.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data50.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... . 440 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . 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=-10296.740802 . ( 1 sec) [ -10294.9392] [GTR parameters ] . ( 1 sec) [ -10294.7927] [Alpha ][ 0.960616] . ( 1 sec) [ -10294.7927] [Topology ] . ( 2 sec) [ -10235.5620] [Topology ] . ( 4 sec) [ -10223.5704] [Topology ] . ( 5 sec) [ -10220.9334] [Topology ] . ( 7 sec) [ -10219.8027] [Topology ] . ( 8 sec) [ -10219.2500] [Topology ] . ( 9 sec) [ -10218.9647] [Topology ] . ( 10 sec) [ -10218.8140] [Topology ] . ( 12 sec) [ -10218.7333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.733311 . ( 21 sec) [ -10218.6801] [GTR parameters ] . ( 21 sec) [ -10218.3007] [Alpha ][ 1.022180] . ( 21 sec) [ -10218.3007] [Topology ] . ( 22 sec) [ -10218.2286] [Topology ] . ( 23 sec) [ -10218.1933] [Topology ] . ( 23 sec) [ -10218.1745] [Topology ] . ( 24 sec) [ -10218.1645] [Topology ] . ( 26 sec) [ -10218.1591] [Topology ] . ( 26 sec) [ -10218.1562] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.156228 . ( 34 sec) [ -10218.1561] [GTR parameters ] . ( 34 sec) [ -10218.1545] [Alpha ][ 1.026389] . ( 34 sec) [ -10218.1545] [Topology ] . ( 35 sec) [ -10218.1527] [Topology ] . ( 37 sec) [ -10218.1518] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.151758 . ( 45 sec) [ -10218.1517] [GTR parameters ] . ( 45 sec) [ -10218.1517] [Alpha ][ 1.026389] . ( 46 sec) [ -10218.1517] [Topology ] . ( 47 sec) [ -10218.1512] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.151240. . Printing the most likely tree in file 'data50.phy_phyml_tree.txt'... . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo