.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2921_54x966_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 397 patterns found. (out of a total of 966 sites) . 643 sites without polymorphism (66.56%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -6773.7497] [GTR parameters ] . ( 2 sec) [ -6662.0020] [Alpha ][ 0.500960] . ( 2 sec) [ -6662.0020] [Topology ] . ( 3 sec) [ -6547.3809] [Topology ] . ( 4 sec) [ -6525.6674] [Topology ] . ( 5 sec) [ -6520.6991] [Topology ] . ( 6 sec) [ -6516.7996] [Topology ] . ( 7 sec) [ -6514.1314] [Topology ] . ( 8 sec) [ -6511.5506] [Topology ] . ( 9 sec) [ -6509.4561] [Topology ] . ( 10 sec) [ -6508.1008] [Topology ] . ( 11 sec) [ -6508.0602] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -6507.6199] [Topology ] . ( 20 sec) [ -6506.3544] [GTR parameters ] . ( 20 sec) [ -6446.9494] [Alpha ][ 0.250961] . ( 20 sec) [ -6446.9494] [Topology ] . ( 21 sec) [ -6446.1760] [Topology ] . ( 23 sec) [ -6445.3926] [Topology ] . ( 24 sec) [ -6444.6345] [Topology ] . ( 25 sec) [ -6444.4249] [Topology ] . ( 26 sec) [ -6444.3550] [Topology ] . ( 27 sec) [ -6444.3291] [Topology ] . ( 27 sec) [ -6444.3194] [Topology ] . Checking for NNIs, optimizing five branches... . ( 35 sec) [ -6443.4624] [Topology ] . ( 36 sec) [ -6442.6721] [GTR parameters ] . ( 36 sec) [ -6441.0623] [Alpha ][ 0.222185] . ( 36 sec) [ -6441.0623] [Topology ] . ( 37 sec) [ -6440.9592] [Topology ] . ( 38 sec) [ -6440.9275] [Topology ] . ( 39 sec) [ -6440.9151] [Topology ] . ( 40 sec) [ -6440.9100] [Topology ] . ( 41 sec) [ -6440.9079] [Topology ] . ( 42 sec) [ -6440.9070] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -6440.8713] [GTR parameters ] . ( 49 sec) [ -6440.8583] [Alpha ][ 0.219892] . ( 49 sec) [ -6440.8583] [Topology ] . ( 50 sec) [ -6440.8564] [Topology ] . ( 51 sec) [ -6440.8556] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -6440.8552] [GTR parameters ] . ( 58 sec) [ -6440.8550] [Alpha ][ 0.219505] . ( 59 sec) [ -6440.8550] [Topology ] . ( 59 sec) [ -6440.8545] [Topology ] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -6440.8545] [GTR parameters ] . ( 66 sec) [ -6440.8545] [Alpha ][ 0.219505] . ( 66 sec) [ -6440.8545] [Topology ] . ( 67 sec) [ -6440.8544] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6440.854359. . Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'... . Time used 0h1m21s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 79.84user 0.00system 1:21.70elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps