.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data42.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... . 279 patterns found. (out of a total of 500 sites) . 203 sites without polymorphism (40.60%). . 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=-4232.026270 . ( 1 sec) [ -4230.2548] [GTR parameters ] . ( 1 sec) [ -4230.1853] [Alpha ][ 0.950604] . ( 1 sec) [ -4230.1853] [Topology ] . ( 2 sec) [ -4215.8559] [Topology ] . ( 3 sec) [ -4214.8475] [Topology ] . ( 4 sec) [ -4214.6692] [Topology ] . ( 5 sec) [ -4214.6239] [Topology ] . ( 6 sec) [ -4214.6092] [Topology ] . ( 6 sec) [ -4214.6031] [Topology ] . ( 7 sec) [ -4214.5999] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.599937 . ( 10 sec) [ -4214.5866] [GTR parameters ] . ( 10 sec) [ -4214.5662] [Alpha ][ 0.976114] . ( 10 sec) [ -4214.5662] [Topology ] . ( 11 sec) [ -4214.5632] [Topology ] . ( 11 sec) [ -4214.5614] [Topology ] . ( 12 sec) [ -4214.5600] [Topology ] . ( 12 sec) [ -4214.5589] [Topology ] . ( 13 sec) [ -4214.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.558087 . ( 17 sec) [ -4214.5580] [GTR parameters ] . ( 17 sec) [ -4214.5580] [Alpha ][ 0.977090] . ( 17 sec) [ -4214.5580] [Topology ] . ( 17 sec) [ -4214.5572] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.557221. . Printing the most likely tree in file 'data42.phy_phyml_tree.txt'... . Time used 0h0m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo