.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data53.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... . 429 patterns found. (out of a total of 500 sites) . 66 sites without polymorphism (13.20%). . 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=-9648.148083 . ( 1 sec) [ -9645.7865] [GTR parameters ] . ( 2 sec) [ -9645.7819] [Alpha ][ 0.992321] . ( 2 sec) [ -9645.7819] [Topology ] . ( 3 sec) [ -9563.6932] [Topology ] . ( 4 sec) [ -9549.6521] [Topology ] . ( 5 sec) [ -9546.6529] [Topology ] . ( 6 sec) [ -9545.4735] [Topology ] . ( 7 sec) [ -9544.9102] [Topology ] . ( 8 sec) [ -9544.6138] [Topology ] . ( 10 sec) [ -9544.4490] [Topology ] . ( 11 sec) [ -9544.3556] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.355619 . ( 21 sec) [ -9544.3056] [GTR parameters ] . ( 21 sec) [ -9544.1564] [Alpha ][ 0.953985] . ( 21 sec) [ -9544.1564] [Topology ] . ( 22 sec) [ -9544.0946] [Topology ] . ( 23 sec) [ -9544.0660] [Topology ] . ( 24 sec) [ -9544.0497] [Topology ] . ( 26 sec) [ -9544.0399] [Topology ] . ( 27 sec) [ -9544.0336] [Topology ] . ( 28 sec) [ -9544.0296] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.029640 . ( 37 sec) [ -9544.0293] [GTR parameters ] . ( 37 sec) [ -9544.0281] [Alpha ][ 0.950438] . ( 37 sec) [ -9544.0281] [Topology ] . ( 38 sec) [ -9544.0253] [Topology ] . ( 39 sec) [ -9544.0235] [Topology ] . ( 40 sec) [ -9544.0223] [Topology ] . ( 41 sec) [ -9544.0215] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.021461 . ( 51 sec) [ -9544.0215] [GTR parameters ] . ( 51 sec) [ -9544.0215] [Alpha ][ 0.950438] . ( 51 sec) [ -9544.0215] [Topology ] . ( 52 sec) [ -9544.0209] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9544.020887. . Printing the most likely tree in file 'data53.phy_phyml_tree.txt'... . Time used 0h1m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo