.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -26079.2058] [GTR parameters ] . ( 3 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 3 sec) [ -25728.9409] [Topology ] . ( 5 sec) [ -25291.2425] [Topology ] . ( 7 sec) [ -25230.3848] [Topology ] . ( 8 sec) [ -25214.3514] [Topology ] . ( 10 sec) [ -25208.4878] [Topology ] . ( 12 sec) [ -25205.8920] [Topology ] . ( 13 sec) [ -25194.6256] [Topology ] . ( 15 sec) [ -25190.1344] [Topology ] . ( 17 sec) [ -25188.5150] [Topology ] . ( 19 sec) [ -25188.1330] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -25146.5950] [GTR parameters ] . ( 40 sec) [ -25136.1397] [Alpha ][ 0.428858] . ( 40 sec) [ -25136.1397] [Topology ] . ( 41 sec) [ -25131.9942] [Topology ] . ( 43 sec) [ -25130.7501] [Topology ] . ( 45 sec) [ -25130.0910] [Topology ] . ( 47 sec) [ -25129.6974] [Topology ] . ( 49 sec) [ -25129.4521] [Topology ] . ( 50 sec) [ -25129.2950] [Topology ] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -25126.2391] [GTR parameters ] . ( 69 sec) [ -25126.1947] [Alpha ][ 0.424452] . ( 69 sec) [ -25126.1947] [Topology ] . ( 70 sec) [ -25125.2580] [Topology ] . ( 72 sec) [ -25124.7461] [Topology ] . ( 74 sec) [ -25124.4178] [Topology ] . ( 75 sec) [ -25124.1998] [Topology ] . ( 77 sec) [ -25124.0522] [Topology ] . ( 79 sec) [ -25123.9521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -25123.3318] [GTR parameters ] . ( 97 sec) [ -25123.3317] [Alpha ][ 0.424028] . ( 97 sec) [ -25123.3317] [Topology ] . ( 99 sec) [ -25123.0192] [Topology ] . ( 101 sec) [ -25122.8253] [Topology ] . ( 102 sec) [ -25122.6945] [Topology ] . ( 104 sec) [ -25122.6048] [Topology ] . ( 106 sec) [ -25122.5424] [Topology ] . ( 108 sec) [ -25122.4990] [Topology ] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -25122.3007] [GTR parameters ] . ( 125 sec) [ -25122.3006] [Alpha ][ 0.423604] . ( 125 sec) [ -25122.3006] [Topology ] . ( 127 sec) [ -25122.1866] [Topology ] . ( 129 sec) [ -25122.1127] [Topology ] . ( 131 sec) [ -25122.0612] [Topology ] . ( 132 sec) [ -25122.0251] [Topology ] . ( 134 sec) [ -25121.9995] [Topology ] . ( 136 sec) [ -25121.9812] [Topology ] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -25121.9076] [GTR parameters ] . ( 153 sec) [ -25121.9073] [Alpha ][ 0.423180] . ( 153 sec) [ -25121.9073] [Topology ] . ( 155 sec) [ -25121.8623] [Topology ] . ( 157 sec) [ -25121.8325] [Topology ] . ( 159 sec) [ -25121.8113] [Topology ] . ( 160 sec) [ -25121.7961] [Topology ] . ( 162 sec) [ -25121.7853] [Topology ] . ( 164 sec) [ -25121.7774] [Topology ] . Checking for NNIs, optimizing five branches... . ( 181 sec) [ -25121.7482] [GTR parameters ] . ( 182 sec) [ -25121.7480] [Alpha ][ 0.422757] . ( 182 sec) [ -25121.7480] [Topology ] . ( 183 sec) [ -25121.7303] [Topology ] . ( 185 sec) [ -25121.7185] [Topology ] . ( 187 sec) [ -25121.7100] [Topology ] . ( 189 sec) [ -25121.7039] [Topology ] . ( 190 sec) [ -25121.6994] [Topology ] . ( 192 sec) [ -25121.6962] [Topology ] . Checking for NNIs, optimizing five branches... . ( 210 sec) [ -25121.6832] [GTR parameters ] . ( 210 sec) [ -25121.6832] [Alpha ][ 0.422757] . ( 210 sec) [ -25121.6832] [Topology ] . ( 212 sec) [ -25121.6754] [Topology ] . ( 213 sec) [ -25121.6702] [Topology ] . ( 215 sec) [ -25121.6663] [Topology ] . ( 217 sec) [ -25121.6636] [Topology ] . ( 219 sec) [ -25121.6616] [Topology ] . ( 220 sec) [ -25121.6601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 238 sec) [ -25121.6553] [GTR parameters ] . ( 238 sec) [ -25121.6549] [Alpha ][ 0.422334] . ( 238 sec) [ -25121.6549] [Topology ] . ( 239 sec) [ -25121.6518] [Topology ] . ( 241 sec) [ -25121.6497] [Topology ] . ( 243 sec) [ -25121.6482] [Topology ] . ( 245 sec) [ -25121.6471] [Topology ] . ( 246 sec) [ -25121.6463] [Topology ] . Checking for NNIs, optimizing five branches... . ( 263 sec) [ -25121.6442] [GTR parameters ] . ( 263 sec) [ -25121.6442] [Alpha ][ 0.422334] . ( 263 sec) [ -25121.6442] [Topology ] . ( 265 sec) [ -25121.6426] [Topology ] . ( 267 sec) [ -25121.6414] [Topology ] . ( 269 sec) [ -25121.6406] [Topology ] . Checking for NNIs, optimizing five branches... . ( 285 sec) [ -25121.6402] [GTR parameters ] . ( 285 sec) [ -25121.6402] [Alpha ][ 0.422334] . ( 285 sec) [ -25121.6402] [Topology ] . ( 287 sec) [ -25121.6393] [Topology ] . Checking for NNIs, optimizing five branches... . ( 303 sec) [ -25121.6393] [GTR parameters ] . ( 303 sec) [ -25121.6393] [Alpha ][ 0.422334] . ( 303 sec) [ -25121.6393] [Topology ] . ( 305 sec) [ -25121.6385] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25121.638540. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 0h5m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 336.01user 0.00system 5:37.51elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps