.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2567_64x1044_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... . 408 patterns found. (out of a total of 1044 sites) . 678 sites without polymorphism (64.94%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -7007.3560] [GTR parameters ] . ( 2 sec) [ -6925.4087] [Alpha ][ 0.500960] . ( 2 sec) [ -6925.4087] [Topology ] . ( 3 sec) [ -6848.6098] [Topology ] . ( 4 sec) [ -6831.2831] [Topology ] . ( 5 sec) [ -6827.5568] [Topology ] . ( 6 sec) [ -6826.0300] [Topology ] . ( 8 sec) [ -6825.4490] [Topology ] . ( 9 sec) [ -6825.2395] [Topology ] . ( 10 sec) [ -6825.1698] [Topology ] . ( 11 sec) [ -6825.1447] [Topology ] . ( 12 sec) [ -6825.1351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -6824.9189] [Topology ] . ( 22 sec) [ -6824.8588] [GTR parameters ] . ( 22 sec) [ -6793.4815] [Alpha ][ 0.278369] . ( 22 sec) [ -6793.4815] [Topology ] . ( 23 sec) [ -6793.2337] [Topology ] . ( 24 sec) [ -6793.1641] [Topology ] . ( 25 sec) [ -6793.1308] [Topology ] . ( 26 sec) [ -6793.1140] [Topology ] . ( 27 sec) [ -6793.1054] [Topology ] . ( 28 sec) [ -6793.1011] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -6792.9534] [Topology ] . ( 38 sec) [ -6792.7485] [GTR parameters ] . ( 38 sec) [ -6792.7442] [Alpha ][ 0.276515] . ( 38 sec) [ -6792.7442] [Topology ] . ( 39 sec) [ -6792.6671] [Topology ] . ( 40 sec) [ -6792.6469] [Topology ] . ( 41 sec) [ -6792.6391] [Topology ] . ( 42 sec) [ -6792.6357] [Topology ] . ( 43 sec) [ -6792.6341] [Topology ] . ( 45 sec) [ -6792.6333] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -6792.5556] [Topology ] . ( 54 sec) [ -6792.5462] [GTR parameters ] . ( 54 sec) [ -6792.5460] [Alpha ][ 0.276824] . ( 54 sec) [ -6792.5460] [Topology ] . ( 55 sec) [ -6792.0186] [Topology ] . ( 56 sec) [ -6791.9663] [Topology ] . ( 57 sec) [ -6791.9610] [Topology ] . ( 58 sec) [ -6791.9601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -6791.9559] [GTR parameters ] . ( 68 sec) [ -6791.9559] [Alpha ][ 0.276824] . ( 68 sec) [ -6791.9559] [Topology ] . ( 69 sec) [ -6791.9557] [Topology ] . Checking for NNIs, optimizing five branches... . ( 78 sec) [ -6791.9556] [GTR parameters ] . ( 78 sec) [ -6791.9556] [Alpha ][ 0.276824] . ( 78 sec) [ -6791.9556] [Topology ] . ( 79 sec) [ -6791.9556] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.955578. . Printing the most likely tree in file 'nucleic_M2567_64x1044_2006.phy_phyml_tree.txt'... . Time used 0h1m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 95.23user 0.00system 1:36.48elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps