.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2566_73x918_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... . 541 patterns found. (out of a total of 918 sites) . 442 sites without polymorphism (48.15%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -12577.0498] [GTR parameters ] . ( 4 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 4 sec) [ -12377.0948] [Topology ] . ( 6 sec) [ -12129.6581] [Topology ] . ( 7 sec) [ -12077.7104] [Topology ] . ( 9 sec) [ -12066.1739] [Topology ] . ( 11 sec) [ -12059.8968] [Topology ] . ( 13 sec) [ -12056.6268] [Topology ] . ( 14 sec) [ -12055.4653] [Topology ] . ( 16 sec) [ -12055.0915] [Topology ] . ( 18 sec) [ -12054.9395] [Topology ] . ( 20 sec) [ -12054.8734] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -12049.4145] [GTR parameters ] . ( 38 sec) [ -12019.0259] [Alpha ][ 0.342808] . ( 38 sec) [ -12019.0259] [Topology ] . ( 40 sec) [ -12018.5158] [Topology ] . ( 42 sec) [ -12018.4764] [Topology ] . ( 44 sec) [ -12018.4681] [Topology ] . ( 45 sec) [ -12018.4656] [Topology ] . ( 47 sec) [ -12018.4647] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -12018.2149] [GTR parameters ] . ( 62 sec) [ -12018.2002] [Alpha ][ 0.339937] . ( 62 sec) [ -12018.2002] [Topology ] . ( 64 sec) [ -12018.1950] [Topology ] . ( 66 sec) [ -12018.1935] [Topology ] . ( 68 sec) [ -12018.1928] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -12018.1923] [GTR parameters ] . ( 81 sec) [ -12018.1923] [Alpha ][ 0.340277] . ( 81 sec) [ -12018.1923] [Topology ] . ( 83 sec) [ -12018.1918] [Topology ] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -12018.1918] [GTR parameters ] . ( 96 sec) [ -12018.1918] [Alpha ][ 0.340277] . ( 96 sec) [ -12018.1918] [Topology ] . ( 98 sec) [ -12018.1916] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12018.191571. . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Time used 0h2m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 124.05user 0.00system 2:05.39elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps