.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data65.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... . 462 patterns found. (out of a total of 500 sites) . 38 sites without polymorphism (7.60%). . 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=-12251.477966 . ( 2 sec) [ -12240.5369] [GTR parameters ] . ( 2 sec) [ -12240.5293] [Alpha ][ 0.991383] . ( 2 sec) [ -12240.5293] [Topology ] . ( 3 sec) [ -12159.4656] [Topology ] . ( 4 sec) [ -12146.8006] [Topology ] . ( 5 sec) [ -12143.2282] [Topology ] . ( 6 sec) [ -12141.6547] [Topology ] . ( 6 sec) [ -12140.8761] [Topology ] . ( 7 sec) [ -12140.4867] [Topology ] . ( 8 sec) [ -12140.2849] [Topology ] . ( 9 sec) [ -12140.1779] [Topology ] . ( 10 sec) [ -12140.1204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -12139.8651] [Topology ] . Before opt ts/t=1.000000 LK=-12139.865084 . ( 20 sec) [ -12139.8452] [GTR parameters ] . ( 20 sec) [ -12139.7702] [Alpha ][ 1.016211] . ( 20 sec) [ -12139.7702] [Topology ] . ( 22 sec) [ -12139.7053] [Topology ] . ( 24 sec) [ -12139.6804] [Topology ] . ( 25 sec) [ -12139.6684] [Topology ] . ( 27 sec) [ -12139.6624] [Topology ] . ( 29 sec) [ -12139.6592] [Topology ] . ( 30 sec) [ -12139.6575] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-12139.657526 . ( 41 sec) [ -12139.6575] [GTR parameters ] . ( 41 sec) [ -12139.6575] [Alpha ][ 1.016211] . ( 41 sec) [ -12139.6575] [Topology ] . ( 43 sec) [ -12139.6566] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.656578. . Printing the most likely tree in file 'data65.phy_phyml_tree.txt'... . Time used 0h1m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo