.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2764_57x803_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... . 628 patterns found. (out of a total of 803 sites) . 286 sites without polymorphism (35.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -10411.1053] [GTR parameters ] . ( 3 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 3 sec) [ -10335.0128] [Topology ] . ( 5 sec) [ -10195.6434] [Topology ] . ( 6 sec) [ -10172.9119] [Topology ] . ( 8 sec) [ -10166.8129] [Topology ] . ( 10 sec) [ -10164.3617] [Topology ] . ( 11 sec) [ -10162.8738] [Topology ] . ( 13 sec) [ -10161.8960] [Topology ] . ( 14 sec) [ -10161.4684] [Topology ] . ( 16 sec) [ -10161.2425] [Topology ] . ( 17 sec) [ -10161.1170] [Topology ] . ( 20 sec) [ -10159.7359] [GTR parameters ] . ( 20 sec) [ -10158.5137] [Alpha ][ 0.551183] . ( 21 sec) [ -10158.5137] [Topology ] . ( 22 sec) [ -10158.2651] [Topology ] . ( 24 sec) [ -10158.0260] [Topology ] . ( 25 sec) [ -10157.8174] [Topology ] . ( 27 sec) [ -10157.7549] [Topology ] . ( 29 sec) [ -10157.7235] [Topology ] . ( 30 sec) [ -10157.7057] [Topology ] . ( 32 sec) [ -10157.6954] [Topology ] . ( 33 sec) [ -10157.6894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -10157.6802] [GTR parameters ] . ( 45 sec) [ -10157.6621] [Alpha ][ 0.557749] . ( 45 sec) [ -10157.6621] [Topology ] . ( 47 sec) [ -10157.6548] [Topology ] . ( 48 sec) [ -10157.6507] [Topology ] . ( 50 sec) [ -10157.6484] [Topology ] . ( 52 sec) [ -10157.6470] [Topology ] . ( 53 sec) [ -10157.6462] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -10157.6460] [GTR parameters ] . ( 65 sec) [ -10157.6459] [Alpha ][ 0.558307] . ( 65 sec) [ -10157.6459] [Topology ] . ( 66 sec) [ -10157.6452] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.645233. . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Time used 0h1m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 88.42user 0.00system 1:29.42elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps