.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2772_77x900_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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 57 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 575 patterns found. (out of a total of 900 sites) . 459 sites without polymorphism (51.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -7535.7731] [GTR parameters ] . ( 3 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 3 sec) [ -7431.0273] [ 1225] [depth= 1] . ( 3 sec) [ -7429.9233] [ 1225] [depth= 1] . ( 3 sec) [ -7410.2809] [ 1223] [depth= 1] . ( 4 sec) [ -7410.1458] [ 1223] [depth= 1] . ( 4 sec) [ -7410.1041] [ 1223] [depth= 1] . ( 4 sec) [ -7409.8023] [ 1223] [depth= 2] . ( 4 sec) [ -7408.9585] [ 1224] [depth= 1] . ( 4 sec) [ -7406.9594] [ 1224] [depth= 2] . ( 4 sec) [ -7404.9846] [ 1223] [depth= 1] . ( 5 sec) [ -7401.0463] [ 1222] [depth= 1] . ( 5 sec) [ -7400.6838] [ 1222] [depth= 1] . ( 5 sec) [ -7400.5019] [ 1222] [depth= 1] . ( 5 sec) [ -7398.4451] [ 1222] [depth= 1] . ( 6 sec) [ -7398.2267] [ 1222] [depth= 1] . ( 6 sec) [ -7396.4619] [ 1222] [depth= 1] . ( 6 sec) [ -7395.6511] [ 1222] [depth= 1] . ( 6 sec) [ -7386.4843] [ 1219] [depth= 1] . ( 6 sec) [ -7385.8609] [ 1219] [depth= 1] . ( 6 sec) [ -7385.8356] [ 1219] [depth= 1] . ( 6 sec) [ -7384.0618] [ 1219] [depth= 1] . ( 7 sec) [ -7380.4750] [ 1218] [depth= 2] . ( 7 sec) [ -7379.5810] [ 1218] [depth= 1] . ( 8 sec) [ -7373.9089] [ 1218] [depth= 1] . ( 8 sec) [ -7371.2656] [ 1219] [depth= 1] . ( 8 sec) [ -7360.0181] [ 1218] [depth= 1] . ( 8 sec) [ -7354.4505] [ 1218] [depth= 1] . ( 9 sec) [ -7352.5763] [ 1218] [depth= 1] . ( 9 sec) [ -7343.0089] [ 1219] [depth= 1] . ( 9 sec) [ -7341.7956] [ 1219] [depth= 1] . ( 9 sec) [ -7340.4186] [ 1222] [depth= 1] . ( 9 sec) [ -7337.1230] [ 1218] [depth= 2] . ( 10 sec) [ -7335.8683] [ 1216] [depth= 1] . ( 10 sec) [ -7332.6406] [ 1218] [depth= 1] . ( 10 sec) [ -7328.7074] [ 1217] [depth= 3] . ( 10 sec) [ -7325.9843] [ 1218] [depth= 1] . ( 10 sec) [ -7323.3650] [ 1217] [depth= 1] . ( 11 sec) [ -7319.1117] [ 1216] [depth= 1] . ( 11 sec) [ -7318.4019] [ 1216] [depth= 1] . ( 11 sec) [ -7315.1916] [ 1215] [depth= 2] . ( 11 sec) [ -7314.6038] [ 1215] [depth= 1] . ( 11 sec) [ -7314.5030] [ 1215] [depth= 1] . ( 12 sec) [ -7307.9502] [ 1215] [depth= 2] . ( 12 sec) [ -7307.0064] [ 1215] [depth= 1] . ( 12 sec) [ -7306.5546] [ 1215] [depth= 1] . ( 12 sec) [ -7306.3905] [ 1215] [depth= 1] . ( 12 sec) [ -7306.2211] [ 1215] [depth= 1] . ( 12 sec) [ -7306.0243] [ 1215] [depth= 2] . ( 12 sec) [ -7305.9469] [ 1215] [depth= 1] . ( 12 sec) [ -7305.9162] [ 1215] [depth= 1] . ( 13 sec) [ -7305.9057] [ 1215] [depth= 2] . ( 13 sec) [ -7305.6603] [ 1215] [depth= 1] . ( 13 sec) [ -7305.4497] [ 1215] [depth= 1] . ( 13 sec) [ -7305.1799] [ 1215] [depth= 1] . ( 14 sec) [ -7303.9590] [ 1215] [depth= 1] . ( 14 sec) [ -7302.3458] [ 1215] [depth= 1] . ( 14 sec) [ -7299.5086] [ 1215] [depth= 1] . ( 14 sec) [ -7296.7986] [ 1214] [depth= 1] . ( 14 sec) [ -7293.6076] [ 1213] [depth= 2] . ( 15 sec) [ -7289.0454] [ 1211] [depth= 1] . ( 15 sec) [ -7287.2859] [ 1213] [depth= 2] . ( 15 sec) [ -7287.2248] [ 1213] [depth= 1] . ( 15 sec) [ -7286.7631] [ 1213] [depth= 1] . ( 15 sec) [ -7284.4897] [ 1213] [depth= 1] . ( 17 sec) [ -7231.5919] [Branch lengths ] . ( 19 sec) [ -7230.9272] [GTR parameters ] . ( 19 sec) [ -7212.0371] [Alpha ][ 0.323736] . ( 22 sec) [ -7210.4648] [ 1214] [depth= 2] . ( 24 sec) [ -7210.4522] [ 1212] [depth= 1] . ( 24 sec) [ -7208.3399] [ 1211] [depth= 7] . ( 24 sec) [ -7207.1767] [ 1211] [depth= 1] . ( 25 sec) [ -7206.9552] [ 1211] [depth= 1] . ( 27 sec) [ -7205.3405] [ 1210] [depth= 2] . ( 27 sec) [ -7205.2683] [ 1210] [depth= 2] . ( 27 sec) [ -7205.2502] [ 1210] [depth= 1] . ( 29 sec) [ -7200.6067] [ 1209] [depth= 2] . ( 31 sec) [ -7195.4785] [Branch lengths ] . ( 33 sec) [ -7194.6416] [GTR parameters ] . ( 33 sec) [ -7194.6193] [Alpha ][ 0.319247] . ( 37 sec) [ -7194.3159] [ 1209] [depth= 1] . ( 44 sec) [ -7193.7440] [Branch lengths ] . ( 46 sec) [ -7193.7385] [GTR parameters ] . ( 46 sec) [ -7193.7380] [Alpha ][ 0.318443] . ( 132 sec) [ -7193.7066] [Branch lengths ] . ( 132 sec) [ -7193.7066] [Topology ] . ( 134 sec) [ -7193.7057] [Topology ] . ( 134 sec) [ -7193.7056] [GTR parameters ] . ( 135 sec) [ -7193.7056] [Alpha ][ 0.318443] . Checking for NNIs, optimizing five branches... . ( 148 sec) [ -7193.4056] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7193.405612. . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Time used 0h2m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 159.09user 0.00system 2:43.04elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps