ 0.935381] . ( 1 sec) [ -10311.6492] [Topology ] . ( 3 sec) [ -10271.7364] [Topology ] . ( 4 sec) [ -10265.0575] [Topology ] . ( 5 sec) [ -10263.2794] [Topology ] . ( 6 sec) [ -10262.6090] [Topology ] . ( 7 sec) [ -10262.2889] [Topology ] . ( 8 sec) [ -10262.1288] [Topology ] . ( 10 sec) [ -10262.0472] [Topology ] . ( 12 sec) [ -10262.0051] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10262.005059 . ( 22 sec) [ -10261.9510] [GTR parameters ] . ( 22 sec) [ -10261.6619] [Alpha ][ 0.986600] . ( 22 sec) [ -10261.6619] [Topology ] . ( 23 sec) [ -10261.6104] [Topology ] . ( 25 sec) [ -10261.5863] [Topology ] . ( 26 sec) [ -10261.5740] [Topology ] . ( 27 sec) [ -10261.5677] [Topology ] . ( 28 sec) [ -10261.5644] [Topology ] . ( 29 sec) [ -10261.5627] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.562735 . ( 38 sec) [ -10261.5626] [GTR parameters ] . ( 39 sec) [ -10261.5600] [Alpha ][ 0.991703] . ( 39 sec) [ -10261.5600] [Topology ] . ( 40 sec) [ -10261.5587] [Topology ] . ( 41 sec) [ -10261.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.558104 . ( 50 sec) [ -10261.5581] [GTR parameters ] . ( 50 sec) [ -10261.5581] [Alpha ][ 0.991703] . ( 50 sec) [ -10261.5581] [Topology ] . ( 52 sec) [ -10261.5578] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557766. . Printing the most likely tree in file 'data43.phy_phyml_tree.txt'... . Time used 0h1m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo