.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 280 patterns found. (out of a total of 1252 sites) . 984 sites without polymorphism (78.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -3429.4082] [GTR parameters ] . ( 2 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 2 sec) [ -3418.4507] [Topology ] . ( 3 sec) [ -3383.7580] [Topology ] . ( 4 sec) [ -3375.4885] [Topology ] . ( 5 sec) [ -3373.8574] [Topology ] . ( 6 sec) [ -3375.5743] [Topology ] . Moving backward . ( 6 sec) [ -3372.6560] [Topology ] . ( 7 sec) [ -3373.0305] [Topology ] . Moving backward . ( 7 sec) [ -3371.8967] [Topology ] . ( 8 sec) [ -3371.9248] [Topology ] . Moving backward . ( 8 sec) [ -3371.5939] [Topology ] . ( 9 sec) [ -3371.1516] [GTR parameters ] . ( 10 sec) [ -3365.0485] [Alpha ][ 0.259276] . ( 10 sec) [ -3365.0485] [Topology ] . ( 10 sec) [ -3364.5439] [Topology ] . ( 11 sec) [ -3364.9588] [Topology ] . Moving backward . ( 11 sec) [ -3363.9789] [Topology ] . ( 12 sec) [ -3364.1521] [Topology ] . Moving backward . ( 12 sec) [ -3363.9097] [Topology ] . ( 13 sec) [ -3363.9390] [Topology ] . Moving backward . ( 13 sec) [ -3363.8773] [Topology ] . ( 14 sec) [ -3363.9045] [Topology ] . Moving backward . ( 14 sec) [ -3363.8521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -3363.8103] [Topology ] . ( 20 sec) [ -3363.6958] [GTR parameters ] . ( 20 sec) [ -3363.6179] [Alpha ][ 0.242419] . ( 20 sec) [ -3363.6179] [Topology ] . ( 21 sec) [ -3363.5719] [Topology ] . ( 22 sec) [ -3363.5643] [Topology ] . ( 22 sec) [ -3363.6368] [Topology ] . Moving backward . ( 23 sec) [ -3363.5567] [Topology ] . ( 23 sec) [ -3363.5928] [Topology ] . Moving backward . ( 23 sec) [ -3363.5488] [Topology ] . ( 24 sec) [ -3363.5884] [Topology ] . Moving backward . ( 24 sec) [ -3363.5425] [Topology ] . ( 25 sec) [ -3363.5619] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -3363.5617] [Topology ] . ( 30 sec) [ -3363.5577] [GTR parameters ] . ( 30 sec) [ -3363.5548] [Alpha ][ 0.239253] . ( 30 sec) [ -3363.5548] [Topology ] . ( 31 sec) [ -3363.9067] [Topology ] . Moving backward . ( 31 sec) [ -3363.5441] [Topology ] . ( 31 sec) [ -3363.6769] [Topology ] . Moving backward . ( 32 sec) [ -3363.5300] [Topology ] . ( 32 sec) [ -3363.7362] [Topology ] . Moving backward . ( 32 sec) [ -3363.5250] [Topology ] . ( 33 sec) [ -3363.6144] [Topology ] . Moving backward . ( 33 sec) [ -3363.5137] [Topology ] . ( 34 sec) [ -3363.6283] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -3363.4943] [Topology ] . ( 39 sec) [ -3363.4941] [GTR parameters ] . ( 39 sec) [ -3363.4939] [Alpha ][ 0.238325] . ( 39 sec) [ -3363.4939] [Topology ] . ( 40 sec) [ -3363.4851] [Topology ] . ( 40 sec) [ -3363.4793] [Topology ] . ( 41 sec) [ -3363.4779] [Topology ] . ( 42 sec) [ -3363.4819] [Topology ] . Moving backward . ( 42 sec) [ -3363.4758] [Topology ] . ( 42 sec) [ -3363.4760] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3363.4729] [Topology ] . ( 47 sec) [ -3363.4729] [GTR parameters ] . ( 47 sec) [ -3363.4729] [Alpha ][ 0.238087] . ( 47 sec) [ -3363.4729] [Topology ] . ( 48 sec) [ -3363.4717] [Topology ] . ( 49 sec) [ -3363.4707] [Topology ] . ( 50 sec) [ -3363.4697] [Topology ] . ( 50 sec) [ -3363.4687] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -3363.4497] [Topology ] . ( 55 sec) [ -3363.4497] [GTR parameters ] . ( 56 sec) [ -3363.4497] [Alpha ][ 0.238087] . ( 56 sec) [ -3363.4497] [Topology ] . ( 56 sec) [ -3363.4489] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -3363.4487] [Topology ] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -3363.4294] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -3363.4235] [Topology ] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -3363.4219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -3363.4203] [Topology ] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -3363.3839] [Topology ] . Checking for NNIs, optimizing five branches... . ( 90 sec) [ -3363.3837] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3363.383651. . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Time used 0h1m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 94.56user 0.00system 1:36.08elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps