.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_2006.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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17741.2296] [Topology ] . ( 10 sec) [ -17315.9427] [Topology ] . ( 13 sec) [ -17203.4981] [Topology ] . ( 16 sec) [ -17151.0051] [Topology ] . ( 19 sec) [ -17128.8187] [Topology ] . ( 22 sec) [ -17112.6803] [Topology ] . ( 25 sec) [ -17105.8340] [Topology ] . ( 29 sec) [ -17101.2221] [Topology ] . ( 32 sec) [ -17099.3400] [Topology ] . ( 35 sec) [ -17097.6209] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -17091.2429] [Topology ] . ( 65 sec) [ -17076.1281] [GTR parameters ] . ( 66 sec) [ -17046.3688] [Alpha ][ 0.369311] . ( 66 sec) [ -17046.3688] [Topology ] . ( 69 sec) [ -17043.4664] [Topology ] . ( 72 sec) [ -17042.4267] [Topology ] . ( 75 sec) [ -17041.4778] [Topology ] . ( 78 sec) [ -17039.1772] [Topology ] . ( 81 sec) [ -17036.4185] [Topology ] . ( 84 sec) [ -17036.0413] [Topology ] . ( 87 sec) [ -17035.9335] [Topology ] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -17034.9214] [GTR parameters ] . ( 113 sec) [ -17034.8933] [Alpha ][ 0.365833] . ( 113 sec) [ -17034.8933] [Topology ] . ( 116 sec) [ -17034.7268] [Topology ] . ( 119 sec) [ -17034.6482] [Topology ] . ( 122 sec) [ -17034.5992] [Topology ] . ( 125 sec) [ -17034.5677] [Topology ] . ( 129 sec) [ -17034.5474] [Topology ] . ( 132 sec) [ -17034.5344] [Topology ] . Checking for NNIs, optimizing five branches... . ( 157 sec) [ -17034.5093] [GTR parameters ] . ( 157 sec) [ -17034.5092] [Alpha ][ 0.365468] . ( 157 sec) [ -17034.5092] [Topology ] . ( 160 sec) [ -17034.4950] [Topology ] . ( 163 sec) [ -17034.4865] [Topology ] . ( 166 sec) [ -17034.4811] [Topology ] . ( 169 sec) [ -17034.4776] [Topology ] . ( 173 sec) [ -17034.4753] [Topology ] . ( 176 sec) [ -17034.4739] [Topology ] . Checking for NNIs, optimizing five branches... . ( 199 sec) [ -17034.4722] [GTR parameters ] . ( 199 sec) [ -17034.4722] [Alpha ][ 0.365468] . ( 199 sec) [ -17034.4722] [Topology ] . ( 203 sec) [ -17034.4709] [Topology ] . ( 206 sec) [ -17034.4700] [Topology ] . Checking for NNIs, optimizing five branches... . ( 229 sec) [ -17034.4698] [GTR parameters ] . ( 229 sec) [ -17034.4698] [Alpha ][ 0.365468] . ( 229 sec) [ -17034.4698] [Topology ] . ( 232 sec) [ -17034.4693] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -17034.469256. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 0h4m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 277.90user 0.00system 4:39.52elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps