.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data6.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... . 376 patterns found. (out of a total of 500 sites) . 113 sites without polymorphism (22.60%). . 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=-7048.952922 . ( 1 sec) [ -7048.3387] [GTR parameters ] . ( 1 sec) [ -7048.3296] [Alpha ][ 0.988108] . ( 1 sec) [ -7048.3296] [Topology ] . ( 1 sec) [ -7027.3699] [Topology ] . ( 2 sec) [ -7025.2151] [Topology ] . ( 3 sec) [ -7024.6546] [Topology ] . ( 4 sec) [ -7024.4334] [Topology ] . ( 5 sec) [ -7024.3338] [Topology ] . ( 5 sec) [ -7024.2861] [Topology ] . ( 6 sec) [ -7024.2626] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.262628 . ( 12 sec) [ -7024.2478] [GTR parameters ] . ( 12 sec) [ -7024.2259] [Alpha ][ 1.007084] . ( 12 sec) [ -7024.2259] [Topology ] . ( 12 sec) [ -7024.2117] [Topology ] . ( 13 sec) [ -7024.2049] [Topology ] . ( 14 sec) [ -7024.2015] [Topology ] . ( 15 sec) [ -7024.1998] [Topology ] . ( 15 sec) [ -7024.1989] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.198936 . ( 20 sec) [ -7024.1989] [GTR parameters ] . ( 21 sec) [ -7024.1988] [Alpha ][ 1.008092] . ( 21 sec) [ -7024.1988] [Topology ] . ( 21 sec) [ -7024.1984] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.198384. . Printing the most likely tree in file 'data6.phy_phyml_tree.txt'... . Time used 0h0m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo