.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -8163.5103] [GTR parameters ] . ( 3 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 3 sec) [ -8080.4464] [Topology ] . ( 5 sec) [ -7998.7983] [Topology ] . ( 6 sec) [ -7955.3559] [Topology ] . ( 8 sec) [ -7942.8529] [Topology ] . ( 10 sec) [ -7938.6627] [Topology ] . ( 11 sec) [ -7938.6180] [Topology ] . ( 13 sec) [ -7936.9159] [Topology ] . ( 15 sec) [ -7937.3880] [Topology ] . Moving backward . ( 15 sec) [ -7936.2310] [Topology ] . ( 16 sec) [ -7935.8656] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -7931.5928] [Topology ] . ( 33 sec) [ -7931.2315] [GTR parameters ] . ( 33 sec) [ -7881.1773] [Alpha ][ 0.250961] . ( 33 sec) [ -7881.1773] [Topology ] . ( 35 sec) [ -7880.5556] [Topology ] . ( 36 sec) [ -7880.3201] [Topology ] . ( 38 sec) [ -7880.2593] [Topology ] . ( 40 sec) [ -7880.2272] [Topology ] . ( 41 sec) [ -7880.2046] [Topology ] . ( 43 sec) [ -7880.1875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7878.0740] [Topology ] . ( 57 sec) [ -7878.0004] [GTR parameters ] . ( 57 sec) [ -7875.6771] [Alpha ][ 0.212336] . ( 57 sec) [ -7875.6771] [Topology ] . ( 58 sec) [ -7875.5666] [Topology ] . ( 60 sec) [ -7875.2585] [Topology ] . ( 61 sec) [ -7873.6080] [Topology ] . ( 63 sec) [ -7869.6012] [Topology ] . ( 65 sec) [ -7868.4627] [Topology ] . ( 66 sec) [ -7868.3538] [Topology ] . ( 68 sec) [ -7868.3402] [Topology ] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -7868.3399] [Topology ] . ( 81 sec) [ -7868.3159] [GTR parameters ] . ( 81 sec) [ -7868.3141] [Alpha ][ 0.211294] . ( 81 sec) [ -7868.3141] [Topology ] . ( 83 sec) [ -7868.3112] [Topology ] . ( 85 sec) [ -7868.3103] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -7868.3029] [Topology ] . ( 97 sec) [ -7868.3029] [GTR parameters ] . ( 97 sec) [ -7868.3029] [Alpha ][ 0.211294] . ( 97 sec) [ -7868.3029] [Topology ] . ( 99 sec) [ -7868.3022] [Topology ] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -7868.3021] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7868.302081. . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 0h2m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 123.09user 0.00system 2:04.78elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps