.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data49.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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 248 patterns found. (out of a total of 500 sites) . 240 sites without polymorphism (48.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3491.381768 . ( 1 sec) [ -3490.8884] [GTR parameters ] . ( 1 sec) [ -3490.7282] [Alpha ][ 1.104161] . ( 1 sec) [ -3490.7282] [Topology ] . ( 2 sec) [ -3485.5616] [Topology ] . ( 2 sec) [ -3485.0246] [Topology ] . ( 3 sec) [ -3484.9129] [Topology ] . ( 4 sec) [ -3484.8770] [Topology ] . Moving backward . ( 4 sec) [ -3484.8327] [Topology ] . ( 5 sec) [ -3484.8068] [Topology ] . ( 6 sec) [ -3484.8045] [Topology ] . ( 7 sec) [ -3484.8042] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3484.804156 . ( 10 sec) [ -3484.7990] [GTR parameters ] . ( 10 sec) [ -3484.7928] [Alpha ][ 1.125754] . ( 10 sec) [ -3484.7928] [Topology ] . ( 11 sec) [ -3484.7926] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3484.792586 . ( 14 sec) [ -3484.7926] [GTR parameters ] . ( 14 sec) [ -3484.7926] [Alpha ][ 1.126879] . ( 14 sec) [ -3484.7926] [Topology ] . ( 15 sec) [ -3484.7925] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 22 sec) [ -3490.8884] [GTR parameters ] . ( 22 sec) [ -3490.7282] [Alpha ][ 1.104161] . ( 22 sec) [ -3490.5952] [ 486] [depth= 1] . ( 22 sec) [ -3490.5730] [ 486] [depth= 1] . ( 23 sec) [ -3490.4514] [ 486] [depth= 1] . ( 23 sec) [ -3489.2123] [ 486] [depth= 1] . ( 23 sec) [ -3488.8578] [ 486] [depth= 1] . ( 23 sec) [ -3488.4670] [ 486] [depth= 1] . ( 23 sec) [ -3488.4157] [ 486] [depth= 1] . ( 24 sec) [ -3487.4073] [ 486] [depth= 2] . ( 24 sec) [ -3487.3836] [ 486] [depth= 2] . ( 24 sec) [ -3487.3454] [ 486] [depth= 2] . ( 25 sec) [ -3487.2853] [ 486] [depth= 2] . ( 25 sec) [ -3487.2702] [ 486] [depth= 2] . ( 25 sec) [ -3487.2406] [ 486] [depth= 1] . ( 25 sec) [ -3484.8259] [Branch lengths ] . ( 25 sec) [ -3484.8205] [GTR parameters ] . ( 25 sec) [ -3484.8154] [Alpha ][ 1.123752] . ( 29 sec) [ -3484.7929] [Branch lengths ] . ( 50 sec) [ -3484.7926] [Branch lengths ] . ( 50 sec) [ -3484.7926] [Topology ] . ( 51 sec) [ -3484.7926] [Topology ] . ( 51 sec) [ -3484.7926] [GTR parameters ] . ( 51 sec) [ -3484.7925] [Alpha ][ 1.126219] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3484.792537 . Log likelihood obtained after SPR moves : -3484.792506 . Log likelihood of the current tree: -3484.792506. . Printing the most likely tree in file 'data49.phy_phyml_tree.txt'... . Time used 0h0m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo