.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_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 . Compressing sequences... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -27626.8600] [Ts/ts ratio ][ 6.532821] . ( 1 sec) [ -27625.5664] [ 5812] [depth= 1] . ( 2 sec) [ -27622.4952] [ 5817] [depth= 1] . ( 2 sec) [ -27609.6606] [ 5812] [depth= 1] . ( 2 sec) [ -27609.3427] [ 5820] [depth= 1] . ( 3 sec) [ -27605.2703] [ 5824] [depth= 1] . ( 3 sec) [ -27593.3813] [ 5820] [depth= 1] . ( 4 sec) [ -27591.0654] [ 5823] [depth= 1] . ( 4 sec) [ -27590.7373] [ 5820] [depth= 1] . ( 5 sec) [ -27584.7822] [ 5821] [depth= 1] . ( 5 sec) [ -27579.1470] [ 5826] [depth= 1] . ( 5 sec) [ -27576.9748] [ 5821] [depth= 1] . ( 6 sec) [ -27574.8309] [ 5823] [depth= 1] . ( 6 sec) [ -27573.7787] [ 5825] [depth= 1] . ( 6 sec) [ -27572.8566] [ 5824] [depth= 1] . ( 7 sec) [ -27571.0179] [ 5819] [depth= 1] . ( 7 sec) [ -27562.1654] [ 5823] [depth= 1] . ( 7 sec) [ -27542.5323] [ 5812] [depth= 4] . ( 8 sec) [ -27542.3027] [ 5817] [depth= 2] . ( 8 sec) [ -27532.1626] [ 5818] [depth= 1] . ( 8 sec) [ -27530.8109] [ 5817] [depth= 1] . ( 9 sec) [ -27524.1250] [ 5816] [depth= 1] . ( 9 sec) [ -27520.8726] [ 5814] [depth= 1] . ( 9 sec) [ -27520.7318] [ 5815] [depth= 1] . ( 9 sec) [ -27520.6878] [ 5814] [depth= 1] . ( 9 sec) [ -27515.3230] [ 5808] [depth= 1] . ( 10 sec) [ -27512.7812] [ 5810] [depth= 1] . ( 10 sec) [ -27500.3012] [ 5802] [depth= 1] . ( 10 sec) [ -27493.3675] [ 5802] [depth= 1] . ( 10 sec) [ -27477.2929] [ 5803] [depth= 3] . ( 11 sec) [ -27470.5132] [ 5807] [depth= 1] . ( 11 sec) [ -27469.4885] [ 5813] [depth= 1] . ( 12 sec) [ -27457.5859] [ 5811] [depth= 2] . ( 12 sec) [ -27449.5598] [ 5819] [depth= 1] . ( 12 sec) [ -27432.7970] [ 5811] [depth= 1] . ( 13 sec) [ -27424.1931] [ 5822] [depth= 1] . ( 13 sec) [ -27409.9986] [ 5811] [depth= 1] . ( 13 sec) [ -27409.8796] [ 5813] [depth= 1] . ( 14 sec) [ -27385.7386] [ 5822] [depth= 2] . ( 14 sec) [ -27372.1713] [ 5816] [depth= 2] . ( 14 sec) [ -27371.1522] [ 5817] [depth= 1] . ( 14 sec) [ -27368.0139] [ 5816] [depth= 1] . ( 15 sec) [ -27360.3745] [ 5812] [depth= 1] . ( 15 sec) [ -27356.7062] [ 5812] [depth= 1] . ( 15 sec) [ -27353.7251] [ 5815] [depth= 1] . ( 16 sec) [ -27352.8865] [ 5814] [depth= 1] . ( 16 sec) [ -27350.7461] [ 5812] [depth= 1] . ( 16 sec) [ -27350.3933] [ 5814] [depth= 1] . ( 17 sec) [ -27350.0610] [ 5813] [depth= 1] . ( 17 sec) [ -27349.5186] [ 5812] [depth= 1] . ( 17 sec) [ -27348.9027] [ 5816] [depth= 1] . ( 17 sec) [ -27333.7063] [ 5820] [depth= 1] . ( 17 sec) [ -27332.1258] [ 5822] [depth= 2] . ( 17 sec) [ -27329.7002] [ 5822] [depth= 1] . ( 18 sec) [ -27328.6416] [ 5822] [depth= 1] . ( 18 sec) [ -27326.3726] [ 5822] [depth= 1] . ( 19 sec) [ -27324.6879] [ 5822] [depth= 1] . ( 19 sec) [ -27321.5868] [ 5822] [depth= 1] . ( 20 sec) [ -27321.1140] [ 5822] [depth= 1] . ( 20 sec) [ -27319.0794] [ 5822] [depth= 1] . ( 20 sec) [ -27317.4188] [ 5824] [depth= 1] . ( 21 sec) [ -27312.5630] [ 5822] [depth= 1] . ( 21 sec) [ -27311.8833] [ 5825] [depth= 1] . ( 21 sec) [ -27306.7231] [ 5822] [depth= 2] . ( 21 sec) [ -27305.7358] [ 5820] [depth= 1] . ( 21 sec) [ -27299.8986] [ 5818] [depth= 1] . ( 22 sec) [ -27295.6911] [ 5820] [depth= 1] . ( 22 sec) [ -27291.3390] [ 5818] [depth= 1] . ( 22 sec) [ -27290.6805] [ 5821] [depth= 1] . ( 22 sec) [ -27287.5361] [ 5818] [depth= 1] . ( 23 sec) [ -27287.4249] [ 5820] [depth= 1] . ( 23 sec) [ -27285.5945] [ 5818] [depth= 1] . ( 24 sec) [ -27285.5086] [ 5822] [depth= 2] . ( 26 sec) [ -27285.3564] [ 5820] [depth= 1] . ( 28 sec) [ -27282.3475] [ 5819] [depth= 1] . ( 28 sec) [ -27281.1651] [ 5819] [depth= 3] . ( 28 sec) [ -27280.9772] [ 5819] [depth= 1] . ( 30 sec) [ -27277.3344] [ 5818] [depth= 1] . ( 30 sec) [ -27275.5730] [ 5818] [depth= 1] . ( 33 sec) [ -27273.3449] [ 5819] [depth= 4] . ( 36 sec) [ -27272.6211] [ 5819] [depth= 1] . ( 37 sec) [ -27272.5224] [ 5819] [depth= 1] . ( 37 sec) [ -27272.4868] [ 5819] [depth= 1] . ( 40 sec) [ -27272.4739] [ 5819] [depth= 1] . ( 43 sec) [ -27272.4547] [ 5819] [depth= 1] . ( 45 sec) [ -27171.8192] [Branch lengths ] . ( 46 sec) [ -27168.9966] [Ts/ts ratio ][ 7.029265] . ( 46 sec) [ -27162.2345] [ 5810] [depth= 1] . ( 49 sec) [ -27161.9943] [ 5812] [depth= 1] . ( 53 sec) [ -27161.7570] [ 5814] [depth= 1] . ( 53 sec) [ -27158.8497] [ 5810] [depth= 1] . ( 53 sec) [ -27153.9081] [ 5809] [depth= 2] . ( 54 sec) [ -27153.1906] [ 5815] [depth= 1] . ( 54 sec) [ -27151.0960] [ 5807] [depth= 1] . ( 55 sec) [ -27148.0937] [ 5808] [depth= 1] . ( 55 sec) [ -27146.2829] [ 5808] [depth= 1] . ( 58 sec) [ -27140.0233] [ 5808] [depth= 3] . ( 58 sec) [ -27137.7715] [ 5804] [depth= 1] . ( 58 sec) [ -27137.5182] [ 5805] [depth= 1] . ( 59 sec) [ -27137.4466] [ 5805] [depth= 2] . ( 60 sec) [ -27132.2338] [ 5809] [depth= 1] . ( 60 sec) [ -27131.8120] [ 5802] [depth= 1] . ( 61 sec) [ -27129.5525] [ 5802] [depth= 1] . ( 63 sec) [ -27128.6813] [ 5806] [depth= 1] . ( 64 sec) [ -27128.5573] [ 5809] [depth= 1] . ( 72 sec) [ -27127.2260] [ 5806] [depth= 3] . ( 75 sec) [ -27127.2143] [ 5806] [depth= 1] . ( 91 sec) [ -27110.8158] [Branch lengths ] . ( 91 sec) [ -27110.5506] [Ts/ts ratio ][ 7.188170] . ( 135 sec) [ -27109.6284] [Branch lengths ] . ( 208 sec) [ -27109.5126] [ 5809] [depth= 1] . ( 271 sec) [ -27109.2717] [Branch lengths ] . ( 272 sec) [ -27109.2599] [Ts/ts ratio ][ 7.223185] . ( 272 sec) [ -27109.2599] [Topology ] . ( 275 sec) [ -27109.2503] [Topology ] . ( 278 sec) [ -27109.2478] [Topology ] . ( 281 sec) [ -27109.2468] [Topology ] . ( 282 sec) [ -27109.2468] [Ts/ts ratio ][ 7.223185] . ( 282 sec) [ -27109.2468] [Topology ] . ( 285 sec) [ -27109.2464] [Topology ] . ( 285 sec) [ -27109.2464] [Ts/ts ratio ][ 7.223185] . Checking for NNIs, optimizing five branches... . ( 309 sec) [ -27109.0852] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -27109.085217. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 165.485631 1.000000 0.081706 34 9.720808 0.841000 0.014581 28 3.157669 0.782000 0.006585 49 17.612928 0.938000 0.026765 100 108.177963 1.000000 0.059774 84 24.016387 0.975000 0.031253 71 8.026525 0.834000 0.025158 91 30.052635 0.959000 0.031761 100 173.030537 1.000000 0.085590 99 18.145418 0.935000 0.014212 49 4.071964 0.697000 0.011344 86 27.468220 0.939000 0.026771 100 71.581166 0.999000 0.056709 100 105.051678 1.000000 0.091612 61 12.179924 0.920000 0.019024 100 411.635558 1.000000 0.176015 81 5.167237 0.849000 0.014471 100 117.200188 1.000000 0.057623 100 80.820326 0.997000 0.027939 92 50.864877 0.995000 0.043336 58 6.475528 0.709000 0.023583 93 28.279254 0.965000 0.033207 45 0.945400 0.118000 0.011913 89 24.939756 0.971000 0.021548 46 1.689399 0.258000 0.004766 100 113.038067 1.000000 0.031132 78 55.432000 0.996000 0.017515 53 10.319226 0.867000 0.003872 42 3.390654 0.741000 0.001137 44 5.913043 0.776000 0.005913 100 64.784259 0.998000 0.024699 100 61.872251 0.995000 0.041648 58 6.888491 0.811000 0.007162 36 0.858663 0.279000 0.005458 69 10.689272 0.871000 0.015963 39 0.322444 0.027000 0.007347 70 12.975925 0.880000 0.006882 100 60.983626 0.997000 0.027486 42 1.031251 0.282000 0.003614 100 58.259860 1.000000 0.039844 54 3.783738 0.644000 0.011673 100 92.150217 1.000000 0.055088 51 2.047034 0.374000 0.011566 98 32.297739 0.982000 0.038716 100 83.143430 0.999000 0.069942 100 75.870156 0.996000 0.048612 98 35.787034 0.992000 0.056035 100 46.688041 0.994000 0.064842 33 6.189527 0.795000 0.010785 100 151.255202 1.000000 0.070288 100 38.148399 0.989000 0.022690 59 5.732547 0.479000 0.009145 93 32.936329 0.982000 0.019239 70 5.052110 0.810000 0.004256 11 0.838989 0.313000 0.004915 48 8.872684 0.885000 0.014145 100 104.729356 1.000000 0.055567 100 61.298158 0.998000 0.046267 99 126.651806 1.000000 0.064453 98 28.032736 0.984000 0.021261 84 34.443539 0.980000 0.014504 100 112.312937 1.000000 0.030163 60 5.159325 0.544000 0.007167 66 6.213463 0.834000 0.004868 100 53.179910 0.997000 0.034915 88 31.467364 0.974000 0.024100 43 0.077472 0.000000 0.003692 72 8.357795 0.851000 0.006645 100 106.084668 1.000000 0.030757 99 30.525716 0.979000 0.019106 100 58.050412 0.989000 0.028170 19 0.066747 0.000000 0.001896 45 11.187140 0.863000 0.011054 26 6.124568 0.720000 0.004779 94 32.160056 0.963000 0.015642 62 4.843276 0.670000 0.006465 95 42.646119 0.976000 0.019636 100 108.021942 0.997000 0.021421 46 11.394773 0.888000 0.005090 26 2.280409 0.364000 0.001043 31 4.826966 0.735000 0.001929 49 1.793806 0.186000 0.005451 100 133.922612 1.000000 0.034386 100 64.241719 1.000000 0.032706 47 2.835919 0.753000 0.002320 50 11.057439 0.889000 0.003517 36 3.956042 0.741000 0.001341 23 8.087500 0.759000 0.001564 87 25.749584 0.935000 0.005293 97 59.224694 0.986000 0.008747 85 26.772247 0.950000 0.004733 100 79.123195 0.999000 0.012564 23 13.330554 0.865000 0.001856 39 16.016520 0.901000 0.002783 100 47.597945 0.975000 0.007630 20 5.495391 0.757000 0.000944 25 7.810478 0.831000 0.002364 57 12.794267 0.834000 0.003667 7 7.257247 0.767000 0.000974 16 3.487743 0.750000 0.000916 35 5.360765 0.813000 0.001852 6 -1.000000 0.000000 0.000000 98 60.739413 0.993000 0.007616 52 32.089845 0.936000 0.003516 74 18.862047 0.910000 0.003032 82 11.659829 0.867000 0.001848 45 4.548682 0.636000 0.001817 . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 10h0m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo