.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data100.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... . 450 patterns found. (out of a total of 500 sites) . 47 sites without polymorphism (9.40%). . 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=-10614.462202 . ( 1 sec) [ -10610.1657] [GTR parameters ] . ( 1 sec) [ -10610.1656] [Alpha ][ 1.001154] . ( 1 sec) [ -10610.1656] [Topology ] . ( 2 sec) [ -10531.3624] [Topology ] . ( 3 sec) [ -10511.2075] [Topology ] . ( 4 sec) [ -10505.1369] [Topology ] . ( 4 sec) [ -10502.3616] [Topology ] . ( 5 sec) [ -10500.9767] [Topology ] . ( 6 sec) [ -10500.2834] [Topology ] . ( 7 sec) [ -10499.9077] [Topology ] . ( 8 sec) [ -10499.6992] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10499.699178 . ( 15 sec) [ -10499.3949] [GTR parameters ] . ( 15 sec) [ -10499.3214] [Alpha ][ 0.975377] . ( 15 sec) [ -10499.3214] [Topology ] . ( 15 sec) [ -10499.1740] [Topology ] . ( 16 sec) [ -10499.0934] [Topology ] . ( 17 sec) [ -10499.0472] [Topology ] . ( 18 sec) [ -10499.0204] [Topology ] . ( 19 sec) [ -10499.0049] [Topology ] . ( 19 sec) [ -10498.9959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.995947 . ( 26 sec) [ -10498.9941] [GTR parameters ] . ( 26 sec) [ -10498.9900] [Alpha ][ 0.969090] . ( 26 sec) [ -10498.9900] [Topology ] . ( 27 sec) [ -10498.9835] [Topology ] . ( 28 sec) [ -10498.9798] [Topology ] . ( 28 sec) [ -10498.9777] [Topology ] . ( 29 sec) [ -10498.9765] [Topology ] . ( 30 sec) [ -10498.9757] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.975740 . ( 36 sec) [ -10498.9757] [GTR parameters ] . ( 36 sec) [ -10498.9755] [Alpha ][ 0.967885] . ( 36 sec) [ -10498.9755] [Topology ] . ( 37 sec) [ -10498.9750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10498.975038. . Printing the most likely tree in file 'data100.phy_phyml_tree.txt'... . Time used 0h0m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo