.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data39.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... . 451 patterns found. (out of a total of 500 sites) . 50 sites without polymorphism (10.00%). . 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=-11018.795404 . ( 1 sec) [ -11014.7165] [GTR parameters ] . ( 1 sec) [ -11014.2861] [Alpha ][ 0.935530] . ( 1 sec) [ -11014.2861] [Topology ] . ( 2 sec) [ -10972.3241] [Topology ] . ( 3 sec) [ -10967.5469] [Topology ] . ( 4 sec) [ -10965.9215] [Topology ] . ( 5 sec) [ -10965.1673] [Topology ] . ( 6 sec) [ -10964.7837] [Topology ] . ( 7 sec) [ -10964.5763] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10964.576298 . ( 15 sec) [ -10964.5099] [GTR parameters ] . ( 15 sec) [ -10963.7218] [Alpha ][ 1.019586] . ( 15 sec) [ -10963.7218] [Topology ] . ( 16 sec) [ -10963.5142] [Topology ] . ( 17 sec) [ -10963.4215] [Topology ] . ( 18 sec) [ -10963.3752] [Topology ] . ( 19 sec) [ -10963.3512] [Topology ] . ( 20 sec) [ -10963.3387] [Topology ] . ( 21 sec) [ -10963.3321] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.332126 . ( 29 sec) [ -10963.3319] [GTR parameters ] . ( 29 sec) [ -10963.3219] [Alpha ][ 1.029584] . ( 29 sec) [ -10963.3219] [Topology ] . ( 30 sec) [ -10963.3171] [Topology ] . ( 31 sec) [ -10963.3147] [Topology ] . ( 33 sec) [ -10963.3135] [Topology ] . ( 34 sec) [ -10963.3128] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.312816 . ( 44 sec) [ -10963.3128] [GTR parameters ] . ( 44 sec) [ -10963.3127] [Alpha ][ 1.030614] . ( 44 sec) [ -10963.3127] [Topology ] . ( 45 sec) [ -10963.3123] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.312327. . Printing the most likely tree in file 'data39.phy_phyml_tree.txt'... . Time used 0h1m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo