.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data74.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... . 241 patterns found. (out of a total of 500 sites) . 238 sites without polymorphism (47.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3431.794665 . ( 1 sec) [ -3430.1324] [GTR parameters ] . ( 1 sec) [ -3429.5047] [Alpha ][ 1.225211] . ( 1 sec) [ -3429.5047] [Topology ] . ( 2 sec) [ -3425.1146] [Topology ] . ( 2 sec) [ -3424.7672] [Topology ] . ( 3 sec) [ -3424.7130] [Topology ] . ( 3 sec) [ -3424.7024] [Topology ] . ( 3 sec) [ -3424.7000] [Topology ] . ( 4 sec) [ -3424.6995] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3424.699457 . ( 8 sec) [ -3424.6991] [GTR parameters ] . ( 8 sec) [ -3424.6928] [Alpha ][ 1.251356] . ( 8 sec) [ -3424.6928] [Topology ] . ( 8 sec) [ -3424.6926] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3424.692568 . ( 13 sec) [ -3424.6925] [GTR parameters ] . ( 13 sec) [ -3424.6925] [Alpha ][ 1.251356] . ( 13 sec) [ -3424.6925] [Topology ] . ( 14 sec) [ -3424.6925] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.692457. . Printing the most likely tree in file 'data74.phy_phyml_tree.txt'... . Time used 0h0m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo