.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data10.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... . 293 patterns found. (out of a total of 500 sites) . 199 sites without polymorphism (39.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4475.291522 . ( 0 sec) [ -4472.4085] [GTR parameters ] . ( 0 sec) [ -4472.4070] [Alpha ][ 1.007326] . ( 0 sec) [ -4472.4070] [Topology ] . ( 1 sec) [ -4462.4908] [Topology ] . ( 2 sec) [ -4461.5449] [Topology ] . ( 2 sec) [ -4461.3788] [Topology ] . ( 3 sec) [ -4461.3404] [Topology ] . ( 4 sec) [ -4461.3305] [Topology ] . ( 4 sec) [ -4461.3278] [Topology ] . ( 5 sec) [ -4461.3270] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4461.327021 . ( 9 sec) [ -4461.3173] [GTR parameters ] . ( 9 sec) [ -4461.3084] [Alpha ][ 1.024609] . ( 9 sec) [ -4461.3084] [Topology ] . ( 10 sec) [ -4461.3078] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4461.307814 . ( 14 sec) [ -4461.3078] [GTR parameters ] . ( 14 sec) [ -4461.3077] [Alpha ][ 1.025633] . ( 14 sec) [ -4461.3077] [Topology ] . ( 15 sec) [ -4461.3075] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 26 sec) [ -4472.4085] [GTR parameters ] . ( 26 sec) [ -4472.4070] [Alpha ][ 1.007326] . ( 27 sec) [ -4469.8470] [ 684] [depth= 1] . ( 27 sec) [ -4468.0896] [ 684] [depth= 1] . ( 28 sec) [ -4467.9747] [ 684] [depth= 1] . ( 28 sec) [ -4467.6254] [ 684] [depth= 1] . ( 28 sec) [ -4467.5436] [ 684] [depth= 1] . ( 30 sec) [ -4467.5156] [ 684] [depth= 1] . ( 30 sec) [ -4461.4086] [Branch lengths ] . ( 30 sec) [ -4461.3997] [GTR parameters ] . ( 30 sec) [ -4461.3956] [Alpha ][ 1.019776] . ( 35 sec) [ -4461.3124] [Branch lengths ] . ( 57 sec) [ -4461.3085] [Branch lengths ] . ( 57 sec) [ -4461.3085] [Topology ] . ( 58 sec) [ -4461.3084] [Topology ] . ( 58 sec) [ -4461.3084] [GTR parameters ] . ( 58 sec) [ -4461.3074] [Alpha ][ 1.025601] . ( 58 sec) [ -4461.3074] [Topology ] . ( 59 sec) [ -4461.3073] [Topology ] . ( 59 sec) [ -4461.3073] [GTR parameters ] . ( 59 sec) [ -4461.3073] [Alpha ][ 1.025601] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4461.307512 . Log likelihood obtained after SPR moves : -4461.307338 . Log likelihood of the current tree: -4461.307338. . Printing the most likely tree in file 'data10.phy_phyml_tree.txt'... . Time used 0h1m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo