.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data38.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... . 417 patterns found. (out of a total of 500 sites) . 82 sites without polymorphism (16.40%). . 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=-9766.742204 . ( 1 sec) [ -9764.5406] [GTR parameters ] . ( 1 sec) [ -9762.3882] [Alpha ][ 0.854371] . ( 1 sec) [ -9762.3882] [Topology ] . ( 3 sec) [ -9719.6165] [Topology ] . ( 4 sec) [ -9712.6303] [Topology ] . ( 5 sec) [ -9710.9518] [Topology ] . ( 6 sec) [ -9710.2725] [Topology ] . ( 7 sec) [ -9709.9654] [Topology ] . ( 8 sec) [ -9709.8205] [Topology ] . ( 9 sec) [ -9709.7502] [Topology ] . ( 10 sec) [ -9709.7153] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.715254 . ( 16 sec) [ -9709.6642] [GTR parameters ] . ( 16 sec) [ -9709.2487] [Alpha ][ 0.913010] . ( 16 sec) [ -9709.2487] [Topology ] . ( 17 sec) [ -9709.1890] [Topology ] . ( 18 sec) [ -9709.1643] [Topology ] . ( 19 sec) [ -9709.1525] [Topology ] . ( 20 sec) [ -9709.1467] [Topology ] . ( 22 sec) [ -9709.1438] [Topology ] . ( 23 sec) [ -9709.1423] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.142282 . ( 31 sec) [ -9709.1416] [GTR parameters ] . ( 31 sec) [ -9709.1373] [Alpha ][ 0.919319] . ( 32 sec) [ -9709.1373] [Topology ] . ( 33 sec) [ -9709.1361] [Topology ] . ( 34 sec) [ -9709.1355] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.135472 . ( 41 sec) [ -9709.1354] [GTR parameters ] . ( 41 sec) [ -9709.1354] [Alpha ][ 0.919319] . ( 42 sec) [ -9709.1354] [Topology ] . ( 42 sec) [ -9709.1352] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.135166. . Printing the most likely tree in file 'data38.phy_phyml_tree.txt'... . Time used 0h0m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo