.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2916_143x897_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 . 73 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 303 patterns found. (out of a total of 897 sites) . 620 sites without polymorphism (69.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -3593.8681] [GTR parameters ] . ( 2 sec) [ -3572.6148] [Alpha ][ 0.500960] . ( 2 sec) [ -3572.6148] [Topology ] . ( 5 sec) [ -3519.3730] [Topology ] . ( 7 sec) [ -3509.5189] [Topology ] . ( 9 sec) [ -3506.2944] [Topology ] . ( 11 sec) [ -3504.2974] [Topology ] . ( 13 sec) [ -3504.1015] [Topology ] . ( 15 sec) [ -3504.0779] [Topology ] . ( 17 sec) [ -3504.7313] [Topology ] . Moving backward . ( 17 sec) [ -3503.2725] [Topology ] . ( 19 sec) [ -3503.0857] [Topology ] . ( 22 sec) [ -3504.2253] [GTR parameters ] . ( 22 sec) [ -3495.1632] [Alpha ][ 0.267622] . ( 22 sec) [ -3495.1632] [Topology ] . ( 24 sec) [ -3493.0420] [Topology ] . ( 26 sec) [ -3493.1186] [Topology ] . Moving backward . ( 26 sec) [ -3492.9346] [Topology ] . ( 28 sec) [ -3493.3411] [Topology ] . Moving backward . ( 28 sec) [ -3492.9330] [Topology ] . ( 29 sec) [ -3493.4804] [Topology ] . Moving backward . ( 30 sec) [ -3492.9140] [Topology ] . ( 31 sec) [ -3493.3163] [Topology ] . Moving backward . ( 31 sec) [ -3492.9024] [Topology ] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -3493.0797] [Topology ] . ( 45 sec) [ -3492.8590] [GTR parameters ] . ( 45 sec) [ -3492.8542] [Alpha ][ 0.264260] . ( 45 sec) [ -3492.8542] [Topology ] . ( 47 sec) [ -3492.8481] [Topology ] . ( 49 sec) [ -3494.2271] [Topology ] . Moving backward . ( 49 sec) [ -3492.6788] [Topology ] . ( 51 sec) [ -3493.0008] [Topology ] . Moving backward . ( 51 sec) [ -3492.6040] [Topology ] . ( 53 sec) [ -3492.6918] [Topology ] . Moving backward . ( 53 sec) [ -3492.5978] [Topology ] . ( 55 sec) [ -3492.6979] [Topology ] . Moving backward . ( 55 sec) [ -3492.5942] [Topology ] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -3492.5890] [Topology ] . ( 68 sec) [ -3492.5873] [GTR parameters ] . ( 68 sec) [ -3492.5873] [Alpha ][ 0.263923] . ( 68 sec) [ -3492.5873] [Topology ] . ( 69 sec) [ -3492.5824] [Topology ] . ( 71 sec) [ -3492.5786] [Topology ] . ( 73 sec) [ -3492.5803] [Topology ] . Moving backward . ( 73 sec) [ -3492.5768] [Topology ] . ( 75 sec) [ -3492.5839] [Topology ] . Moving backward . ( 75 sec) [ -3492.5758] [Topology ] . ( 77 sec) [ -3492.5983] [Topology ] . Moving backward . ( 77 sec) [ -3492.5751] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -3492.5700] [Topology ] . ( 88 sec) [ -3492.5699] [GTR parameters ] . ( 88 sec) [ -3492.5699] [Alpha ][ 0.263923] . ( 88 sec) [ -3492.5699] [Topology ] . ( 90 sec) [ -3492.5657] [Topology ] . ( 91 sec) [ -3492.5632] [Topology ] . ( 93 sec) [ -3492.5785] [Topology ] . Moving backward . ( 93 sec) [ -3492.5615] [Topology ] . ( 95 sec) [ -3492.5855] [Topology ] . Moving backward . ( 95 sec) [ -3492.5595] [Topology ] . ( 97 sec) [ -3492.5860] [Topology ] . Moving backward . ( 97 sec) [ -3492.5564] [Topology ] . ( 99 sec) [ -3492.5628] [Topology ] . Checking for NNIs, optimizing five branches... . ( 109 sec) [ -3492.5521] [Topology ] . ( 109 sec) [ -3492.5521] [GTR parameters ] . ( 109 sec) [ -3492.5521] [Alpha ][ 0.263923] . ( 110 sec) [ -3492.5521] [Topology ] . ( 111 sec) [ -3492.5512] [Topology ] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -3492.5414] [Topology ] . ( 122 sec) [ -3492.5414] [GTR parameters ] . ( 122 sec) [ -3492.5414] [Alpha ][ 0.263923] . ( 122 sec) [ -3492.5414] [Topology ] . ( 124 sec) [ -3492.5409] [Topology ] . Checking for NNIs, optimizing five branches... . ( 134 sec) [ -3492.5408] [Topology ] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -3492.5404] [Topology ] . Checking for NNIs, optimizing five branches... . ( 154 sec) [ -3492.5390] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -3492.5377] [Topology ] . Checking for NNIs, optimizing five branches... . ( 175 sec) [ -3492.5355] [Topology ] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -3492.5346] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -3492.5345] [Topology ] . Checking for NNIs, optimizing five branches... . ( 206 sec) [ -3492.5316] [Topology ] . Checking for NNIs, optimizing five branches... . ( 216 sec) [ -3492.5315] [Topology ] . Checking for NNIs, optimizing five branches... . ( 226 sec) [ -3492.5314] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3492.531436. . Printing the most likely tree in file 'nucleic_M2916_143x897_2006.phy_phyml_tree.txt'... . Time used 0h3m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 236.29user 0.00system 3:57.98elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps