.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data40.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... . 426 patterns found. (out of a total of 500 sites) . 70 sites without polymorphism (14.00%). . 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=-9827.155972 . ( 1 sec) [ -9824.3441] [GTR parameters ] . ( 1 sec) [ -9824.0535] [Alpha ][ 0.943410] . ( 1 sec) [ -9824.0535] [Topology ] . ( 1 sec) [ -9781.0533] [Topology ] . ( 2 sec) [ -9771.4895] [Topology ] . ( 3 sec) [ -9769.0992] [Topology ] . ( 4 sec) [ -9768.2834] [Topology ] . ( 5 sec) [ -9767.8984] [Topology ] . ( 5 sec) [ -9767.7052] [Topology ] . ( 6 sec) [ -9767.6057] [Topology ] . ( 7 sec) [ -9767.5536] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9767.553606 . ( 13 sec) [ -9767.4435] [GTR parameters ] . ( 13 sec) [ -9767.0408] [Alpha ][ 1.007628] . ( 13 sec) [ -9767.0408] [Topology ] . ( 14 sec) [ -9766.9849] [Topology ] . ( 15 sec) [ -9766.9584] [Topology ] . ( 16 sec) [ -9766.9447] [Topology ] . ( 16 sec) [ -9766.9375] [Topology ] . ( 17 sec) [ -9766.9336] [Topology ] . ( 18 sec) [ -9766.9315] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.931452 . ( 24 sec) [ -9766.9314] [GTR parameters ] . ( 24 sec) [ -9766.9301] [Alpha ][ 1.011385] . ( 24 sec) [ -9766.9301] [Topology ] . ( 24 sec) [ -9766.9288] [Topology ] . ( 25 sec) [ -9766.9280] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.928011 . ( 31 sec) [ -9766.9280] [GTR parameters ] . ( 31 sec) [ -9766.9280] [Alpha ][ 1.011385] . ( 31 sec) [ -9766.9280] [Topology ] . ( 32 sec) [ -9766.9276] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.927571. . Printing the most likely tree in file 'data40.phy_phyml_tree.txt'... . Time used 0h0m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo