.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_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 . Compressing sequences... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3268.3123] [GTR parameters ] . ( 0 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 0 sec) [ -3255.0160] [Topology ] . ( 1 sec) [ -3235.7288] [Topology ] . ( 1 sec) [ -3225.5065] [Topology ] . ( 2 sec) [ -3221.9728] [Topology ] . ( 3 sec) [ -3221.2756] [Topology ] . ( 3 sec) [ -3221.1176] [Topology ] . ( 4 sec) [ -3221.0803] [Topology ] . ( 4 sec) [ -3221.0709] [Topology ] . ( 4 sec) [ -3221.0686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8 sec) [ -3111.9592] [GTR parameters ] . ( 8 sec) [ -3101.6790] [Alpha ][ 0.250961] . ( 8 sec) [ -3101.6790] [Topology ] . ( 9 sec) [ -3101.2469] [Topology ] . ( 9 sec) [ -3101.1951] [Topology ] . ( 10 sec) [ -3101.1835] [Topology ] . ( 10 sec) [ -3101.1807] [Topology ] . ( 11 sec) [ -3101.1800] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -3096.7030] [GTR parameters ] . ( 14 sec) [ -3094.6692] [Alpha ][ 0.159093] . ( 14 sec) [ -3094.6692] [Topology ] . ( 15 sec) [ -3094.6282] [Topology ] . ( 15 sec) [ -3094.6257] [Topology ] . ( 16 sec) [ -3094.6253] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -3089.9543] [GTR parameters ] . ( 20 sec) [ -3089.9515] [Alpha ][ 0.156168] . ( 20 sec) [ -3089.9515] [Topology ] . ( 20 sec) [ -3089.9489] [Topology ] . ( 20 sec) [ -3089.9485] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -3085.2057] [GTR parameters ] . ( 24 sec) [ -3085.2053] [Alpha ][ 0.154998] . ( 24 sec) [ -3085.2053] [Topology ] . ( 25 sec) [ -3085.2010] [Topology ] . ( 25 sec) [ -3085.2002] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -3080.3925] [GTR parameters ] . ( 29 sec) [ -3080.3922] [Alpha ][ 0.153972] . ( 29 sec) [ -3080.3922] [Topology ] . ( 30 sec) [ -3080.3863] [Topology ] . ( 30 sec) [ -3080.3852] [Topology ] . ( 30 sec) [ -3080.3848] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -3075.5240] [GTR parameters ] . ( 34 sec) [ -3075.5237] [Alpha ][ 0.152988] . ( 34 sec) [ -3075.5237] [Topology ] . ( 35 sec) [ -3075.5172] [Topology ] . ( 35 sec) [ -3075.5160] [Topology ] . ( 36 sec) [ -3075.5157] [Topology ] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -3039.0349] [GTR parameters ] . ( 40 sec) [ -3038.7796] [Alpha ][ 0.128324] . ( 40 sec) [ -3038.7796] [Topology ] . ( 41 sec) [ -3037.3507] [Topology ] . ( 41 sec) [ -3037.1439] [Topology ] . ( 41 sec) [ -3037.0788] [Topology ] . ( 42 sec) [ -3037.0592] [Topology ] . ( 42 sec) [ -3037.0539] [Topology ] . ( 43 sec) [ -3037.0525] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3036.9165] [GTR parameters ] . ( 47 sec) [ -3036.9104] [Alpha ][ 0.131591] . ( 47 sec) [ -3036.9104] [Topology ] . ( 48 sec) [ -3036.8963] [Topology ] . ( 48 sec) [ -3036.8936] [Topology ] . ( 49 sec) [ -3036.8929] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -3036.8920] [GTR parameters ] . ( 53 sec) [ -3036.8918] [Alpha ][ 0.132183] . ( 53 sec) [ -3036.8918] [Topology ] . ( 53 sec) [ -3036.8913] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -3036.8913] [GTR parameters ] . ( 57 sec) [ -3036.8913] [Alpha ][ 0.132315] . ( 57 sec) [ -3036.8913] [Topology ] . ( 57 sec) [ -3036.8912] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3036.891188. . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 64.37user 0.00system 1:05.44elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps