.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data8.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... . 419 patterns found. (out of a total of 500 sites) . 76 sites without polymorphism (15.20%). . 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=-8988.698459 . ( 1 sec) [ -8984.7515] [GTR parameters ] . ( 1 sec) [ -8984.0081] [Alpha ][ 0.908527] . ( 1 sec) [ -8984.0081] [Topology ] . ( 2 sec) [ -8898.6998] [Topology ] . ( 3 sec) [ -8882.6992] [Topology ] . ( 3 sec) [ -8878.8739] [Topology ] . ( 4 sec) [ -8877.7173] [Topology ] . ( 5 sec) [ -8877.2412] [Topology ] . ( 6 sec) [ -8876.9976] [Topology ] . ( 6 sec) [ -8876.8604] [Topology ] . ( 7 sec) [ -8876.7778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -8876.3657] [Topology ] . Before opt ts/t=1.000000 LK=-8876.365684 . ( 15 sec) [ -8875.9438] [GTR parameters ] . ( 15 sec) [ -8875.8939] [Alpha ][ 0.888108] . ( 15 sec) [ -8875.8939] [Topology ] . ( 15 sec) [ -8875.7268] [Topology ] . ( 16 sec) [ -8875.0780] [Topology ] . ( 17 sec) [ -8874.8683] [Topology ] . ( 18 sec) [ -8874.7383] [Topology ] . ( 18 sec) [ -8874.6503] [Topology ] . ( 19 sec) [ -8874.5883] [Topology ] . ( 20 sec) [ -8874.5429] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.542850 . ( 27 sec) [ -8874.5400] [GTR parameters ] . ( 27 sec) [ -8874.5400] [Alpha ][ 0.888108] . ( 27 sec) [ -8874.5400] [Topology ] . ( 28 sec) [ -8874.5064] [Topology ] . ( 28 sec) [ -8874.4814] [Topology ] . ( 29 sec) [ -8874.4629] [Topology ] . ( 30 sec) [ -8874.4489] [Topology ] . ( 31 sec) [ -8874.4384] [Topology ] . ( 31 sec) [ -8874.4303] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.430347 . ( 38 sec) [ -8874.4303] [GTR parameters ] . ( 38 sec) [ -8874.4303] [Alpha ][ 0.888108] . ( 38 sec) [ -8874.4303] [Topology ] . ( 39 sec) [ -8874.4241] [Topology ] . ( 40 sec) [ -8874.4193] [Topology ] . ( 41 sec) [ -8874.4156] [Topology ] . ( 42 sec) [ -8874.4128] [Topology ] . ( 42 sec) [ -8874.4105] [Topology ] . ( 43 sec) [ -8874.4088] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.408835 . ( 50 sec) [ -8874.4088] [GTR parameters ] . ( 50 sec) [ -8874.4088] [Alpha ][ 0.888108] . ( 50 sec) [ -8874.4088] [Topology ] . ( 51 sec) [ -8874.4075] [Topology ] . ( 51 sec) [ -8874.4065] [Topology ] . ( 52 sec) [ -8874.4057] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.405690 . ( 59 sec) [ -8874.4057] [GTR parameters ] . ( 59 sec) [ -8874.4057] [Alpha ][ 0.888108] . ( 59 sec) [ -8874.4057] [Topology ] . ( 60 sec) [ -8874.4051] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.405073. . Printing the most likely tree in file 'data8.phy_phyml_tree.txt'... . Time used 0h1m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo