.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2944_80x1495_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 494 patterns found. (out of a total of 1495 sites) . 1077 sites without polymorphism (72.04%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -9336.8033] [GTR parameters ] . ( 4 sec) [ -9236.3667] [Alpha ][ 0.500960] . ( 4 sec) [ -9236.3667] [Topology ] . ( 6 sec) [ -9106.7265] [Topology ] . ( 8 sec) [ -9073.5495] [Topology ] . ( 10 sec) [ -9062.8635] [Topology ] . ( 11 sec) [ -9058.7107] [Topology ] . ( 13 sec) [ -9056.6216] [Topology ] . ( 15 sec) [ -9055.9627] [Topology ] . ( 17 sec) [ -9055.6109] [Topology ] . ( 19 sec) [ -9055.0866] [Topology ] . ( 21 sec) [ -9053.7351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -9052.4667] [GTR parameters ] . ( 37 sec) [ -9024.8575] [Alpha ][ 0.313875] . ( 37 sec) [ -9024.8575] [Topology ] . ( 39 sec) [ -9024.3363] [Topology ] . ( 41 sec) [ -9024.0852] [Topology ] . ( 43 sec) [ -9023.9339] [Topology ] . ( 45 sec) [ -9023.8381] [Topology ] . ( 46 sec) [ -9023.7762] [Topology ] . ( 48 sec) [ -9023.7359] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -9023.4456] [GTR parameters ] . ( 63 sec) [ -9023.4363] [Alpha ][ 0.311241] . ( 63 sec) [ -9023.4363] [Topology ] . ( 65 sec) [ -9023.4001] [Topology ] . ( 67 sec) [ -9023.3767] [Topology ] . ( 68 sec) [ -9023.3613] [Topology ] . ( 70 sec) [ -9023.3512] [Topology ] . ( 72 sec) [ -9023.3445] [Topology ] . ( 74 sec) [ -9023.3401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -9023.3391] [GTR parameters ] . ( 87 sec) [ -9023.3390] [Alpha ][ 0.310868] . ( 87 sec) [ -9023.3390] [Topology ] . ( 89 sec) [ -9023.3357] [Topology ] . ( 90 sec) [ -9023.3336] [Topology ] . ( 92 sec) [ -9023.3322] [Topology ] . ( 94 sec) [ -9023.3312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -9023.3306] [GTR parameters ] . ( 107 sec) [ -9023.3306] [Alpha ][ 0.310868] . ( 107 sec) [ -9023.3306] [Topology ] . ( 109 sec) [ -9023.3300] [Topology ] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -9023.3299] [GTR parameters ] . ( 122 sec) [ -9023.3299] [Alpha ][ 0.310868] . ( 122 sec) [ -9023.3299] [Topology ] . ( 124 sec) [ -9023.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9023.329451. . Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'... . Time used 0h2m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 149.06user 0.00system 2:30.96elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps