.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data12.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... . 349 patterns found. (out of a total of 500 sites) . 135 sites without polymorphism (27.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6050.947914 . ( 0 sec) [ -6049.3553] [GTR parameters ] . ( 0 sec) [ -6049.3232] [Alpha ][ 0.974396] . ( 1 sec) [ -6049.3232] [Topology ] . ( 1 sec) [ -6034.4456] [Topology ] . ( 2 sec) [ -6032.8652] [Topology ] . ( 3 sec) [ -6032.4749] [Topology ] . ( 4 sec) [ -6032.3420] [Topology ] . ( 4 sec) [ -6032.2915] [Topology ] . ( 5 sec) [ -6032.2714] [Topology ] . ( 7 sec) [ -6032.2632] [Topology ] . Checking for NNIs, optimizing five branches... . ( 11 sec) [ -6031.9929] [Topology ] . Before opt ts/t=1.000000 LK=-6031.992854 . ( 12 sec) [ -6031.9701] [GTR parameters ] . ( 12 sec) [ -6031.9311] [Alpha ][ 1.001414] . ( 12 sec) [ -6031.9311] [Topology ] . ( 13 sec) [ -6031.9038] [Topology ] . ( 13 sec) [ -6031.8983] [Topology ] . ( 14 sec) [ -6031.8966] [Topology ] . ( 15 sec) [ -6031.8959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6031.895930 . ( 23 sec) [ -6031.8959] [GTR parameters ] . ( 23 sec) [ -6031.8958] [Alpha ][ 1.002853] . ( 23 sec) [ -6031.8958] [Topology ] . ( 24 sec) [ -6031.8955] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895482. . Printing the most likely tree in file 'data12.phy_phyml_tree.txt'... . Time used 0h0m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo