.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data93.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... . 402 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8471.601432 . ( 2 sec) [ -8466.7709] [GTR parameters ] . ( 2 sec) [ -8465.8651] [Alpha ][ 0.896372] . ( 2 sec) [ -8465.8651] [Topology ] . ( 4 sec) [ -8427.9263] [Topology ] . ( 5 sec) [ -8421.9128] [Topology ] . ( 6 sec) [ -8420.1616] [Topology ] . ( 7 sec) [ -8419.4102] [Topology ] . ( 7 sec) [ -8419.0903] [Topology ] . ( 8 sec) [ -8418.9520] [Topology ] . ( 9 sec) [ -8418.8875] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.887512 . ( 15 sec) [ -8418.8409] [GTR parameters ] . ( 15 sec) [ -8418.5825] [Alpha ][ 0.947946] . ( 15 sec) [ -8418.5825] [Topology ] . ( 16 sec) [ -8418.5235] [Topology ] . ( 17 sec) [ -8418.4968] [Topology ] . ( 18 sec) [ -8418.4836] [Topology ] . ( 19 sec) [ -8418.4771] [Topology ] . ( 20 sec) [ -8418.4738] [Topology ] . ( 21 sec) [ -8418.4721] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.472118 . ( 30 sec) [ -8418.4720] [GTR parameters ] . ( 30 sec) [ -8418.4699] [Alpha ][ 0.952739] . ( 30 sec) [ -8418.4699] [Topology ] . ( 31 sec) [ -8418.4688] [Topology ] . ( 32 sec) [ -8418.4683] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.468264 . ( 42 sec) [ -8418.4683] [GTR parameters ] . ( 42 sec) [ -8418.4683] [Alpha ][ 0.952739] . ( 42 sec) [ -8418.4683] [Topology ] . ( 43 sec) [ -8418.4680] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.467977. . Printing the most likely tree in file 'data93.phy_phyml_tree.txt'... . Time used 0h1m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo