.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2921_54x966_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 397 patterns found. (out of a total of 966 sites) . 643 sites without polymorphism (66.56%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6750.9979] [Ts/ts ratio ][ 4.861438] . ( 1 sec) [ -6749.5712] [ 1015] [depth= 1] . ( 1 sec) [ -6746.0818] [ 1017] [depth= 1] . ( 1 sec) [ -6745.7063] [ 1015] [depth= 1] . ( 1 sec) [ -6733.6696] [ 1019] [depth= 2] . ( 1 sec) [ -6730.3703] [ 1019] [depth= 1] . ( 1 sec) [ -6728.4194] [ 1019] [depth= 1] . ( 1 sec) [ -6719.6685] [ 1019] [depth= 1] . ( 1 sec) [ -6717.0733] [ 1019] [depth= 1] . ( 2 sec) [ -6716.0137] [ 1019] [depth= 1] . ( 2 sec) [ -6712.0964] [ 1017] [depth= 1] . ( 2 sec) [ -6710.7120] [ 1018] [depth= 1] . ( 2 sec) [ -6706.8299] [ 1017] [depth= 1] . ( 2 sec) [ -6696.8818] [ 1015] [depth= 1] . ( 2 sec) [ -6689.2646] [ 1013] [depth= 1] . ( 3 sec) [ -6686.6452] [ 1015] [depth= 1] . ( 3 sec) [ -6683.9349] [ 1015] [depth= 1] . ( 3 sec) [ -6678.0478] [ 1015] [depth= 1] . ( 3 sec) [ -6676.6974] [ 1015] [depth= 1] . ( 4 sec) [ -6675.3891] [ 1015] [depth= 1] . ( 4 sec) [ -6675.2258] [ 1015] [depth= 1] . ( 4 sec) [ -6673.0195] [ 1016] [depth= 1] . ( 4 sec) [ -6670.4726] [ 1015] [depth= 1] . ( 4 sec) [ -6669.4616] [ 1015] [depth= 1] . ( 4 sec) [ -6667.9501] [ 1015] [depth= 1] . ( 4 sec) [ -6667.1081] [ 1016] [depth= 1] . ( 4 sec) [ -6666.8940] [ 1015] [depth= 1] . ( 4 sec) [ -6663.0025] [ 1015] [depth= 1] . ( 4 sec) [ -6659.4372] [ 1014] [depth= 2] . ( 5 sec) [ -6659.2258] [ 1019] [depth= 2] . ( 5 sec) [ -6659.1847] [ 1015] [depth= 2] . ( 5 sec) [ -6657.2826] [ 1014] [depth= 1] . ( 5 sec) [ -6656.5628] [ 1014] [depth= 1] . ( 5 sec) [ -6656.5333] [ 1017] [depth= 1] . ( 6 sec) [ -6656.1466] [ 1018] [depth= 1] . ( 6 sec) [ -6655.8011] [ 1020] [depth= 1] . ( 6 sec) [ -6653.1473] [ 1022] [depth= 2] . ( 7 sec) [ -6651.5972] [ 1021] [depth= 1] . ( 8 sec) [ -6650.8795] [ 1018] [depth= 2] . ( 9 sec) [ -6643.5387] [ 1018] [depth= 1] . ( 9 sec) [ -6641.3751] [ 1016] [depth= 1] . ( 10 sec) [ -6634.0964] [ 1012] [depth= 2] . ( 10 sec) [ -6589.0756] [Branch lengths ] . ( 10 sec) [ -6588.1421] [Ts/ts ratio ][ 5.348871] . ( 10 sec) [ -6588.0675] [ 1011] [depth= 1] . ( 10 sec) [ -6587.8316] [ 1010] [depth= 1] . ( 10 sec) [ -6587.0835] [ 1009] [depth= 1] . ( 11 sec) [ -6587.0686] [ 1009] [depth= 1] . ( 12 sec) [ -6586.2421] [ 1010] [depth= 1] . ( 12 sec) [ -6582.3771] [ 1008] [depth= 2] . ( 16 sec) [ -6580.9971] [ 1008] [depth= 1] . ( 19 sec) [ -6580.6994] [ 1007] [depth= 2] . ( 19 sec) [ -6576.5839] [Branch lengths ] . ( 19 sec) [ -6576.5806] [Ts/ts ratio ][ 5.379367] . ( 28 sec) [ -6576.4157] [Branch lengths ] . ( 66 sec) [ -6576.4037] [Branch lengths ] . ( 66 sec) [ -6576.4037] [Topology ] . ( 67 sec) [ -6576.4032] [Topology ] . ( 67 sec) [ -6576.4019] [Ts/ts ratio ][ 5.399635] . ( 67 sec) [ -6576.4019] [Topology ] . ( 68 sec) [ -6576.4018] [Topology ] . ( 68 sec) [ -6576.4018] [Ts/ts ratio ][ 5.399635] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6576.401766. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 71 8.413851 0.786000 0.001722 48 0.494548 0.606000 0.001303 100 220.512743 1.000000 0.099692 46 1.203125 0.263000 0.008510 98 66.631469 0.994000 0.039859 85 7.843373 0.856000 0.011069 100 34.964834 0.973000 0.019358 67 3.420762 0.727000 0.001658 35 1.099347 0.158000 0.006317 100 100.811445 1.000000 0.063071 100 31.845314 0.973000 0.034272 54 10.369242 0.882000 0.014292 91 29.838512 0.956000 0.011105 48 1.725494 0.698000 0.004371 86 33.575351 0.965000 0.017545 92 33.710758 0.969000 0.018750 65 4.394963 0.698000 0.004823 73 17.173746 0.907000 0.012854 81 15.059551 0.924000 0.011594 96 20.790923 0.958000 0.016322 59 2.330784 0.742000 0.002295 100 77.625375 0.998000 0.022771 78 17.032429 0.942000 0.019376 37 5.078616 0.569000 0.013089 44 1.356661 0.187000 0.011018 100 136.571300 1.000000 0.059107 30 -1.000000 0.000000 0.000000 87 29.811777 0.974000 0.028193 25 2.427036 0.449000 0.008983 100 55.765543 0.999000 0.035685 33 4.862710 0.771000 0.006917 51 4.598682 0.827000 0.010005 100 163.996229 1.000000 0.072504 88 8.918112 0.862000 0.007277 50 2.389682 0.325000 0.004163 61 17.132037 0.939000 0.016680 25 2.986183 0.717000 0.003944 40 27.055251 0.948000 0.011403 55 9.862392 0.869000 0.006804 87 31.345691 0.960000 0.014029 90 20.664538 0.942000 0.012017 30 28.741334 0.960000 0.014363 10 10.582130 0.861000 0.007581 77 11.789309 0.887000 0.008311 11 9.617099 0.884000 0.007308 79 11.366775 0.875000 0.006693 100 78.747904 1.000000 0.021892 99 15.919588 0.936000 0.007942 19 20.757770 0.963000 0.012109 67 15.279831 0.908000 0.011099 20 0.399849 0.037000 0.003471 . Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'... . Time used 1h54m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo