.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_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... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14783.6519] [Ts/ts ratio ][ 3.729321] . ( 1 sec) [ -14782.6530] [ 2562] [depth= 2] . ( 1 sec) [ -14779.3835] [ 2562] [depth= 1] . ( 1 sec) [ -14779.1364] [ 2562] [depth= 1] . ( 2 sec) [ -14774.8786] [ 2562] [depth= 2] . ( 2 sec) [ -14772.7357] [ 2561] [depth= 2] . ( 2 sec) [ -14772.4123] [ 2561] [depth= 1] . ( 2 sec) [ -14771.9058] [ 2562] [depth= 1] . ( 2 sec) [ -14771.5033] [ 2561] [depth= 1] . ( 3 sec) [ -14762.0469] [ 2559] [depth= 2] . ( 4 sec) [ -14761.8319] [ 2563] [depth= 1] . ( 4 sec) [ -14755.3823] [ 2562] [depth= 1] . ( 4 sec) [ -14754.3037] [ 2563] [depth= 1] . ( 4 sec) [ -14749.3267] [ 2561] [depth= 1] . ( 5 sec) [ -14748.5059] [ 2562] [depth= 1] . ( 5 sec) [ -14744.9425] [ 2561] [depth= 1] . ( 5 sec) [ -14743.2479] [ 2567] [depth= 1] . ( 5 sec) [ -14736.9721] [ 2561] [depth= 1] . ( 5 sec) [ -14727.9877] [ 2565] [depth= 5] . ( 6 sec) [ -14726.2119] [ 2565] [depth= 1] . ( 6 sec) [ -14722.6641] [ 2565] [depth= 1] . ( 6 sec) [ -14706.4335] [ 2571] [depth= 6] . ( 6 sec) [ -14700.6545] [ 2560] [depth= 6] . ( 6 sec) [ -14696.9142] [ 2561] [depth= 1] . ( 6 sec) [ -14696.8670] [ 2560] [depth= 1] . ( 6 sec) [ -14691.6716] [ 2561] [depth= 1] . ( 6 sec) [ -14688.2041] [ 2560] [depth= 1] . ( 7 sec) [ -14683.9648] [ 2557] [depth= 1] . ( 7 sec) [ -14680.0475] [ 2561] [depth= 2] . ( 7 sec) [ -14672.9040] [ 2558] [depth= 2] . ( 7 sec) [ -14669.0919] [ 2561] [depth= 1] . ( 7 sec) [ -14666.9350] [ 2558] [depth= 1] . ( 7 sec) [ -14663.6126] [ 2562] [depth= 1] . ( 8 sec) [ -14658.8323] [ 2558] [depth= 2] . ( 8 sec) [ -14638.0707] [ 2555] [depth= 2] . ( 8 sec) [ -14636.2421] [ 2551] [depth= 1] . ( 8 sec) [ -14633.2272] [ 2551] [depth= 1] . ( 8 sec) [ -14632.8654] [ 2559] [depth= 1] . ( 8 sec) [ -14632.5358] [ 2559] [depth= 1] . ( 8 sec) [ -14631.7412] [ 2563] [depth= 1] . ( 8 sec) [ -14631.1739] [ 2559] [depth= 1] . ( 8 sec) [ -14624.5602] [ 2560] [depth= 1] . ( 9 sec) [ -14621.8683] [ 2564] [depth= 1] . ( 9 sec) [ -14619.6013] [ 2566] [depth= 3] . ( 9 sec) [ -14615.9021] [ 2560] [depth= 3] . ( 9 sec) [ -14605.4364] [ 2562] [depth= 3] . ( 9 sec) [ -14604.6731] [ 2560] [depth= 1] . ( 10 sec) [ -14601.3418] [ 2558] [depth= 1] . ( 10 sec) [ -14601.0898] [ 2559] [depth= 1] . ( 10 sec) [ -14594.8842] [ 2558] [depth= 1] . ( 10 sec) [ -14586.7106] [ 2554] [depth= 2] . ( 10 sec) [ -14586.1733] [ 2553] [depth= 1] . ( 11 sec) [ -14586.0221] [ 2554] [depth= 1] . ( 11 sec) [ -14584.8769] [ 2556] [depth= 1] . ( 11 sec) [ -14583.7927] [ 2556] [depth= 8] . ( 11 sec) [ -14583.0967] [ 2556] [depth= 1] . ( 12 sec) [ -14581.1637] [ 2553] [depth= 2] . ( 12 sec) [ -14581.0291] [ 2553] [depth= 1] . ( 13 sec) [ -14580.9682] [ 2553] [depth= 1] . ( 13 sec) [ -14580.7889] [ 2554] [depth= 1] . ( 14 sec) [ -14578.8522] [ 2555] [depth= 1] . ( 14 sec) [ -14575.9414] [ 2554] [depth= 1] . ( 14 sec) [ -14573.8295] [ 2553] [depth= 1] . ( 14 sec) [ -14572.1047] [ 2555] [depth= 3] . ( 14 sec) [ -14571.4177] [ 2554] [depth= 1] . ( 15 sec) [ -14567.0500] [ 2552] [depth= 2] . ( 16 sec) [ -14566.0189] [ 2553] [depth= 1] . ( 16 sec) [ -14565.6413] [ 2555] [depth= 1] . ( 16 sec) [ -14565.4656] [ 2555] [depth= 1] . ( 17 sec) [ -14519.3319] [Branch lengths ] . ( 17 sec) [ -14519.1928] [Ts/ts ratio ][ 3.812828] . ( 18 sec) [ -14509.5088] [ 2548] [depth= 1] . ( 20 sec) [ -14508.8166] [ 2545] [depth= 1] . ( 21 sec) [ -14508.1513] [ 2544] [depth= 1] . ( 23 sec) [ -14508.0578] [ 2545] [depth= 1] . ( 24 sec) [ -14508.0071] [ 2545] [depth= 1] . ( 25 sec) [ -14506.9236] [ 2546] [depth= 1] . ( 26 sec) [ -14506.4207] [ 2546] [depth= 1] . ( 27 sec) [ -14506.2459] [ 2547] [depth= 1] . ( 28 sec) [ -14505.7976] [ 2547] [depth= 1] . ( 31 sec) [ -14505.3451] [ 2553] [depth= 3] . ( 39 sec) [ -14497.9896] [Branch lengths ] . ( 39 sec) [ -14497.9213] [Ts/ts ratio ][ 3.872677] . ( 52 sec) [ -14497.9098] [ 2553] [depth= 1] . ( 64 sec) [ -14497.0932] [Branch lengths ] . ( 64 sec) [ -14497.0920] [Ts/ts ratio ][ 3.880826] . ( 135 sec) [ -14496.9561] [Branch lengths ] . ( 135 sec) [ -14496.9561] [Topology ] . ( 137 sec) [ -14496.4952] [Topology ] . ( 139 sec) [ -14496.0636] [Topology ] . ( 140 sec) [ -14496.0322] [Topology ] . ( 142 sec) [ -14496.0281] [Topology ] . ( 144 sec) [ -14496.0271] [Topology ] . ( 145 sec) [ -14496.0267] [Topology ] . ( 146 sec) [ -14496.0260] [Ts/ts ratio ][ 3.875018] . ( 146 sec) [ -14496.0260] [Topology ] . ( 147 sec) [ -14496.0258] [Topology ] . ( 147 sec) [ -14496.0258] [Ts/ts ratio ][ 3.875018] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14496.025825. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 135.267470 0.999000 0.024846 78 19.514092 0.934000 0.006088 82 15.752023 0.913000 0.006690 100 73.919694 0.997000 0.018061 53 9.982844 0.856000 0.002517 44 1.355740 0.681000 0.001733 98 35.999933 0.979000 0.010501 100 115.683456 1.000000 0.020767 53 11.413027 0.838000 0.003997 7 -1.000000 0.000000 0.000000 25 2.086241 0.448000 0.002433 41 1.838477 0.360000 0.003190 100 126.256977 1.000000 0.027995 99 31.796335 0.967000 0.008854 100 48.981262 0.990000 0.013309 71 4.180558 0.410000 0.008903 91 22.739153 0.951000 0.008654 71 6.622705 0.810000 0.004463 48 8.361063 0.765000 0.004113 61 4.467425 0.814000 0.004514 86 15.122302 0.898000 0.006159 35 2.655336 0.577000 0.002756 22 4.319038 0.783000 0.003532 16 6.463086 0.593000 0.004321 23 0.668132 0.675000 0.001345 54 14.318245 0.918000 0.010166 45 20.970035 0.938000 0.007999 19 3.000350 0.690000 0.002974 1 19.210271 0.921000 0.004644 1 38.334765 0.970000 0.007376 9 12.925015 0.897000 0.004322 18 5.323946 0.724000 0.008151 3 -1.000000 0.000000 0.000000 23 22.272285 0.957000 0.008153 4 -1.000000 0.000000 0.000000 23 1.830852 0.166000 0.005601 1 2.974500 0.751000 0.001181 27 37.568681 0.966000 0.007690 19 7.155712 0.843000 0.004680 95 35.268623 0.989000 0.019972 96 24.593490 0.966000 0.019924 26 1.375221 0.706000 0.003915 10 9.825165 0.756000 0.005952 21 8.468774 0.834000 0.003967 16 1.539400 0.394000 0.002937 22 9.823654 0.895000 0.012157 4 31.968754 0.980000 0.009255 34 18.873081 0.956000 0.016574 0 2.884747 0.523000 0.002689 1 6.756062 0.854000 0.005634 15 19.758103 0.964000 0.017274 51 8.874641 0.871000 0.011534 70 9.670888 0.820000 0.014900 25 1.056017 0.347000 0.005624 4 1.066848 0.262000 0.002577 27 11.134429 0.880000 0.010083 57 14.035738 0.938000 0.015020 . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 4h22m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo