.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data31.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... . 380 patterns found. (out of a total of 500 sites) . 109 sites without polymorphism (21.80%). . 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=-7232.842533 . ( 1 sec) [ -7230.4040] [GTR parameters ] . ( 1 sec) [ -7229.6204] [Alpha ][ 0.896021] . ( 1 sec) [ -7229.6204] [Topology ] . ( 2 sec) [ -7192.0939] [Topology ] . ( 3 sec) [ -7187.0334] [Topology ] . ( 4 sec) [ -7185.9593] [Topology ] . ( 5 sec) [ -7185.6067] [Topology ] . ( 6 sec) [ -7185.4697] [Topology ] . ( 6 sec) [ -7185.4114] [Topology ] . ( 7 sec) [ -7185.3852] [Topology ] . ( 8 sec) [ -7185.3059] [Topology ] . ( 9 sec) [ -7182.8083] [Topology ] . Before opt ts/t=1.000000 LK=-7182.649243 . ( 11 sec) [ -7182.5732] [GTR parameters ] . ( 11 sec) [ -7182.4728] [Alpha ][ 0.929875] . ( 11 sec) [ -7182.4728] [Topology ] . ( 12 sec) [ -7181.7891] [Topology ] . ( 13 sec) [ -7179.9913] [Topology ] . ( 14 sec) [ -7179.6157] [Topology ] . ( 15 sec) [ -7179.5869] [Topology ] . ( 15 sec) [ -7179.5798] [Topology ] . ( 16 sec) [ -7179.5776] [Topology ] . ( 17 sec) [ -7179.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.576932 . ( 25 sec) [ -7179.5752] [GTR parameters ] . ( 25 sec) [ -7179.5673] [Alpha ][ 0.939938] . ( 25 sec) [ -7179.5673] [Topology ] . ( 26 sec) [ -7179.5669] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.566930 . ( 33 sec) [ -7179.5669] [GTR parameters ] . ( 33 sec) [ -7179.5669] [Alpha ][ 0.939938] . ( 33 sec) [ -7179.5669] [Topology ] . ( 34 sec) [ -7179.5668] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.566849. . Printing the most likely tree in file 'data31.phy_phyml_tree.txt'... . Time used 0h0m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo