.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2839_470x829_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 . 52 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 733 patterns found. (out of a total of 829 sites) . 93 sites without polymorphism (11.22%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 184Mo of memory space... . Maximizing likelihood (using NNI moves)... . ( 45 sec) [ -44518.3396] [GTR parameters ] . ( 48 sec) [ -44263.3238] [Alpha ][ 0.500960] . ( 48 sec) [ -44263.3238] [Topology ] . ( 89 sec) [ -43246.8275] [Topology ] . ( 131 sec) [ -42997.7888] [Topology ] . ( 172 sec) [ -42888.5833] [Topology ] . ( 213 sec) [ -42840.4345] [Topology ] . ( 253 sec) [ -42815.4677] [Topology ] . ( 293 sec) [ -42793.9669] [Topology ] . ( 332 sec) [ -42759.5810] [Topology ] . ( 372 sec) [ -42703.5941] [Topology ] . ( 411 sec) [ -42637.5887] [Topology ] . ( 464 sec) [ -42570.3083] [GTR parameters ] . ( 466 sec) [ -42531.0370] [Alpha ][ 0.670551] . ( 466 sec) [ -42531.0370] [Topology ] . ( 506 sec) [ -42506.2669] [Topology ] . ( 545 sec) [ -42499.3432] [Topology ] . ( 584 sec) [ -42495.7670] [Topology ] . ( 623 sec) [ -42493.6223] [Topology ] . ( 662 sec) [ -42492.1393] [Topology ] . ( 701 sec) [ -42491.0552] [Topology ] . ( 740 sec) [ -42490.3124] [Topology ] . ( 780 sec) [ -42489.7890] [Topology ] . ( 819 sec) [ -42489.4201] [Topology ] . Checking for NNIs, optimizing five branches... . ( 957 sec) [ -42488.5908] [Topology ] . ( 971 sec) [ -42488.4658] [GTR parameters ] . ( 973 sec) [ -42484.5920] [Alpha ][ 0.730835] . ( 973 sec) [ -42484.5920] [Topology ] . ( 1012 sec) [ -42483.7075] [Topology ] . ( 1051 sec) [ -42483.1764] [Topology ] . ( 1090 sec) [ -42482.8220] [Topology ] . ( 1129 sec) [ -42482.5837] [Topology ] . ( 1168 sec) [ -42482.4232] [Topology ] . ( 1207 sec) [ -42482.3152] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1307 sec) [ -42481.9906] [Topology ] . ( 1319 sec) [ -42481.9534] [GTR parameters ] . ( 1320 sec) [ -42481.7934] [Alpha ][ 0.742845] . ( 1321 sec) [ -42481.7934] [Topology ] . ( 1360 sec) [ -42481.2909] [Topology ] . ( 1399 sec) [ -42481.1797] [Topology ] . ( 1438 sec) [ -42481.0740] [Topology ] . ( 1477 sec) [ -42480.9438] [Topology ] . ( 1516 sec) [ -42480.8929] [Topology ] . ( 1555 sec) [ -42480.8634] [Topology ] . ( 1594 sec) [ -42480.8446] [Topology ] . ( 1633 sec) [ -42480.8322] [Topology ] . ( 1672 sec) [ -42480.8241] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1772 sec) [ -42480.5311] [Topology ] . ( 1784 sec) [ -42480.5238] [GTR parameters ] . ( 1785 sec) [ -42480.4983] [Alpha ][ 0.747714] . ( 1786 sec) [ -42480.4983] [Topology ] . ( 1825 sec) [ -42480.3205] [Topology ] . ( 1864 sec) [ -42480.1877] [Topology ] . ( 1903 sec) [ -42479.6032] [Topology ] . ( 1942 sec) [ -42478.0597] [Topology ] . ( 1981 sec) [ -42476.2743] [Topology ] . ( 2020 sec) [ -42474.8341] [Topology ] . ( 2059 sec) [ -42473.6268] [Topology ] . ( 2098 sec) [ -42472.8343] [Topology ] . ( 2137 sec) [ -42472.7757] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2275 sec) [ -42472.5605] [Topology ] . ( 2283 sec) [ -42472.5546] [GTR parameters ] . ( 2284 sec) [ -42472.5507] [Alpha ][ 0.749610] . ( 2285 sec) [ -42472.5507] [Topology ] . ( 2324 sec) [ -42472.5471] [Topology ] . ( 2363 sec) [ -42472.5459] [Topology ] . ( 2402 sec) [ -42472.5455] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2501 sec) [ -42472.5206] [Topology ] . ( 2510 sec) [ -42472.5198] [GTR parameters ] . ( 2511 sec) [ -42472.5198] [Alpha ][ 0.749610] . ( 2511 sec) [ -42472.5198] [Topology ] . ( 2550 sec) [ -42472.5074] [Topology ] . ( 2590 sec) [ -42472.5062] [Topology ] . ( 2629 sec) [ -42472.5060] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2728 sec) [ -42472.5054] [Topology ] . ( 2731 sec) [ -42472.5054] [GTR parameters ] . ( 2732 sec) [ -42472.5054] [Alpha ][ 0.749610] . ( 2732 sec) [ -42472.5054] [Topology ] . ( 2771 sec) [ -42472.4880] [Topology ] . ( 2810 sec) [ -42468.4909] [Topology ] . ( 2849 sec) [ -42465.5751] [Topology ] . ( 2888 sec) [ -42464.9936] [Topology ] . ( 2927 sec) [ -42464.9425] [Topology ] . ( 2966 sec) [ -42464.9158] [Topology ] . ( 3005 sec) [ -42464.8936] [Topology ] . ( 3045 sec) [ -42464.8735] [Topology ] . ( 3084 sec) [ -42464.8552] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3183 sec) [ -42464.8546] [Topology ] . ( 3195 sec) [ -42464.8531] [GTR parameters ] . ( 3196 sec) [ -42464.8531] [Alpha ][ 0.749610] . ( 3196 sec) [ -42464.8531] [Topology ] . ( 3235 sec) [ -42464.8310] [Topology ] . ( 3274 sec) [ -42464.7999] [Topology ] . ( 3313 sec) [ -42464.7824] [Topology ] . ( 3352 sec) [ -42464.7756] [Topology ] . ( 3392 sec) [ -42464.7737] [Topology ] . ( 3431 sec) [ -42464.7732] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3530 sec) [ -42464.7730] [Topology ] . ( 3533 sec) [ -42464.7730] [GTR parameters ] . ( 3534 sec) [ -42464.7730] [Alpha ][ 0.749610] . ( 3534 sec) [ -42464.7730] [Topology ] . ( 3573 sec) [ -42464.7728] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3673 sec) [ -42464.7726] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3772 sec) [ -42464.7725] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -42464.772518. . Printing the most likely tree in file 'nucleic_M2839_470x829_2006.phy_phyml_tree.txt'... . Time used 1h4m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3890.77user 0.00system 1:04:52elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps