.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2932_68x1712_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 . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1264 patterns found. (out of a total of 1712 sites) . 601 sites without polymorphism (35.11%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 45Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -15465.7212] [GTR parameters ] . ( 8 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 8 sec) [ -15431.9484] [Topology ] . ( 11 sec) [ -15123.7998] [Topology ] . ( 15 sec) [ -15045.1303] [Topology ] . ( 19 sec) [ -15019.2652] [Topology ] . ( 22 sec) [ -15009.7959] [Topology ] . ( 26 sec) [ -15006.3124] [Topology ] . ( 30 sec) [ -15003.2852] [Topology ] . ( 33 sec) [ -14997.0189] [Topology ] . ( 36 sec) [ -14981.6104] [Topology ] . ( 40 sec) [ -14966.8514] [Topology ] . ( 53 sec) [ -14941.8760] [GTR parameters ] . ( 53 sec) [ -14941.7245] [Alpha ][ 0.597689] . ( 53 sec) [ -14941.7245] [Topology ] . ( 57 sec) [ -14938.9688] [Topology ] . ( 60 sec) [ -14938.5298] [Topology ] . ( 63 sec) [ -14938.0933] [Topology ] . ( 67 sec) [ -14937.9609] [Topology ] . ( 70 sec) [ -14937.9156] [Topology ] . ( 74 sec) [ -14937.6606] [Topology ] . ( 77 sec) [ -14937.8851] [Topology ] . Moving backward . ( 77 sec) [ -14932.9840] [Topology ] . ( 81 sec) [ -14932.5999] [Topology ] . Checking for NNIs, optimizing five branches... . ( 116 sec) [ -14932.8775] [Topology ] . ( 122 sec) [ -14932.6234] [GTR parameters ] . ( 123 sec) [ -14932.3411] [Alpha ][ 0.576687] . ( 123 sec) [ -14932.3411] [Topology ] . ( 127 sec) [ -14931.4471] [Topology ] . ( 130 sec) [ -14931.6178] [Topology ] . Moving backward . ( 130 sec) [ -14931.3953] [Topology ] . ( 134 sec) [ -14931.7351] [Topology ] . Moving backward . ( 134 sec) [ -14931.3471] [Topology ] . ( 138 sec) [ -14931.4047] [Topology ] . Moving backward . ( 138 sec) [ -14931.3258] [Topology ] . ( 141 sec) [ -14931.5111] [Topology ] . Moving backward . ( 142 sec) [ -14931.3137] [Topology ] . Checking for NNIs, optimizing five branches... . ( 176 sec) [ -14930.6260] [Topology ] . ( 178 sec) [ -14930.6075] [GTR parameters ] . ( 178 sec) [ -14930.5855] [Alpha ][ 0.570794] . ( 178 sec) [ -14930.5855] [Topology ] . ( 182 sec) [ -14930.1129] [Topology ] . ( 185 sec) [ -14930.3959] [Topology ] . Moving backward . ( 186 sec) [ -14929.8056] [Topology ] . ( 189 sec) [ -14929.9694] [Topology ] . Moving backward . ( 189 sec) [ -14929.6610] [Topology ] . ( 193 sec) [ -14929.6374] [Topology ] . ( 196 sec) [ -14929.6416] [Topology ] . Moving backward . ( 197 sec) [ -14929.6332] [Topology ] . ( 200 sec) [ -14929.6352] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 230 sec) [ -14929.6291] [Topology ] . ( 235 sec) [ -14929.6260] [GTR parameters ] . ( 235 sec) [ -14929.6239] [Alpha ][ 0.568931] . ( 235 sec) [ -14929.6239] [Topology ] . ( 239 sec) [ -14929.6195] [Topology ] . ( 242 sec) [ -14929.6177] [Topology ] . ( 245 sec) [ -14929.6180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 275 sec) [ -14929.6162] [Topology ] . ( 278 sec) [ -14929.6157] [GTR parameters ] . ( 278 sec) [ -14929.6154] [Alpha ][ 0.568261] . ( 278 sec) [ -14929.6154] [Topology ] . ( 282 sec) [ -14929.6146] [Topology ] . Checking for NNIs, optimizing five branches... . ( 312 sec) [ -14929.6140] [Topology ] . ( 313 sec) [ -14929.6139] [GTR parameters ] . ( 313 sec) [ -14929.6139] [Alpha ][ 0.568261] . ( 313 sec) [ -14929.6139] [Topology ] . ( 317 sec) [ -14929.6134] [Topology ] . Checking for NNIs, optimizing five branches... . ( 346 sec) [ -14929.6131] [Topology ] . Checking for NNIs, optimizing five branches... . ( 378 sec) [ -14929.6092] [Topology ] . Checking for NNIs, optimizing five branches... . ( 410 sec) [ -14929.6091] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14929.609064. . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 0h7m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 440.59user 0.00system 7:22.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps