.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2661_66x1027_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 . 9 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 596 patterns found. (out of a total of 1027 sites) . 417 sites without polymorphism (40.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -9359.5522] [GTR parameters ] . ( 3 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 4 sec) [ -9317.1645] [ 1834] [depth= 1] . ( 4 sec) [ -9315.6040] [ 1834] [depth= 1] . ( 4 sec) [ -9315.1052] [ 1833] [depth= 1] . ( 5 sec) [ -9315.0255] [ 1833] [depth= 1] . ( 5 sec) [ -9314.3793] [ 1833] [depth= 1] . ( 6 sec) [ -9314.2353] [ 1833] [depth= 1] . ( 6 sec) [ -9262.9945] [ 1860] [depth= 1] . ( 6 sec) [ -9248.7438] [ 1833] [depth= 1] . ( 6 sec) [ -9247.9524] [ 1833] [depth= 1] . ( 6 sec) [ -9247.8331] [ 1833] [depth= 1] . ( 7 sec) [ -9247.8211] [ 1833] [depth= 1] . ( 7 sec) [ -9247.8078] [ 1833] [depth= 1] . ( 7 sec) [ -9235.3607] [ 1830] [depth= 1] . ( 7 sec) [ -9234.3904] [ 1833] [depth= 1] . ( 7 sec) [ -9233.9232] [ 1830] [depth= 1] . ( 8 sec) [ -9233.1588] [ 1830] [depth= 2] . ( 8 sec) [ -9233.0346] [ 1830] [depth= 1] . ( 8 sec) [ -9232.9893] [ 1830] [depth= 1] . ( 8 sec) [ -9232.9739] [ 1830] [depth= 1] . ( 9 sec) [ -9232.9450] [ 1830] [depth= 3] . ( 11 sec) [ -9231.8949] [ 1832] [depth= 1] . ( 11 sec) [ -9229.6619] [ 1830] [depth= 1] . ( 12 sec) [ -9215.3303] [ 1835] [depth= 1] . ( 12 sec) [ -9204.6040] [ 1830] [depth= 1] . ( 13 sec) [ -9188.8289] [ 1829] [depth= 1] . ( 13 sec) [ -9188.7212] [ 1829] [depth= 1] . ( 13 sec) [ -9187.8323] [ 1829] [depth= 1] . ( 13 sec) [ -9187.7954] [ 1829] [depth= 1] . ( 14 sec) [ -9184.3888] [ 1829] [depth= 1] . ( 14 sec) [ -9179.3403] [ 1840] [depth= 1] . ( 15 sec) [ -9177.1602] [ 1829] [depth= 1] . ( 16 sec) [ -9174.3976] [ 1832] [depth= 1] . ( 16 sec) [ -9174.2815] [ 1832] [depth= 1] . ( 16 sec) [ -9173.9300] [ 1832] [depth= 1] . ( 16 sec) [ -9173.6882] [ 1832] [depth= 1] . ( 18 sec) [ -9171.2726] [ 1835] [depth= 1] . ( 18 sec) [ -9170.1518] [ 1832] [depth= 1] . ( 18 sec) [ -9170.1235] [ 1832] [depth= 1] . ( 19 sec) [ -9170.0995] [ 1832] [depth= 1] . ( 20 sec) [ -9149.5675] [Branch lengths ] . ( 22 sec) [ -9144.1259] [GTR parameters ] . ( 23 sec) [ -9144.1055] [Alpha ][ 0.497716] . ( 25 sec) [ -9144.0484] [ 1832] [depth= 1] . ( 26 sec) [ -9143.1183] [ 1829] [depth= 1] . ( 32 sec) [ -9143.0920] [ 1829] [depth= 1] . ( 39 sec) [ -9136.8309] [Branch lengths ] . ( 41 sec) [ -9136.7563] [GTR parameters ] . ( 41 sec) [ -9136.7065] [Alpha ][ 0.488466] . ( 50 sec) [ -9136.6799] [ 1829] [depth= 1] . ( 55 sec) [ -9136.0985] [Branch lengths ] . ( 56 sec) [ -9136.0933] [GTR parameters ] . ( 56 sec) [ -9136.0920] [Alpha ][ 0.486910] . ( 111 sec) [ -9135.9733] [Branch lengths ] . ( 111 sec) [ -9135.9733] [Topology ] . ( 113 sec) [ -9135.8505] [Topology ] . ( 114 sec) [ -9135.2320] [Topology ] . ( 116 sec) [ -9133.1923] [Topology ] . ( 118 sec) [ -9131.6586] [Topology ] . ( 119 sec) [ -9131.5822] [Topology ] . ( 121 sec) [ -9131.5678] [Topology ] . ( 122 sec) [ -9131.5600] [GTR parameters ] . ( 122 sec) [ -9131.5600] [Alpha ][ 0.486910] . ( 122 sec) [ -9131.5600] [Topology ] . ( 124 sec) [ -9131.5560] [Topology ] . ( 125 sec) [ -9131.5546] [Topology ] . ( 127 sec) [ -9131.5540] [Topology ] . ( 127 sec) [ -9131.5539] [GTR parameters ] . ( 128 sec) [ -9131.5539] [Alpha ][ 0.486910] . ( 128 sec) [ -9131.5539] [Topology ] . ( 129 sec) [ -9131.5535] [Topology ] . ( 130 sec) [ -9131.5535] [GTR parameters ] . ( 130 sec) [ -9131.5535] [Alpha ][ 0.486910] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.553478. . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Time used 0h2m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 141.03user 0.00system 2:22.37elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps