.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17993.6320] [Ts/ts ratio ][ 3.950320] . ( 1 sec) [ -17983.0006] [ 3536] [depth= 1] . ( 1 sec) [ -17978.9443] [ 3536] [depth= 1] . ( 1 sec) [ -17961.6022] [ 3536] [depth= 1] . ( 2 sec) [ -17949.9066] [ 3527] [depth= 2] . ( 2 sec) [ -17942.6833] [ 3527] [depth= 2] . ( 2 sec) [ -17930.0505] [ 3525] [depth= 2] . ( 2 sec) [ -17928.0778] [ 3524] [depth= 1] . ( 4 sec) [ -17927.7821] [ 3524] [depth= 1] . ( 4 sec) [ -17924.9707] [ 3523] [depth= 1] . ( 4 sec) [ -17924.2904] [ 3523] [depth= 1] . ( 5 sec) [ -17921.4953] [ 3523] [depth= 1] . ( 5 sec) [ -17921.3129] [ 3523] [depth= 1] . ( 6 sec) [ -17907.2201] [ 3525] [depth= 1] . ( 6 sec) [ -17906.5123] [ 3522] [depth= 2] . ( 6 sec) [ -17905.3125] [ 3522] [depth= 1] . ( 6 sec) [ -17905.0534] [ 3522] [depth= 1] . ( 7 sec) [ -17902.3242] [ 3519] [depth= 1] . ( 7 sec) [ -17902.2435] [ 3517] [depth= 1] . ( 8 sec) [ -17900.3641] [ 3519] [depth= 1] . ( 8 sec) [ -17899.6465] [ 3517] [depth= 1] . ( 8 sec) [ -17898.8907] [ 3522] [depth= 1] . ( 8 sec) [ -17892.3877] [ 3531] [depth= 3] . ( 8 sec) [ -17884.9295] [ 3521] [depth= 1] . ( 9 sec) [ -17884.6295] [ 3521] [depth= 1] . ( 9 sec) [ -17882.2224] [ 3521] [depth= 1] . ( 9 sec) [ -17881.8551] [ 3521] [depth= 1] . ( 9 sec) [ -17874.6622] [ 3520] [depth= 1] . ( 9 sec) [ -17874.2189] [ 3520] [depth= 1] . ( 10 sec) [ -17873.2179] [ 3520] [depth= 1] . ( 10 sec) [ -17872.7357] [ 3520] [depth= 1] . ( 10 sec) [ -17870.3047] [ 3519] [depth= 1] . ( 11 sec) [ -17866.4920] [ 3521] [depth= 1] . ( 11 sec) [ -17856.3557] [ 3520] [depth= 1] . ( 11 sec) [ -17855.9317] [ 3521] [depth= 1] . ( 11 sec) [ -17855.5738] [ 3522] [depth= 1] . ( 12 sec) [ -17850.4991] [ 3524] [depth= 1] . ( 12 sec) [ -17845.5074] [ 3523] [depth= 1] . ( 13 sec) [ -17830.9812] [ 3523] [depth= 3] . ( 13 sec) [ -17829.0978] [ 3523] [depth= 1] . ( 13 sec) [ -17822.9900] [ 3523] [depth= 1] . ( 13 sec) [ -17817.2336] [ 3525] [depth= 4] . ( 14 sec) [ -17813.0536] [ 3520] [depth= 3] . ( 14 sec) [ -17802.1400] [ 3520] [depth= 1] . ( 14 sec) [ -17801.6784] [ 3520] [depth= 1] . ( 15 sec) [ -17800.2767] [ 3520] [depth= 1] . ( 15 sec) [ -17794.1306] [ 3516] [depth= 2] . ( 16 sec) [ -17792.5961] [ 3516] [depth= 1] . ( 16 sec) [ -17791.5357] [ 3516] [depth= 2] . ( 16 sec) [ -17784.8723] [ 3514] [depth= 2] . ( 17 sec) [ -17782.8668] [ 3514] [depth= 1] . ( 17 sec) [ -17767.6469] [ 3514] [depth= 1] . ( 17 sec) [ -17761.3850] [ 3513] [depth= 3] . ( 17 sec) [ -17750.9067] [ 3511] [depth= 7] . ( 18 sec) [ -17749.8447] [ 3515] [depth= 1] . ( 18 sec) [ -17748.6940] [ 3516] [depth= 1] . ( 18 sec) [ -17746.9196] [ 3516] [depth= 1] . ( 19 sec) [ -17745.8140] [ 3520] [depth= 1] . ( 19 sec) [ -17741.3457] [ 3520] [depth= 1] . ( 19 sec) [ -17736.7916] [ 3521] [depth= 2] . ( 19 sec) [ -17729.5284] [ 3523] [depth= 3] . ( 19 sec) [ -17727.8616] [ 3520] [depth= 1] . ( 19 sec) [ -17722.4745] [ 3517] [depth= 1] . ( 20 sec) [ -17720.8919] [ 3520] [depth= 1] . ( 20 sec) [ -17710.3750] [ 3518] [depth= 1] . ( 20 sec) [ -17709.8951] [ 3518] [depth= 1] . ( 20 sec) [ -17709.8778] [ 3522] [depth= 1] . ( 20 sec) [ -17708.3921] [ 3519] [depth= 1] . ( 21 sec) [ -17707.7686] [ 3518] [depth= 1] . ( 21 sec) [ -17706.6277] [ 3515] [depth= 1] . ( 21 sec) [ -17705.4101] [ 3517] [depth= 1] . ( 21 sec) [ -17699.4044] [ 3515] [depth= 1] . ( 22 sec) [ -17684.9727] [ 3517] [depth= 2] . ( 22 sec) [ -17681.9135] [ 3513] [depth= 1] . ( 22 sec) [ -17655.9811] [ 3507] [depth= 5] . ( 23 sec) [ -17649.4171] [ 3512] [depth= 1] . ( 23 sec) [ -17640.8930] [ 3510] [depth= 2] . ( 24 sec) [ -17636.9488] [ 3512] [depth= 2] . ( 24 sec) [ -17635.8955] [ 3511] [depth= 5] . ( 25 sec) [ -17619.8659] [ 3503] [depth= 1] . ( 25 sec) [ -17610.8013] [ 3502] [depth= 2] . ( 26 sec) [ -17608.2703] [ 3500] [depth= 1] . ( 26 sec) [ -17606.6048] [ 3504] [depth= 1] . ( 26 sec) [ -17598.5110] [ 3507] [depth= 1] . ( 26 sec) [ -17578.9167] [ 3499] [depth= 1] . ( 26 sec) [ -17576.0890] [ 3496] [depth= 3] . ( 27 sec) [ -17572.9084] [ 3491] [depth= 3] . ( 27 sec) [ -17566.9934] [ 3495] [depth= 2] . ( 27 sec) [ -17566.9834] [ 3497] [depth= 1] . ( 27 sec) [ -17560.0992] [ 3488] [depth= 2] . ( 27 sec) [ -17559.6228] [ 3491] [depth= 1] . ( 28 sec) [ -17557.7544] [ 3488] [depth= 1] . ( 28 sec) [ -17548.0745] [ 3484] [depth= 2] . ( 29 sec) [ -17547.2127] [ 3486] [depth= 5] . ( 29 sec) [ -17539.9949] [ 3486] [depth= 5] . ( 29 sec) [ -17536.3514] [ 3485] [depth= 1] . ( 29 sec) [ -17530.2356] [ 3486] [depth= 1] . ( 30 sec) [ -17527.8300] [ 3487] [depth= 1] . ( 30 sec) [ -17527.1366] [ 3484] [depth= 2] . ( 30 sec) [ -17523.0226] [ 3483] [depth= 1] . ( 30 sec) [ -17522.9084] [ 3482] [depth= 1] . ( 30 sec) [ -17519.1133] [ 3482] [depth= 1] . ( 30 sec) [ -17515.9803] [ 3484] [depth= 1] . ( 31 sec) [ -17509.7777] [ 3483] [depth= 1] . ( 33 sec) [ -17507.5419] [ 3481] [depth= 1] . ( 33 sec) [ -17506.5441] [ 3482] [depth= 1] . ( 33 sec) [ -17505.2220] [ 3482] [depth= 1] . ( 33 sec) [ -17504.2416] [ 3482] [depth= 2] . ( 35 sec) [ -17500.3183] [ 3482] [depth= 1] . ( 36 sec) [ -17319.2989] [Branch lengths ] . ( 36 sec) [ -17312.1511] [Ts/ts ratio ][ 4.544581] . ( 38 sec) [ -17310.3406] [ 3483] [depth= 1] . ( 41 sec) [ -17310.1697] [ 3479] [depth= 2] . ( 41 sec) [ -17306.6508] [ 3480] [depth= 1] . ( 42 sec) [ -17306.6329] [ 3480] [depth= 1] . ( 50 sec) [ -17302.4486] [ 3479] [depth= 1] . ( 58 sec) [ -17302.1220] [ 3479] [depth= 1] . ( 58 sec) [ -17299.3200] [ 3478] [depth= 1] . ( 59 sec) [ -17299.0831] [ 3477] [depth= 1] . ( 59 sec) [ -17298.7243] [ 3480] [depth= 1] . ( 60 sec) [ -17293.0929] [ 3480] [depth= 3] . ( 61 sec) [ -17290.1842] [ 3484] [depth= 1] . ( 64 sec) [ -17288.8334] [ 3483] [depth= 1] . ( 65 sec) [ -17287.3506] [ 3485] [depth= 4] . ( 67 sec) [ -17285.9564] [ 3483] [depth= 1] . ( 74 sec) [ -17243.1458] [Branch lengths ] . ( 74 sec) [ -17242.7536] [Ts/ts ratio ][ 4.697157] . ( 82 sec) [ -17242.6770] [ 3483] [depth= 1] . ( 82 sec) [ -17242.6433] [ 3483] [depth= 1] . ( 88 sec) [ -17242.3368] [ 3480] [depth= 1] . ( 90 sec) [ -17242.1727] [ 3480] [depth= 2] . ( 91 sec) [ -17241.9998] [ 3482] [depth= 1] . ( 92 sec) [ -17241.5610] [ 3479] [depth= 1] . ( 112 sec) [ -17230.8743] [Branch lengths ] . ( 112 sec) [ -17230.7779] [Ts/ts ratio ][ 4.777048] . ( 120 sec) [ -17230.7609] [ 3479] [depth= 1] . ( 120 sec) [ -17230.7494] [ 3479] [depth= 1] . ( 150 sec) [ -17228.4866] [Branch lengths ] . ( 150 sec) [ -17228.4590] [Ts/ts ratio ][ 4.817741] . ( 188 sec) [ -17227.9283] [Branch lengths ] . ( 327 sec) [ -17227.8042] [Branch lengths ] . ( 328 sec) [ -17227.8042] [Topology ] . ( 331 sec) [ -17227.7858] [Topology ] . ( 334 sec) [ -17227.7780] [Topology ] . ( 337 sec) [ -17227.7736] [Topology ] . ( 340 sec) [ -17227.7709] [Topology ] . ( 343 sec) [ -17227.7694] [Topology ] . ( 346 sec) [ -17227.7685] [Topology ] . ( 346 sec) [ -17227.7440] [Ts/ts ratio ][ 4.856160] . ( 346 sec) [ -17227.7440] [Topology ] . ( 349 sec) [ -17227.7417] [Topology ] . ( 352 sec) [ -17227.7405] [Topology ] . ( 356 sec) [ -17227.7399] [Topology ] . ( 356 sec) [ -17227.7396] [Ts/ts ratio ][ 4.863645] . ( 356 sec) [ -17227.7396] [Topology ] . ( 359 sec) [ -17227.7390] [Topology ] . ( 359 sec) [ -17227.7390] [Ts/ts ratio ][ 4.863645] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -17227.739030. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 72 20.553389 0.964000 0.114400 100 45.773706 0.992000 0.113943 67 13.035439 0.861000 0.089889 100 107.271549 1.000000 0.250315 51 3.012172 0.770000 0.015983 95 65.905051 0.996000 0.059578 99 20.837162 0.956000 0.030154 100 58.117660 0.998000 0.051230 99 52.656419 0.995000 0.052131 71 5.219610 0.695000 0.013651 84 19.392003 0.905000 0.026370 100 96.788343 1.000000 0.080062 84 12.152897 0.895000 0.015857 64 6.996269 0.698000 0.009979 42 6.030331 0.644000 0.021716 100 171.469707 1.000000 0.191908 96 23.210931 0.933000 0.037395 75 59.884960 0.995000 0.079710 27 6.567682 0.756000 0.007117 35 15.236602 0.894000 0.015578 100 173.892228 1.000000 0.116767 97 31.448754 0.961000 0.030347 100 70.579076 0.998000 0.054317 87 20.743210 0.959000 0.026414 70 8.373449 0.848000 0.007703 51 1.061947 0.702000 0.001934 95 18.635572 0.902000 0.024771 87 6.592808 0.834000 0.009494 99 54.138265 0.993000 0.044642 26 0.934857 0.385000 0.007821 80 29.382408 0.971000 0.044046 66 3.359725 0.790000 0.010852 98 36.262935 0.986000 0.068740 100 103.827416 1.000000 0.117627 48 6.740877 0.863000 0.028997 79 44.551872 0.993000 0.171327 38 0.370623 0.026000 0.039647 82 8.241779 0.696000 0.066424 84 6.905880 0.868000 0.050745 40 8.110448 0.892000 0.041919 40 20.250838 0.907000 0.020866 92 34.869619 0.989000 0.041508 15 -1.000000 0.000000 0.000001 100 60.508335 0.991000 0.036334 35 14.875851 0.898000 0.016504 50 8.779945 0.887000 0.017430 54 6.218167 0.842000 0.012721 100 101.378090 1.000000 0.062293 28 0.044035 0.000000 0.001651 96 60.614509 0.997000 0.051558 41 14.110905 0.863000 0.007833 100 130.885673 1.000000 0.075206 32 5.971748 0.847000 0.011565 71 36.940570 0.970000 0.042068 55 10.921313 0.886000 0.021117 24 0.045691 0.000000 0.009668 90 20.931699 0.896000 0.013810 51 22.036565 0.950000 0.026249 71 6.977782 0.790000 0.011603 62 5.918537 0.773000 0.003158 33 -1.000000 0.000000 0.000000 68 18.723130 0.887000 0.019043 43 35.657729 0.982000 0.040230 95 41.266873 0.978000 0.032727 86 11.438055 0.897000 0.012739 90 12.167149 0.910000 0.013091 64 3.259404 0.436000 0.006748 21 3.402821 0.491000 0.010705 75 22.285147 0.949000 0.026080 100 94.654816 1.000000 0.068284 55 21.442143 0.969000 0.032737 25 1.709647 0.322000 0.005398 40 14.180855 0.877000 0.012216 27 1.960314 0.803000 0.004687 54 37.090839 0.981000 0.026668 100 68.885475 0.994000 0.039326 43 -1.000000 0.000000 0.000000 100 88.069205 1.000000 0.025448 19 0.739043 0.098000 0.009299 23 3.271755 0.823000 0.012832 24 6.064615 0.801000 0.007868 27 4.922010 0.813000 0.015126 47 24.584329 0.962000 0.054344 100 127.730308 1.000000 0.138959 47 12.316613 0.910000 0.026477 99 42.567372 0.981000 0.053988 97 82.098976 1.000000 0.083805 45 8.119006 0.863000 0.018129 68 19.274356 0.910000 0.022850 9 2.748341 0.696000 0.010912 100 68.909779 1.000000 0.043709 8 10.082400 0.879000 0.015764 7 9.123056 0.850000 0.013352 17 6.968994 0.833000 0.010410 41 8.686787 0.871000 0.018043 6 7.137444 0.833000 0.012229 65 32.996461 0.972000 0.029265 34 2.659481 0.759000 0.007010 6 5.332103 0.647000 0.011657 10 3.442220 0.758000 0.005570 100 64.460846 0.994000 0.032173 6 0.462520 0.119000 0.006260 76 57.521880 0.989000 0.045477 73 9.027945 0.792000 0.016770 57 4.385314 0.790000 0.009324 69 8.624191 0.810000 0.013670 100 48.402402 0.988000 0.028203 . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 12h13m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo