.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2792_166x812_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... . 616 patterns found. (out of a total of 812 sites) . 322 sites without polymorphism (39.66%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 54Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10886.2360] [Ts/ts ratio ][ 3.331247] . ( 2 sec) [ -10878.9311] [ 1899] [depth= 1] . ( 2 sec) [ -10870.3165] [ 1899] [depth= 1] . ( 3 sec) [ -10862.6695] [ 1901] [depth= 1] . ( 3 sec) [ -10837.5811] [ 1898] [depth= 4] . ( 4 sec) [ -10836.5770] [ 1902] [depth= 2] . ( 4 sec) [ -10834.5815] [ 1902] [depth= 2] . ( 5 sec) [ -10830.5932] [ 1897] [depth= 3] . ( 5 sec) [ -10829.0247] [ 1896] [depth= 1] . ( 5 sec) [ -10828.1985] [ 1901] [depth= 1] . ( 6 sec) [ -10826.9957] [ 1899] [depth= 2] . ( 6 sec) [ -10823.1276] [ 1897] [depth= 1] . ( 6 sec) [ -10819.8229] [ 1896] [depth= 1] . ( 7 sec) [ -10819.6902] [ 1897] [depth= 1] . ( 8 sec) [ -10818.6190] [ 1897] [depth= 1] . ( 8 sec) [ -10818.2324] [ 1897] [depth= 1] . ( 9 sec) [ -10816.5725] [ 1898] [depth= 2] . ( 9 sec) [ -10816.5465] [ 1898] [depth= 1] . ( 12 sec) [ -10816.2279] [ 1898] [depth= 1] . ( 12 sec) [ -10815.7381] [ 1898] [depth= 1] . ( 12 sec) [ -10815.6683] [ 1898] [depth= 1] . ( 12 sec) [ -10815.6522] [ 1898] [depth= 2] . ( 14 sec) [ -10805.6552] [ 1897] [depth= 1] . ( 14 sec) [ -10804.2857] [ 1897] [depth= 1] . ( 16 sec) [ -10801.3441] [ 1896] [depth= 1] . ( 18 sec) [ -10801.2554] [ 1896] [depth= 1] . ( 18 sec) [ -10800.9271] [ 1896] [depth= 1] . ( 19 sec) [ -10799.7181] [ 1896] [depth= 2] . ( 19 sec) [ -10799.2821] [ 1897] [depth= 1] . ( 20 sec) [ -10798.6363] [ 1896] [depth= 2] . ( 21 sec) [ -10798.1145] [ 1901] [depth= 1] . ( 21 sec) [ -10791.3241] [ 1903] [depth= 1] . ( 22 sec) [ -10791.2430] [ 1903] [depth= 1] . ( 23 sec) [ -10789.8311] [ 1903] [depth= 2] . ( 23 sec) [ -10789.7820] [ 1903] [depth= 1] . ( 23 sec) [ -10789.1691] [ 1903] [depth= 4] . ( 23 sec) [ -10782.3549] [ 1902] [depth= 2] . ( 24 sec) [ -10782.2721] [ 1902] [depth= 2] . ( 24 sec) [ -10781.9708] [ 1902] [depth= 1] . ( 24 sec) [ -10781.8117] [ 1902] [depth= 1] . ( 27 sec) [ -10781.7468] [ 1902] [depth= 2] . ( 28 sec) [ -10779.4075] [ 1901] [depth= 3] . ( 28 sec) [ -10775.1665] [ 1901] [depth= 1] . ( 29 sec) [ -10775.1502] [ 1901] [depth= 3] . ( 30 sec) [ -10775.1155] [ 1901] [depth= 2] . ( 33 sec) [ -10771.9008] [ 1903] [depth= 1] . ( 33 sec) [ -10770.1798] [ 1901] [depth= 1] . ( 34 sec) [ -10769.4442] [ 1899] [depth= 1] . ( 34 sec) [ -10767.9591] [ 1899] [depth= 1] . ( 34 sec) [ -10766.8532] [ 1899] [depth= 1] . ( 35 sec) [ -10765.4767] [ 1899] [depth= 1] . ( 35 sec) [ -10763.3977] [ 1898] [depth= 1] . ( 38 sec) [ -10762.5480] [ 1898] [depth= 1] . ( 38 sec) [ -10762.1024] [ 1898] [depth= 1] . ( 39 sec) [ -10762.0469] [ 1898] [depth= 1] . ( 39 sec) [ -10761.4491] [ 1899] [depth= 1] . ( 40 sec) [ -10760.6686] [ 1899] [depth= 1] . ( 41 sec) [ -10759.7925] [ 1899] [depth= 1] . ( 41 sec) [ -10759.3191] [ 1899] [depth= 1] . ( 44 sec) [ -10759.2879] [ 1899] [depth= 1] . ( 44 sec) [ -10759.2581] [ 1899] [depth= 1] . ( 45 sec) [ -10759.1744] [ 1899] [depth= 1] . ( 47 sec) [ -10759.1512] [ 1899] [depth= 1] . ( 47 sec) [ -10758.6160] [ 1899] [depth= 1] . ( 47 sec) [ -10758.2820] [ 1899] [depth= 1] . ( 53 sec) [ -10758.2700] [ 1899] [depth= 1] . ( 53 sec) [ -10758.1515] [ 1899] [depth= 1] . ( 53 sec) [ -10758.1148] [ 1899] [depth= 1] . ( 54 sec) [ -10758.1041] [ 1899] [depth= 1] . ( 54 sec) [ -10757.3049] [ 1899] [depth= 1] . ( 54 sec) [ -10756.8591] [ 1899] [depth= 1] . ( 55 sec) [ -10756.7961] [ 1899] [depth= 1] . ( 58 sec) [ -10755.1444] [ 1899] [depth= 1] . ( 62 sec) [ -10754.9828] [ 1899] [depth= 2] . ( 62 sec) [ -10753.6800] [ 1899] [depth= 1] . ( 63 sec) [ -10753.1860] [ 1898] [depth= 2] . ( 63 sec) [ -10753.0304] [ 1898] [depth= 1] . ( 63 sec) [ -10752.9284] [ 1899] [depth= 2] . ( 64 sec) [ -10752.8789] [ 1899] [depth= 2] . ( 64 sec) [ -10752.4030] [ 1898] [depth= 2] . ( 64 sec) [ -10752.1595] [ 1898] [depth= 1] . ( 65 sec) [ -10752.0357] [ 1898] [depth= 2] . ( 65 sec) [ -10751.7180] [ 1898] [depth= 2] . ( 65 sec) [ -10751.3773] [ 1898] [depth= 2] . ( 66 sec) [ -10751.3551] [ 1898] [depth= 2] . ( 66 sec) [ -10751.2228] [ 1898] [depth= 2] . ( 67 sec) [ -10751.1857] [ 1898] [depth= 3] . ( 67 sec) [ -10750.9861] [ 1898] [depth= 4] . ( 69 sec) [ -10748.5313] [ 1900] [depth= 1] . ( 71 sec) [ -10748.1137] [ 1902] [depth= 1] . ( 71 sec) [ -10734.7352] [ 1900] [depth= 1] . ( 73 sec) [ -10733.6667] [ 1902] [depth= 1] . ( 73 sec) [ -10731.3626] [ 1900] [depth= 1] . ( 74 sec) [ -10730.8624] [ 1899] [depth= 1] . ( 74 sec) [ -10725.3658] [ 1897] [depth= 1] . ( 74 sec) [ -10725.1236] [ 1898] [depth= 1] . ( 75 sec) [ -10724.4499] [ 1902] [depth= 1] . ( 76 sec) [ -10723.9265] [ 1903] [depth= 4] . ( 76 sec) [ -10723.8320] [ 1902] [depth= 1] . ( 76 sec) [ -10723.7569] [ 1903] [depth= 1] . ( 77 sec) [ -10722.5272] [ 1902] [depth= 1] . ( 77 sec) [ -10720.3780] [ 1901] [depth= 1] . ( 77 sec) [ -10718.2952] [ 1902] [depth= 1] . ( 77 sec) [ -10716.3378] [ 1901] [depth= 2] . ( 78 sec) [ -10716.2517] [ 1901] [depth= 1] . ( 78 sec) [ -10716.0322] [ 1901] [depth= 1] . ( 78 sec) [ -10715.5752] [ 1901] [depth= 1] . ( 79 sec) [ -10715.5585] [ 1901] [depth= 2] . ( 79 sec) [ -10715.2325] [ 1901] [depth= 1] . ( 80 sec) [ -10715.1202] [ 1901] [depth= 1] . ( 80 sec) [ -10715.0850] [ 1901] [depth= 2] . ( 80 sec) [ -10715.0657] [ 1901] [depth= 1] . ( 82 sec) [ -10713.7139] [ 1901] [depth= 3] . ( 83 sec) [ -10712.6863] [ 1902] [depth= 1] . ( 85 sec) [ -10712.4407] [ 1903] [depth= 1] . ( 86 sec) [ -10711.5002] [ 1902] [depth= 1] . ( 87 sec) [ -10711.1654] [ 1902] [depth= 1] . ( 88 sec) [ -10710.8495] [ 1903] [depth= 4] . ( 88 sec) [ -10710.4575] [ 1904] [depth= 2] . ( 89 sec) [ -10709.9918] [ 1904] [depth= 1] . ( 89 sec) [ -10709.4300] [ 1904] [depth= 2] . ( 89 sec) [ -10708.3547] [ 1905] [depth= 1] . ( 90 sec) [ -10708.3374] [ 1905] [depth= 1] . ( 90 sec) [ -10704.8592] [ 1903] [depth= 1] . ( 92 sec) [ -10703.3326] [ 1905] [depth= 2] . ( 94 sec) [ -10702.9006] [ 1905] [depth= 2] . ( 94 sec) [ -10702.4515] [ 1905] [depth= 3] . ( 95 sec) [ -10702.4411] [ 1905] [depth= 1] . ( 97 sec) [ -10700.7503] [ 1905] [depth= 2] . ( 100 sec) [ -10700.5491] [ 1907] [depth= 1] . ( 100 sec) [ -10700.5299] [ 1907] [depth= 1] . ( 100 sec) [ -10699.2202] [ 1906] [depth= 2] . ( 100 sec) [ -10698.4408] [ 1906] [depth= 2] . ( 103 sec) [ -10697.7602] [ 1906] [depth= 1] . ( 107 sec) [ -10693.2568] [ 1905] [depth= 2] . ( 116 sec) [ -10693.1309] [ 1905] [depth= 2] . ( 116 sec) [ -10692.5178] [ 1905] [depth= 2] . ( 117 sec) [ -10692.4960] [ 1905] [depth= 1] . ( 117 sec) [ -10692.3314] [ 1905] [depth= 3] . ( 117 sec) [ -10692.2553] [ 1905] [depth= 1] . ( 117 sec) [ -10692.2072] [ 1905] [depth= 3] . ( 118 sec) [ -10692.1935] [ 1905] [depth= 1] . ( 118 sec) [ -10692.0247] [ 1905] [depth= 1] . ( 118 sec) [ -10691.9909] [ 1905] [depth= 2] . ( 125 sec) [ -10641.3195] [Branch lengths ] . ( 126 sec) [ -10640.4602] [Ts/ts ratio ][ 3.554436] . ( 126 sec) [ -10640.3070] [ 1902] [depth= 1] . ( 127 sec) [ -10638.5055] [ 1898] [depth= 4] . ( 129 sec) [ -10635.5190] [ 1897] [depth= 1] . ( 131 sec) [ -10633.7687] [ 1896] [depth= 1] . ( 155 sec) [ -10632.6699] [ 1896] [depth= 5] . ( 156 sec) [ -10632.4207] [ 1896] [depth= 3] . ( 156 sec) [ -10632.3989] [ 1896] [depth= 4] . ( 159 sec) [ -10630.1072] [ 1896] [depth= 1] . ( 161 sec) [ -10630.0478] [ 1896] [depth= 2] . ( 165 sec) [ -10630.0115] [ 1895] [depth= 1] . ( 195 sec) [ -10628.8453] [ 1893] [depth= 1] . ( 215 sec) [ -10628.6304] [ 1894] [depth= 3] . ( 221 sec) [ -10628.5334] [ 1893] [depth= 2] . ( 221 sec) [ -10627.6109] [ 1892] [depth= 1] . ( 223 sec) [ -10627.1041] [ 1894] [depth= 1] . ( 223 sec) [ -10625.8919] [ 1894] [depth= 1] . ( 225 sec) [ -10625.7203] [ 1891] [depth= 1] . ( 229 sec) [ -10625.6490] [ 1891] [depth= 1] . ( 229 sec) [ -10624.3456] [ 1886] [depth= 1] . ( 232 sec) [ -10624.3006] [ 1887] [depth= 1] . ( 240 sec) [ -10623.9799] [ 1888] [depth= 1] . ( 241 sec) [ -10623.2803] [ 1887] [depth= 1] . ( 271 sec) [ -10615.4041] [Branch lengths ] . ( 272 sec) [ -10615.3996] [Ts/ts ratio ][ 3.570796] . ( 272 sec) [ -10614.8569] [ 1891] [depth= 1] . ( 274 sec) [ -10614.3209] [ 1887] [depth= 1] . ( 298 sec) [ -10614.2514] [ 1887] [depth= 2] . ( 315 sec) [ -10612.5443] [ 1886] [depth= 1] . ( 421 sec) [ -10610.6327] [Branch lengths ] . ( 422 sec) [ -10610.6301] [Ts/ts ratio ][ 3.583099] . ( 570 sec) [ -10610.4931] [Branch lengths ] . ( 815 sec) [ -10610.4072] [Branch lengths ] . ( 815 sec) [ -10610.4072] [Topology ] . ( 820 sec) [ -10610.0432] [Topology ] . ( 825 sec) [ -10608.5941] [Topology ] . ( 830 sec) [ -10606.5726] [Topology ] . ( 834 sec) [ -10606.1876] [Topology ] . ( 839 sec) [ -10606.1476] [Topology ] . ( 844 sec) [ -10606.1391] [Topology ] . ( 845 sec) [ -10606.1338] [Ts/ts ratio ][ 3.601286] . ( 845 sec) [ -10606.1338] [Topology ] . ( 849 sec) [ -10606.1308] [Topology ] . ( 854 sec) [ -10606.1292] [Topology ] . ( 859 sec) [ -10606.1279] [Topology ] . ( 864 sec) [ -10606.1268] [Topology ] . ( 868 sec) [ -10606.1256] [Topology ] . ( 873 sec) [ -10606.1245] [Topology ] . ( 874 sec) [ -10606.1245] [Ts/ts ratio ][ 3.601286] . ( 874 sec) [ -10606.1245] [Topology ] . ( 878 sec) [ -10606.1234] [Topology ] . ( 883 sec) [ -10606.1226] [Topology ] . ( 884 sec) [ -10606.1226] [Ts/ts ratio ][ 3.601286] . ( 884 sec) [ -10606.1226] [Topology ] . ( 889 sec) [ -10606.1222] [Topology ] . ( 889 sec) [ -10606.1222] [Ts/ts ratio ][ 3.601286] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10606.122168. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 84.189523 1.000000 0.192665 47 0.339370 0.034000 0.044452 99 53.917927 0.998000 0.141299 91 11.219107 0.894000 0.026009 32 6.162257 0.724000 0.018933 6 6.597091 0.826000 0.011202 23 3.148739 0.559000 0.011931 100 94.656300 1.000000 0.077979 50 1.070795 0.071000 0.014734 90 15.941717 0.899000 0.020705 13 4.192830 0.787000 0.009226 26 7.051519 0.860000 0.016748 91 7.493715 0.857000 0.020176 26 6.596165 0.843000 0.015317 49 14.593485 0.943000 0.033830 100 50.932251 0.997000 0.069635 100 176.622298 1.000000 0.164264 99 22.668551 0.964000 0.054060 53 2.774522 0.258000 0.021735 100 45.726904 0.992000 0.029286 66 13.761563 0.938000 0.019142 82 15.214370 0.912000 0.012039 97 16.946649 0.917000 0.005921 26 0.254079 0.584000 0.000798 3 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 55 9.507233 0.822000 0.001673 7 -1.000000 0.000000 0.000000 65 18.638766 0.894000 0.003369 5 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 83 13.380770 0.878000 0.009490 100 130.201592 1.000000 0.046890 84 3.557266 0.754000 0.001684 83 26.343481 0.961000 0.012504 21 -1.000000 0.000000 0.000000 83 10.898619 0.851000 0.004852 49 3.793957 0.704000 0.001676 100 89.256472 1.000000 0.025288 64 5.634181 0.626000 0.005197 76 11.702704 0.869000 0.003918 33 -1.000000 0.000000 0.000000 61 11.798807 0.864000 0.003830 35 2.497391 0.397000 0.001638 79 19.491648 0.874000 0.003291 81 12.441191 0.861000 0.003284 24 -1.000000 0.000000 0.000000 79 5.989272 0.759000 0.009941 100 63.148025 0.992000 0.026720 64 4.365722 0.739000 0.001718 50 7.444963 0.808000 0.001702 15 -1.000000 0.000000 0.000000 17 -1.000000 0.000000 0.000000 67 17.194987 0.961000 0.050847 83 15.941315 0.934000 0.018962 92 25.979696 0.924000 0.008930 88 11.397377 0.861000 0.003678 89 11.217603 0.856000 0.004349 90 32.228410 0.941000 0.007546 25 -1.000000 0.000000 0.000000 97 29.967939 0.940000 0.007228 40 2.304870 0.312000 0.002257 96 29.539378 0.961000 0.010173 98 21.560945 0.924000 0.007419 40 -1.000000 0.000000 0.000000 99 34.244462 0.968000 0.013682 28 5.009604 0.804000 0.008640 100 189.460893 1.000000 0.086571 99 52.444760 0.997000 0.030691 80 7.420142 0.819000 0.003238 9 0.980918 0.322000 0.004471 85 14.747060 0.902000 0.012015 99 39.478939 0.964000 0.020822 86 13.930526 0.913000 0.005777 62 7.279580 0.813000 0.003656 48 7.036793 0.765000 0.001769 59 19.303538 0.930000 0.023127 100 74.576470 1.000000 0.049697 66 14.395411 0.874000 0.013723 81 12.578417 0.859000 0.004792 15 -1.000000 0.000000 0.000000 35 14.553371 0.912000 0.001764 16 -1.000000 0.000000 0.000000 54 7.260832 0.656000 0.006115 30 -1.000000 0.000000 0.000000 69 19.518918 0.915000 0.003572 3 -1.000000 0.000000 0.000000 45 16.733358 0.910000 0.001789 5 -1.000000 0.000000 0.000000 41 11.097069 0.837000 0.001784 73 14.323196 0.853000 0.001793 73 17.941287 0.890000 0.001794 14 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 57 15.681743 0.842000 0.001798 7 -1.000000 0.000000 0.000000 93 29.266320 0.952000 0.005381 95 17.659397 0.916000 0.005414 88 11.277257 0.839000 0.003585 66 3.456154 0.775000 0.004911 60 2.387785 0.748000 0.003152 81 18.586670 0.907000 0.003610 30 -1.000000 0.000000 0.000000 47 4.617442 0.733000 0.001767 87 19.682628 0.910000 0.005421 81 39.447963 0.974000 0.037417 51 8.567889 0.864000 0.011021 37 2.833290 0.438000 0.002130 100 111.362332 0.999000 0.031555 65 5.628822 0.761000 0.003366 8 3.533020 0.799000 0.003225 24 1.342314 0.726000 0.001995 99 33.097134 0.969000 0.013599 17 16.250458 0.930000 0.009793 95 31.445380 0.967000 0.011895 16 1.371538 0.570000 0.004532 100 56.893504 0.996000 0.028082 79 50.673888 0.995000 0.037000 18 0.114240 0.000000 0.003371 10 -1.000000 0.000000 0.000022 75 28.186652 0.948000 0.009295 100 36.867510 0.979000 0.014033 99 24.047887 0.947000 0.009558 23 -1.000000 0.000000 0.000000 27 -1.000000 0.000000 0.000000 60 1.417636 0.718000 0.002496 100 62.088909 0.996000 0.017585 93 26.519137 0.937000 0.012106 85 11.317708 0.844000 0.003837 15 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 83 7.666350 0.843000 0.003972 95 17.157872 0.909000 0.005918 69 24.103735 0.950000 0.008074 44 5.725745 0.827000 0.008023 100 200.652624 1.000000 0.093366 100 46.148982 0.991000 0.025895 78 5.863349 0.763000 0.002040 14 1.517119 0.727000 0.001584 100 84.325436 1.000000 0.019370 54 10.197719 0.853000 0.004840 87 23.331676 0.928000 0.006201 17 5.150459 0.774000 0.002476 100 72.921576 0.999000 0.019094 12 6.258866 0.821000 0.003636 1 -1.000000 0.000000 0.000000 5 6.115760 0.761000 0.002114 100 51.949405 0.989000 0.013017 63 16.060615 0.890000 0.004100 23 9.419650 0.844000 0.002032 9 -1.000000 0.000000 0.000000 21 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 36 9.427746 0.834000 0.002022 54 10.165504 0.851000 0.002051 2 -1.000000 0.000000 0.000000 73 23.067174 0.906000 0.004108 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 68 11.345145 0.806000 0.002017 67 11.713088 0.849000 0.002053 23 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2792_166x812_2006.phy_phyml_tree.txt'... . Time used 23h43m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo