.......................... 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 : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . '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)... . ( 0 sec) [ -9288.4373] [Ts/ts ratio ][ 2.775534] . ( 1 sec) [ -9288.3968] [ 1837] [depth= 1] . ( 1 sec) [ -9286.7043] [ 1837] [depth= 1] . ( 1 sec) [ -9286.2465] [ 1836] [depth= 1] . ( 1 sec) [ -9255.0686] [ 1863] [depth= 1] . ( 1 sec) [ -9241.8896] [ 1836] [depth= 1] . ( 2 sec) [ -9241.8747] [ 1836] [depth= 1] . ( 2 sec) [ -9241.8218] [ 1836] [depth= 1] . ( 2 sec) [ -9241.6333] [ 1836] [depth= 1] . ( 2 sec) [ -9241.4892] [ 1836] [depth= 1] . ( 3 sec) [ -9240.7624] [ 1836] [depth= 1] . ( 3 sec) [ -9240.6595] [ 1836] [depth= 1] . ( 4 sec) [ -9240.6394] [ 1836] [depth= 1] . ( 4 sec) [ -9228.2350] [ 1833] [depth= 1] . ( 4 sec) [ -9227.7207] [ 1836] [depth= 1] . ( 4 sec) [ -9227.2127] [ 1833] [depth= 1] . ( 5 sec) [ -9226.3932] [ 1833] [depth= 1] . ( 5 sec) [ -9226.2650] [ 1833] [depth= 1] . ( 5 sec) [ -9226.2172] [ 1833] [depth= 1] . ( 5 sec) [ -9226.1965] [ 1833] [depth= 1] . ( 5 sec) [ -9222.4661] [ 1830] [depth= 1] . ( 5 sec) [ -9222.4395] [ 1830] [depth= 3] . ( 7 sec) [ -9221.5096] [ 1832] [depth= 1] . ( 7 sec) [ -9219.0387] [ 1830] [depth= 1] . ( 9 sec) [ -9208.7847] [ 1835] [depth= 1] . ( 9 sec) [ -9198.4150] [ 1830] [depth= 1] . ( 9 sec) [ -9184.0250] [ 1829] [depth= 1] . ( 9 sec) [ -9179.6111] [ 1840] [depth= 1] . ( 9 sec) [ -9179.5134] [ 1840] [depth= 1] . ( 10 sec) [ -9178.5890] [ 1840] [depth= 1] . ( 10 sec) [ -9178.5279] [ 1840] [depth= 1] . ( 10 sec) [ -9175.0493] [ 1840] [depth= 1] . ( 11 sec) [ -9174.9735] [ 1840] [depth= 1] . ( 11 sec) [ -9173.2005] [ 1829] [depth= 1] . ( 12 sec) [ -9171.5322] [ 1832] [depth= 1] . ( 12 sec) [ -9171.4226] [ 1832] [depth= 1] . ( 12 sec) [ -9171.0938] [ 1832] [depth= 1] . ( 12 sec) [ -9170.8514] [ 1832] [depth= 1] . ( 14 sec) [ -9168.5664] [ 1835] [depth= 1] . ( 14 sec) [ -9167.6018] [ 1832] [depth= 1] . ( 14 sec) [ -9167.5644] [ 1832] [depth= 1] . ( 14 sec) [ -9167.5356] [ 1832] [depth= 1] . ( 16 sec) [ -9150.2077] [Branch lengths ] . ( 16 sec) [ -9147.4446] [Ts/ts ratio ][ 3.162284] . ( 18 sec) [ -9147.4071] [ 1832] [depth= 1] . ( 20 sec) [ -9146.5302] [ 1829] [depth= 1] . ( 25 sec) [ -9146.5153] [ 1829] [depth= 1] . ( 31 sec) [ -9140.7493] [Branch lengths ] . ( 31 sec) [ -9140.7108] [Ts/ts ratio ][ 3.212693] . ( 40 sec) [ -9140.6844] [ 1829] [depth= 1] . ( 46 sec) [ -9140.1534] [Branch lengths ] . ( 46 sec) [ -9140.1522] [Ts/ts ratio ][ 3.220477] . ( 103 sec) [ -9140.0526] [Branch lengths ] . ( 103 sec) [ -9140.0526] [Topology ] . ( 104 sec) [ -9139.9787] [Topology ] . ( 106 sec) [ -9139.5902] [Topology ] . ( 107 sec) [ -9138.0830] [Topology ] . ( 109 sec) [ -9136.1340] [Topology ] . ( 111 sec) [ -9135.8270] [Topology ] . ( 112 sec) [ -9135.7898] [Topology ] . ( 113 sec) [ -9135.7886] [Ts/ts ratio ][ 3.228376] . ( 113 sec) [ -9135.7886] [Topology ] . ( 114 sec) [ -9135.7808] [Topology ] . ( 116 sec) [ -9135.7786] [Topology ] . ( 118 sec) [ -9135.7779] [Topology ] . ( 118 sec) [ -9135.7779] [Ts/ts ratio ][ 3.228376] . ( 118 sec) [ -9135.7779] [Topology ] . ( 119 sec) [ -9135.7775] [Topology ] . ( 120 sec) [ -9135.7775] [Ts/ts ratio ][ 3.228376] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9135.777516. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 46.250834 0.992000 0.183760 23 4.319018 0.812000 0.062406 90 35.007021 0.991000 0.064292 51 0.938458 0.382000 0.001214 91 32.665603 0.929000 0.003673 39 -1.000000 0.000000 0.000000 34 31.711033 0.988000 0.075704 38 7.592319 0.774000 0.030188 98 206.450147 1.000000 0.178765 74 2.760725 0.765000 0.016229 100 135.870135 1.000000 0.076053 100 83.050470 1.000000 0.038762 22 -1.000000 0.000000 0.000000 54 11.166828 0.807000 0.001318 99 11.145300 0.933000 0.015030 24 -1.000000 0.000000 0.000000 99 48.202711 0.991000 0.039007 86 6.925597 0.842000 0.007406 100 124.449932 1.000000 0.037102 24 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 100 38.012437 0.988000 0.018012 100 64.086077 0.997000 0.015995 87 5.326550 0.797000 0.002557 77 11.349899 0.835000 0.001294 10 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 90 19.175445 0.917000 0.046052 99 29.164913 0.985000 0.043312 100 109.735964 1.000000 0.076735 33 -1.000000 0.000000 0.000000 100 87.866098 0.998000 0.065159 73 0.281211 0.563000 0.000677 58 9.915290 0.901000 0.030126 87 87.087275 1.000000 0.099462 76 1.395845 0.693000 0.002793 75 15.623934 0.863000 0.003617 96 123.408286 1.000000 0.109358 99 26.687559 0.974000 0.023827 73 11.984725 0.908000 0.030319 100 154.524587 1.000000 0.090452 52 -1.000000 0.000000 0.000000 54 6.325328 0.743000 0.001217 65 7.240713 0.766000 0.001213 30 -1.000000 0.000000 0.000000 72 19.826245 0.957000 0.028279 87 61.945892 0.995000 0.042639 80 11.562276 0.832000 0.007191 89 8.332318 0.864000 0.002416 55 -1.000000 0.000000 0.000000 81 5.790030 0.812000 0.003986 90 74.492003 1.000000 0.057307 75 4.054297 0.806000 0.008183 100 61.655129 0.998000 0.028963 100 51.372701 0.991000 0.016929 100 46.531389 0.989000 0.016165 94 72.196720 1.000000 0.035471 71 6.228311 0.818000 0.003580 100 83.157677 0.998000 0.015314 41 -1.000000 0.000000 0.000000 92 8.834934 0.859000 0.002565 42 8.586304 0.898000 0.348208 . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Time used 4h8m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo