.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2708_78x1107_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 . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 1107 sites) . 505 sites without polymorphism (45.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 25Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -6941.4211] [GTR parameters ] . ( 3 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 3 sec) [ -6899.8793] [Topology ] . ( 5 sec) [ -6669.7753] [Topology ] . ( 8 sec) [ -6620.7511] [Topology ] . ( 10 sec) [ -6610.4959] [Topology ] . ( 12 sec) [ -6599.3357] [Topology ] . ( 14 sec) [ -6609.3373] [Topology ] . Moving backward . ( 14 sec) [ -6597.4246] [Topology ] . ( 16 sec) [ -6595.4764] [Topology ] . ( 18 sec) [ -6607.0982] [Topology ] . Moving backward . ( 18 sec) [ -6590.6067] [Topology ] . ( 23 sec) [ -6576.6676] [GTR parameters ] . ( 23 sec) [ -6570.7826] [Alpha ][ 0.397913] . ( 23 sec) [ -6570.7826] [Topology ] . ( 25 sec) [ -6564.4184] [Topology ] . ( 27 sec) [ -6560.3072] [Topology ] . ( 29 sec) [ -6558.6608] [Topology ] . ( 31 sec) [ -6554.1380] [Topology ] . ( 33 sec) [ -6555.8576] [Topology ] . Moving backward . ( 33 sec) [ -6547.5431] [Topology ] . ( 35 sec) [ -6546.5753] [Topology ] . ( 37 sec) [ -6545.8661] [Topology ] . ( 39 sec) [ -6545.4234] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -6544.7079] [Topology ] . ( 59 sec) [ -6544.4729] [GTR parameters ] . ( 59 sec) [ -6543.5007] [Alpha ][ 0.364367] . ( 59 sec) [ -6543.5007] [Topology ] . ( 61 sec) [ -6543.0475] [Topology ] . ( 63 sec) [ -6542.9259] [Topology ] . ( 65 sec) [ -6542.8611] [Topology ] . ( 66 sec) [ -6542.8201] [Topology ] . ( 68 sec) [ -6542.7894] [Topology ] . ( 70 sec) [ -6542.7655] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -6542.3276] [Topology ] . ( 88 sec) [ -6542.3035] [GTR parameters ] . ( 88 sec) [ -6542.1103] [Alpha ][ 0.350598] . ( 88 sec) [ -6542.1103] [Topology ] . ( 90 sec) [ -6541.8049] [Topology ] . ( 92 sec) [ -6541.7034] [Topology ] . ( 94 sec) [ -6541.6334] [Topology ] . ( 95 sec) [ -6541.6074] [Topology ] . ( 97 sec) [ -6541.5899] [Topology ] . ( 99 sec) [ -6541.5776] [Topology ] . ( 101 sec) [ -6541.5669] [Topology ] . ( 102 sec) [ -6541.5598] [Topology ] . Checking for NNIs, optimizing five branches... . ( 120 sec) [ -6541.0115] [Topology ] . ( 121 sec) [ -6541.0040] [GTR parameters ] . ( 121 sec) [ -6540.9757] [Alpha ][ 0.345346] . ( 121 sec) [ -6540.9757] [Topology ] . ( 123 sec) [ -6540.9545] [Topology ] . ( 125 sec) [ -6540.9485] [Topology ] . ( 126 sec) [ -6540.9454] [Topology ] . ( 128 sec) [ -6540.9436] [Topology ] . ( 130 sec) [ -6540.9428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 146 sec) [ -6540.7077] [Topology ] . ( 146 sec) [ -6540.7072] [GTR parameters ] . ( 147 sec) [ -6540.7023] [Alpha ][ 0.343170] . ( 147 sec) [ -6540.7023] [Topology ] . ( 148 sec) [ -6540.6981] [Topology ] . ( 150 sec) [ -6540.6973] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -6540.5640] [Topology ] . ( 166 sec) [ -6540.5638] [GTR parameters ] . ( 166 sec) [ -6540.5634] [Alpha ][ 0.342534] . ( 166 sec) [ -6540.5634] [Topology ] . ( 168 sec) [ -6540.5620] [Topology ] . ( 170 sec) [ -6540.5615] [Topology ] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -6540.5611] [Topology ] . ( 185 sec) [ -6540.5611] [GTR parameters ] . ( 185 sec) [ -6540.5610] [Alpha ][ 0.342191] . ( 185 sec) [ -6540.5610] [Topology ] . ( 187 sec) [ -6540.5602] [Topology ] . Checking for NNIs, optimizing five branches... . ( 202 sec) [ -6540.5596] [Topology ] . ( 202 sec) [ -6540.5596] [GTR parameters ] . ( 203 sec) [ -6540.5594] [Alpha ][ 0.341744] . ( 203 sec) [ -6540.5594] [Topology ] . ( 204 sec) [ -6540.5589] [Topology ] . Checking for NNIs, optimizing five branches... . ( 219 sec) [ -6540.5581] [Topology ] . ( 220 sec) [ -6540.5581] [GTR parameters ] . ( 220 sec) [ -6540.5581] [Alpha ][ 0.342085] . ( 220 sec) [ -6540.5581] [Topology ] . ( 222 sec) [ -6540.5569] [Topology ] . ( 223 sec) [ -6540.5564] [Topology ] . Checking for NNIs, optimizing five branches... . ( 238 sec) [ -6540.5564] [GTR parameters ] . ( 239 sec) [ -6540.5564] [Alpha ][ 0.342085] . ( 239 sec) [ -6540.5564] [Topology ] . ( 240 sec) [ -6540.5559] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6540.555880. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h4m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 268.92user 0.00system 4:30.36elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps