.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data79.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... . 397 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=-7990.949843 . ( 1 sec) [ -7988.1958] [GTR parameters ] . ( 1 sec) [ -7988.1956] [Alpha ][ 0.998171] . ( 1 sec) [ -7988.1956] [Topology ] . ( 2 sec) [ -7946.8898] [Topology ] . ( 2 sec) [ -7942.5047] [Topology ] . ( 3 sec) [ -7940.3008] [Topology ] . ( 4 sec) [ -7939.1196] [Topology ] . ( 5 sec) [ -7938.8803] [Topology ] . ( 6 sec) [ -7938.7734] [Topology ] . ( 7 sec) [ -7938.7010] [Topology ] . ( 9 sec) [ -7938.5453] [Topology ] . ( 10 sec) [ -7936.6980] [Topology ] . Before opt ts/t=1.000000 LK=-7935.798149 . ( 12 sec) [ -7935.7576] [GTR parameters ] . ( 12 sec) [ -7935.6997] [Alpha ][ 1.026029] . ( 12 sec) [ -7935.6997] [Topology ] . ( 13 sec) [ -7935.4675] [Topology ] . ( 14 sec) [ -7935.3702] [Topology ] . ( 15 sec) [ -7935.3500] [Topology ] . ( 16 sec) [ -7935.3422] [Topology ] . ( 17 sec) [ -7935.3386] [Topology ] . ( 18 sec) [ -7935.3369] [Topology ] . ( 19 sec) [ -7935.3360] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.336011 . ( 25 sec) [ -7935.3345] [GTR parameters ] . ( 25 sec) [ -7935.3344] [Alpha ][ 1.027305] . ( 25 sec) [ -7935.3344] [Topology ] . ( 26 sec) [ -7935.3339] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.333949 . ( 33 sec) [ -7935.3339] [GTR parameters ] . ( 34 sec) [ -7935.3339] [Alpha ][ 1.027305] . ( 34 sec) [ -7935.3339] [Topology ] . ( 35 sec) [ -7935.3337] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.333689. . Printing the most likely tree in file 'data79.phy_phyml_tree.txt'... . Time used 0h0m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo