.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2932_68x1712_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 . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1264 patterns found. (out of a total of 1712 sites) . 601 sites without polymorphism (35.11%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 45Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15461.6595] [Ts/ts ratio ][ 2.602816] . ( 2 sec) [ -15459.2896] [ 3263] [depth= 3] . ( 2 sec) [ -15450.2087] [ 3256] [depth= 1] . ( 2 sec) [ -15421.9107] [ 3281] [depth= 1] . ( 4 sec) [ -15421.3835] [ 3281] [depth= 1] . ( 4 sec) [ -15416.2044] [ 3282] [depth= 1] . ( 5 sec) [ -15411.6603] [ 3284] [depth= 3] . ( 5 sec) [ -15411.1612] [ 3281] [depth= 1] . ( 6 sec) [ -15410.8165] [ 3282] [depth= 1] . ( 6 sec) [ -15400.6861] [ 3281] [depth= 1] . ( 6 sec) [ -15378.1211] [ 3276] [depth= 1] . ( 6 sec) [ -15375.8137] [ 3277] [depth= 1] . ( 7 sec) [ -15375.6010] [ 3277] [depth= 1] . ( 7 sec) [ -15368.8359] [ 3277] [depth= 1] . ( 8 sec) [ -15360.7694] [ 3277] [depth= 1] . ( 8 sec) [ -15357.8139] [ 3278] [depth= 2] . ( 8 sec) [ -15344.2629] [ 3264] [depth= 1] . ( 8 sec) [ -15341.9723] [ 3264] [depth= 1] . ( 9 sec) [ -15294.3610] [ 3261] [depth= 2] . ( 9 sec) [ -15290.4961] [ 3261] [depth= 1] . ( 9 sec) [ -15286.2089] [ 3255] [depth= 1] . ( 9 sec) [ -15283.8887] [ 3244] [depth= 1] . ( 10 sec) [ -15266.9088] [ 3237] [depth= 1] . ( 10 sec) [ -15265.2994] [ 3237] [depth= 1] . ( 11 sec) [ -15263.2811] [ 3234] [depth= 1] . ( 11 sec) [ -15256.7971] [ 3233] [depth= 1] . ( 11 sec) [ -15242.7025] [ 3237] [depth= 1] . ( 11 sec) [ -15239.4114] [ 3231] [depth= 2] . ( 12 sec) [ -15238.6904] [ 3231] [depth= 1] . ( 12 sec) [ -15237.6356] [ 3231] [depth= 1] . ( 12 sec) [ -15237.6181] [ 3231] [depth= 5] . ( 13 sec) [ -15235.3019] [ 3231] [depth= 7] . ( 14 sec) [ -15230.5291] [ 3230] [depth= 5] . ( 14 sec) [ -15228.9698] [ 3230] [depth= 3] . ( 14 sec) [ -15219.2201] [ 3230] [depth= 1] . ( 14 sec) [ -15212.3569] [ 3229] [depth= 1] . ( 14 sec) [ -15209.9340] [ 3230] [depth= 3] . ( 15 sec) [ -15209.5816] [ 3230] [depth= 2] . ( 16 sec) [ -15207.1521] [ 3230] [depth= 2] . ( 17 sec) [ -15205.1064] [ 3231] [depth= 2] . ( 17 sec) [ -15203.8825] [ 3231] [depth= 1] . ( 17 sec) [ -15200.0787] [ 3231] [depth= 2] . ( 17 sec) [ -15199.1800] [ 3231] [depth= 5] . ( 18 sec) [ -15198.7381] [ 3231] [depth= 4] . ( 18 sec) [ -15198.1813] [ 3231] [depth= 1] . ( 19 sec) [ -15192.6821] [ 3234] [depth= 1] . ( 19 sec) [ -15191.8100] [ 3232] [depth= 6] . ( 19 sec) [ -15191.6588] [ 3233] [depth= 1] . ( 19 sec) [ -15188.6019] [ 3238] [depth= 2] . ( 20 sec) [ -15186.3452] [ 3236] [depth= 1] . ( 20 sec) [ -15182.2214] [ 3251] [depth= 1] . ( 23 sec) [ -15180.3074] [ 3251] [depth= 1] . ( 23 sec) [ -15178.4416] [ 3259] [depth= 2] . ( 23 sec) [ -15177.0077] [ 3261] [depth= 1] . ( 24 sec) [ -15176.1010] [ 3261] [depth= 3] . ( 24 sec) [ -15174.1574] [ 3258] [depth= 1] . ( 24 sec) [ -15171.1159] [ 3255] [depth= 2] . ( 28 sec) [ -15169.1535] [ 3255] [depth= 1] . ( 29 sec) [ -15169.0244] [ 3255] [depth= 1] . ( 32 sec) [ -15168.4850] [ 3254] [depth= 2] . ( 33 sec) [ -15163.6661] [ 3253] [depth= 4] . ( 33 sec) [ -15163.5834] [ 3253] [depth= 2] . ( 35 sec) [ -15163.5708] [ 3253] [depth= 3] . ( 35 sec) [ -15163.3163] [ 3253] [depth= 1] . ( 36 sec) [ -15163.0360] [ 3253] [depth= 1] . ( 37 sec) [ -15162.9283] [ 3253] [depth= 2] . ( 38 sec) [ -15162.6939] [ 3253] [depth= 1] . ( 38 sec) [ -15162.6426] [ 3253] [depth= 2] . ( 38 sec) [ -15162.4243] [ 3253] [depth= 2] . ( 40 sec) [ -15162.3055] [ 3253] [depth= 1] . ( 41 sec) [ -15162.2676] [ 3253] [depth= 3] . ( 49 sec) [ -15058.5080] [Branch lengths ] . ( 49 sec) [ -15050.3274] [Ts/ts ratio ][ 3.108007] . ( 53 sec) [ -15046.7057] [ 3218] [depth= 1] . ( 59 sec) [ -15045.9777] [ 3219] [depth= 3] . ( 60 sec) [ -15045.8697] [ 3219] [depth= 3] . ( 71 sec) [ -15045.7787] [ 3219] [depth= 3] . ( 73 sec) [ -15045.6705] [ 3222] [depth= 2] . ( 75 sec) [ -15045.1395] [ 3220] [depth= 1] . ( 75 sec) [ -15043.8473] [ 3213] [depth= 1] . ( 76 sec) [ -15041.3132] [ 3197] [depth= 3] . ( 76 sec) [ -15037.9950] [ 3199] [depth= 1] . ( 77 sec) [ -15034.8493] [ 3199] [depth= 1] . ( 77 sec) [ -15034.8049] [ 3199] [depth= 1] . ( 78 sec) [ -15034.3865] [ 3199] [depth= 1] . ( 78 sec) [ -15034.2071] [ 3199] [depth= 1] . ( 79 sec) [ -15033.4856] [ 3198] [depth= 1] . ( 79 sec) [ -15033.1864] [ 3199] [depth= 1] . ( 81 sec) [ -15032.9229] [ 3199] [depth= 1] . ( 81 sec) [ -15032.8193] [ 3199] [depth= 1] . ( 88 sec) [ -15032.7136] [ 3199] [depth= 1] . ( 110 sec) [ -15010.6195] [Branch lengths ] . ( 111 sec) [ -15010.2622] [Ts/ts ratio ][ 3.226266] . ( 127 sec) [ -15010.0996] [ 3191] [depth= 5] . ( 131 sec) [ -15010.0413] [ 3191] [depth= 5] . ( 136 sec) [ -15009.6957] [ 3189] [depth= 1] . ( 173 sec) [ -15004.9587] [Branch lengths ] . ( 173 sec) [ -15004.9579] [Ts/ts ratio ][ 3.232334] . ( 235 sec) [ -15004.4019] [Branch lengths ] . ( 254 sec) [ -15003.4337] [ 3199] [depth= 1] . ( 259 sec) [ -15002.4614] [ 3198] [depth= 2] . ( 266 sec) [ -15002.3849] [ 3198] [depth= 1] . ( 288 sec) [ -15001.7019] [ 3207] [depth= 2] . ( 290 sec) [ -15001.4581] [ 3207] [depth= 2] . ( 296 sec) [ -15001.4016] [ 3207] [depth= 5] . ( 299 sec) [ -15001.3319] [ 3207] [depth= 3] . ( 370 sec) [ -15000.0219] [Branch lengths ] . ( 370 sec) [ -15000.0109] [Ts/ts ratio ][ 3.253758] . ( 510 sec) [ -14999.7912] [Branch lengths ] . ( 510 sec) [ -14999.7912] [Topology ] . ( 513 sec) [ -14999.4156] [Topology ] . ( 516 sec) [ -14997.5744] [Topology ] . ( 520 sec) [ -14993.7842] [Topology ] . ( 523 sec) [ -14993.0659] [Topology ] . ( 527 sec) [ -14992.9253] [Topology ] . ( 530 sec) [ -14992.8664] [Topology ] . ( 531 sec) [ -14992.8628] [Ts/ts ratio ][ 3.242181] . ( 531 sec) [ -14992.8628] [Topology ] . ( 534 sec) [ -14992.8284] [Topology ] . ( 538 sec) [ -14992.8079] [Topology ] . ( 541 sec) [ -14992.7979] [Topology ] . ( 544 sec) [ -14992.8082] [Topology ] . Moving backward . ( 545 sec) [ -14992.7901] [Topology ] . ( 548 sec) [ -14992.7871] [Topology ] . ( 552 sec) [ -14992.8025] [Topology ] . ( 552 sec) [ -14992.8024] [Ts/ts ratio ][ 3.238939] . ( 552 sec) [ -14992.8024] [Topology ] . ( 556 sec) [ -14992.8441] [Topology ] . Moving backward . ( 556 sec) [ -14992.7822] [Topology ] . ( 560 sec) [ -14992.8030] [Topology ] . Moving backward . ( 560 sec) [ -14992.7776] [Topology ] . ( 563 sec) [ -14992.7803] [Topology ] . Moving backward . ( 564 sec) [ -14992.7755] [Topology ] . ( 567 sec) [ -14992.7756] [Topology ] . ( 568 sec) [ -14992.7756] [Ts/ts ratio ][ 3.238939] . ( 568 sec) [ -14992.7756] [Topology ] . ( 571 sec) [ -14992.7789] [Topology ] . Moving backward . ( 571 sec) [ -14992.7740] [Topology ] . ( 575 sec) [ -14992.7745] [Topology ] . ( 575 sec) [ -14992.7745] [Ts/ts ratio ][ 3.238939] . ( 575 sec) [ -14992.7745] [Topology ] . ( 579 sec) [ -14992.7780] [Topology ] . Moving backward . ( 579 sec) [ -14992.7732] [Topology ] . ( 583 sec) [ -14992.7740] [Topology ] . ( 583 sec) [ -14992.7740] [Ts/ts ratio ][ 3.238939] . Checking for NNIs, optimizing five branches... . ( 615 sec) [ -14992.6993] [Topology ] . Checking for NNIs, optimizing five branches... . ( 646 sec) [ -14992.6942] [Topology ] . Checking for NNIs, optimizing five branches... . ( 679 sec) [ -14992.6918] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14992.691752. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 73.666894 1.000000 0.433619 77 13.370873 0.592000 0.424720 90 51.469677 0.996000 0.179202 78 7.972854 0.869000 0.033183 100 110.501085 1.000000 0.683117 65 9.700337 0.942000 0.123291 99 54.476705 0.996000 0.170383 55 9.468863 0.857000 0.088298 53 1.111975 0.226000 0.049611 100 121.698766 0.999000 0.210663 76 0.158798 0.000000 0.002952 92 27.852011 0.979000 0.105892 100 201.973968 1.000000 0.291508 46 1.122498 0.196000 0.029778 100 52.552935 0.999000 0.101280 83 19.727349 0.933000 0.044362 100 28.473587 0.973000 0.032550 76 2.818091 0.757000 0.005636 19 -1.000000 0.000000 0.000000 100 44.210656 0.967000 0.017828 65 6.305496 0.822000 0.012951 66 4.167237 0.815000 0.076578 100 272.291029 1.000000 0.600461 1 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 20 11.008595 0.855000 0.004463 17 -1.000000 0.000000 0.000000 89 57.449732 0.996000 0.013563 73 11.749640 0.803000 0.002184 31 3.398271 0.418000 0.002313 60 16.428826 0.932000 0.028435 93 21.211105 0.941000 0.033599 100 51.751413 0.999000 0.274361 82 7.173215 0.889000 0.047258 100 105.200687 1.000000 0.058413 43 20.972679 0.961000 0.026724 99 45.976366 0.990000 0.026775 80 18.360835 0.908000 0.009173 83 20.110159 0.942000 0.008042 6 -1.000000 0.000000 0.000000 45 28.665487 0.925000 0.003094 61 13.516533 0.892000 0.002703 8 -1.000000 0.000000 0.000000 28 9.622936 0.824000 0.001033 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000069 2 -1.000000 0.000000 0.000491 7 -1.000000 0.000000 0.000140 9 -1.000000 0.000000 0.000327 7 -1.000000 0.000000 0.000000 20 0.149828 0.000000 0.004110 100 67.463654 0.999000 0.034030 50 0.161797 0.000000 0.001058 75 8.833949 0.818000 0.004417 64 0.884892 0.662000 0.016526 57 5.226701 0.827000 0.061651 82 17.691786 0.931000 0.061885 99 39.775528 0.985000 0.069259 90 19.574091 0.956000 0.040301 80 7.559523 0.860000 0.073208 51 1.206662 0.242000 0.038885 . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 15h47m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo