.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2772_77x900_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 . 57 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 575 patterns found. (out of a total of 900 sites) . 459 sites without polymorphism (51.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7535.7731] [GTR parameters ] . ( 3 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 3 sec) [ -7436.5581] [Topology ] . ( 5 sec) [ -7272.4837] [Topology ] . ( 7 sec) [ -7248.9131] [Topology ] . ( 9 sec) [ -7242.2258] [Topology ] . ( 11 sec) [ -7239.3759] [Topology ] . ( 13 sec) [ -7237.7430] [Topology ] . ( 15 sec) [ -7235.4982] [Topology ] . ( 17 sec) [ -7232.9129] [Topology ] . ( 19 sec) [ -7229.8674] [Topology ] . ( 21 sec) [ -7226.3877] [Topology ] . ( 24 sec) [ -7224.6006] [GTR parameters ] . ( 24 sec) [ -7205.9195] [Alpha ][ 0.327414] . ( 24 sec) [ -7205.9195] [Topology ] . ( 26 sec) [ -7204.3575] [Topology ] . ( 28 sec) [ -7202.4492] [Topology ] . ( 30 sec) [ -7200.1107] [Topology ] . ( 33 sec) [ -7199.6426] [Topology ] . ( 35 sec) [ -7199.5423] [Topology ] . ( 37 sec) [ -7199.5102] [Topology ] . ( 39 sec) [ -7199.4996] [Topology ] . ( 41 sec) [ -7199.4959] [Topology ] . ( 43 sec) [ -7199.4946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -7199.4129] [Topology ] . ( 58 sec) [ -7199.2768] [GTR parameters ] . ( 58 sec) [ -7199.1884] [Alpha ][ 0.318202] . ( 58 sec) [ -7199.1884] [Topology ] . ( 60 sec) [ -7199.1112] [Topology ] . ( 62 sec) [ -7199.0965] [Topology ] . ( 64 sec) [ -7199.0928] [Topology ] . ( 66 sec) [ -7199.0918] [Topology ] . ( 67 sec) [ -7199.0916] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -7199.0904] [GTR parameters ] . ( 82 sec) [ -7199.0902] [Alpha ][ 0.317709] . ( 83 sec) [ -7199.0902] [Topology ] . ( 84 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -7199.0900] [GTR parameters ] . ( 99 sec) [ -7199.0900] [Alpha ][ 0.317709] . ( 99 sec) [ -7199.0900] [Topology ] . ( 100 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7199.090001. . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Time used 0h2m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 126.42user 0.00system 2:07.76elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps