.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_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... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -15009.3920] [GTR parameters ] . ( 4 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 4 sec) [ -14725.6209] [Topology ] . ( 5 sec) [ -14531.9053] [Topology ] . ( 7 sec) [ -14493.0754] [Topology ] . ( 8 sec) [ -14474.2240] [Topology ] . ( 10 sec) [ -14466.5015] [Topology ] . ( 12 sec) [ -14464.3817] [Topology ] . ( 13 sec) [ -14463.4422] [Topology ] . ( 15 sec) [ -14462.9907] [Topology ] . ( 16 sec) [ -14462.7666] [Topology ] . ( 18 sec) [ -14462.6528] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -14460.8041] [GTR parameters ] . ( 34 sec) [ -14371.0264] [Alpha ][ 0.279990] . ( 34 sec) [ -14371.0264] [Topology ] . ( 36 sec) [ -14370.0783] [Topology ] . ( 37 sec) [ -14369.8437] [Topology ] . ( 39 sec) [ -14369.4994] [Topology ] . ( 41 sec) [ -14369.4254] [Topology ] . ( 42 sec) [ -14369.3901] [Topology ] . ( 44 sec) [ -14369.3698] [Topology ] . ( 46 sec) [ -14369.3578] [Topology ] . ( 47 sec) [ -14369.3507] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -14368.8958] [GTR parameters ] . ( 61 sec) [ -14368.7192] [Alpha ][ 0.273158] . ( 61 sec) [ -14368.7192] [Topology ] . ( 63 sec) [ -14368.6894] [Topology ] . ( 64 sec) [ -14368.6736] [Topology ] . ( 66 sec) [ -14368.6645] [Topology ] . ( 67 sec) [ -14368.6593] [Topology ] . ( 69 sec) [ -14368.6562] [Topology ] . ( 71 sec) [ -14368.6545] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -14368.6527] [GTR parameters ] . ( 83 sec) [ -14368.6463] [Alpha ][ 0.271777] . ( 83 sec) [ -14368.6463] [Topology ] . ( 85 sec) [ -14368.6434] [Topology ] . ( 87 sec) [ -14368.6418] [Topology ] . ( 88 sec) [ -14368.6408] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -14368.6398] [GTR parameters ] . ( 102 sec) [ -14368.6396] [Alpha ][ 0.271504] . ( 102 sec) [ -14368.6396] [Topology ] . ( 103 sec) [ -14368.6388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 115 sec) [ -14368.6388] [GTR parameters ] . ( 116 sec) [ -14368.6388] [Alpha ][ 0.271504] . ( 116 sec) [ -14368.6388] [Topology ] . ( 117 sec) [ -14368.6384] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14368.638364. . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 0h2m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 140.26user 0.00system 2:21.80elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps