.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data1.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... . 437 patterns found. (out of a total of 500 sites) . 64 sites without polymorphism (12.80%). . 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=-10670.638885 . ( 1 sec) [ -10666.7778] [GTR parameters ] . ( 1 sec) [ -10666.2120] [Alpha ][ 0.925980] . ( 1 sec) [ -10666.2120] [Topology ] . ( 2 sec) [ -10610.0666] [Topology ] . ( 3 sec) [ -10586.1511] [Topology ] . ( 3 sec) [ -10581.2066] [Topology ] . ( 4 sec) [ -10580.2747] [Topology ] . ( 5 sec) [ -10579.9449] [Topology ] . ( 6 sec) [ -10579.7943] [Topology ] . ( 7 sec) [ -10579.7182] [Topology ] . ( 8 sec) [ -10579.6779] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.677901 . ( 14 sec) [ -10579.6411] [GTR parameters ] . ( 14 sec) [ -10579.3155] [Alpha ][ 0.979846] . ( 14 sec) [ -10579.3155] [Topology ] . ( 15 sec) [ -10579.2624] [Topology ] . ( 16 sec) [ -10579.2389] [Topology ] . ( 17 sec) [ -10579.2266] [Topology ] . ( 18 sec) [ -10579.2199] [Topology ] . ( 18 sec) [ -10579.2162] [Topology ] . ( 19 sec) [ -10579.2142] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.214195 . ( 26 sec) [ -10579.2140] [GTR parameters ] . ( 26 sec) [ -10579.2110] [Alpha ][ 0.985268] . ( 26 sec) [ -10579.2110] [Topology ] . ( 27 sec) [ -10579.2094] [Topology ] . ( 27 sec) [ -10579.2086] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.208575 . ( 34 sec) [ -10579.2086] [GTR parameters ] . ( 34 sec) [ -10579.2086] [Alpha ][ 0.985268] . ( 34 sec) [ -10579.2086] [Topology ] . ( 35 sec) [ -10579.2081] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.208118. . Printing the most likely tree in file 'data1.phy_phyml_tree.txt'... . Time used 0h0m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo