.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -16171.4937] [GTR parameters ] . ( 6 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 6 sec) [ -16055.6228] [Topology ] . ( 10 sec) [ -15746.4015] [Topology ] . ( 13 sec) [ -15704.7329] [Topology ] . ( 17 sec) [ -15695.3163] [Topology ] . ( 20 sec) [ -15693.0363] [Topology ] . ( 24 sec) [ -15692.2250] [Topology ] . ( 27 sec) [ -15691.7236] [Topology ] . ( 31 sec) [ -15691.0034] [Topology ] . ( 34 sec) [ -15689.1725] [Topology ] . ( 38 sec) [ -15687.5621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -15687.0077] [Topology ] . ( 71 sec) [ -15674.2751] [GTR parameters ] . ( 72 sec) [ -15673.3524] [Alpha ][ 0.534838] . ( 72 sec) [ -15673.3524] [Topology ] . ( 75 sec) [ -15671.9309] [Topology ] . ( 79 sec) [ -15671.3290] [Topology ] . ( 82 sec) [ -15670.9763] [Topology ] . ( 86 sec) [ -15670.7498] [Topology ] . ( 89 sec) [ -15670.5983] [Topology ] . ( 93 sec) [ -15670.4943] [Topology ] . Checking for NNIs, optimizing five branches... . ( 118 sec) [ -15670.4657] [Topology ] . ( 124 sec) [ -15670.3857] [GTR parameters ] . ( 124 sec) [ -15670.3285] [Alpha ][ 0.543674] . ( 124 sec) [ -15670.3285] [Topology ] . ( 127 sec) [ -15670.1641] [Topology ] . ( 131 sec) [ -15670.0851] [Topology ] . ( 134 sec) [ -15670.0324] [Topology ] . ( 138 sec) [ -15669.9950] [Topology ] . ( 141 sec) [ -15669.9680] [Topology ] . ( 145 sec) [ -15669.9482] [Topology ] . Checking for NNIs, optimizing five branches... . ( 171 sec) [ -15669.9480] [Topology ] . ( 173 sec) [ -15669.9440] [GTR parameters ] . ( 174 sec) [ -15669.9395] [Alpha ][ 0.546104] . ( 174 sec) [ -15669.9395] [Topology ] . ( 177 sec) [ -15669.9214] [Topology ] . ( 181 sec) [ -15669.9081] [Topology ] . ( 184 sec) [ -15669.8982] [Topology ] . ( 188 sec) [ -15669.8909] [Topology ] . ( 191 sec) [ -15669.8854] [Topology ] . ( 195 sec) [ -15669.8813] [Topology ] . Checking for NNIs, optimizing five branches... . ( 222 sec) [ -15669.8803] [GTR parameters ] . ( 222 sec) [ -15669.8797] [Alpha ][ 0.547002] . ( 222 sec) [ -15669.8797] [Topology ] . ( 225 sec) [ -15669.8759] [Topology ] . ( 229 sec) [ -15669.8731] [Topology ] . ( 232 sec) [ -15669.8710] [Topology ] . ( 236 sec) [ -15669.8694] [Topology ] . ( 239 sec) [ -15669.8681] [Topology ] . ( 243 sec) [ -15669.8672] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -15669.8667] [GTR parameters ] . ( 271 sec) [ -15669.8666] [Alpha ][ 0.547549] . ( 271 sec) [ -15669.8666] [Topology ] . ( 275 sec) [ -15669.8657] [Topology ] . Checking for NNIs, optimizing five branches... . ( 301 sec) [ -15669.8657] [GTR parameters ] . ( 301 sec) [ -15669.8657] [Alpha ][ 0.547549] . ( 301 sec) [ -15669.8657] [Topology ] . ( 305 sec) [ -15669.8650] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15669.865032. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 0h5m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 355.85user 0.00system 5:57.71elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps