.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2933_99x1634_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 578 patterns found. (out of a total of 1634 sites) . 1151 sites without polymorphism (70.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7940.5492] [Ts/ts ratio ][ 3.202333] . ( 1 sec) [ -7930.0518] [ 1132] [depth= 1] . ( 1 sec) [ -7900.9358] [ 1127] [depth= 1] . ( 1 sec) [ -7895.4675] [ 1124] [depth= 3] . ( 1 sec) [ -7885.7001] [ 1122] [depth= 2] . ( 1 sec) [ -7885.5422] [ 1122] [depth= 1] . ( 2 sec) [ -7885.3819] [ 1127] [depth= 1] . ( 3 sec) [ -7885.0940] [ 1127] [depth= 1] . ( 3 sec) [ -7884.8390] [ 1127] [depth= 1] . ( 3 sec) [ -7884.7979] [ 1127] [depth= 1] . ( 3 sec) [ -7884.7850] [ 1127] [depth= 2] . ( 6 sec) [ -7876.4068] [ 1126] [depth= 1] . ( 6 sec) [ -7872.6900] [ 1126] [depth= 1] . ( 7 sec) [ -7871.0054] [ 1126] [depth= 1] . ( 7 sec) [ -7870.7153] [ 1126] [depth= 1] . ( 8 sec) [ -7851.2745] [ 1127] [depth= 2] . ( 8 sec) [ -7850.5432] [ 1126] [depth= 2] . ( 8 sec) [ -7850.0937] [ 1126] [depth= 1] . ( 8 sec) [ -7847.7544] [ 1128] [depth= 1] . ( 9 sec) [ -7847.7124] [ 1128] [depth= 2] . ( 9 sec) [ -7845.2987] [ 1127] [depth= 2] . ( 10 sec) [ -7841.7454] [ 1127] [depth= 2] . ( 10 sec) [ -7839.5998] [ 1124] [depth= 1] . ( 12 sec) [ -7838.6469] [ 1122] [depth= 1] . ( 12 sec) [ -7837.6475] [ 1122] [depth= 1] . ( 13 sec) [ -7807.0970] [ 1116] [depth= 8] . ( 13 sec) [ -7803.9958] [ 1115] [depth= 1] . ( 14 sec) [ -7803.7016] [ 1118] [depth= 2] . ( 14 sec) [ -7800.4486] [ 1116] [depth= 1] . ( 15 sec) [ -7799.2627] [ 1115] [depth= 1] . ( 15 sec) [ -7797.4173] [ 1114] [depth= 1] . ( 15 sec) [ -7797.3405] [ 1116] [depth= 1] . ( 15 sec) [ -7795.0388] [ 1108] [depth= 1] . ( 15 sec) [ -7795.0196] [ 1108] [depth= 1] . ( 16 sec) [ -7794.3233] [ 1106] [depth= 1] . ( 16 sec) [ -7793.5910] [ 1108] [depth= 1] . ( 17 sec) [ -7790.3439] [ 1111] [depth= 1] . ( 17 sec) [ -7790.1825] [ 1116] [depth= 2] . ( 17 sec) [ -7790.0237] [ 1116] [depth= 1] . ( 17 sec) [ -7789.8821] [ 1116] [depth= 1] . ( 17 sec) [ -7789.4124] [ 1116] [depth= 1] . ( 18 sec) [ -7782.9891] [ 1115] [depth= 5] . ( 18 sec) [ -7782.5518] [ 1115] [depth= 3] . ( 18 sec) [ -7782.4681] [ 1115] [depth= 2] . ( 18 sec) [ -7782.3736] [ 1115] [depth= 1] . ( 18 sec) [ -7781.7836] [ 1115] [depth= 3] . ( 21 sec) [ -7777.0320] [ 1114] [depth= 2] . ( 22 sec) [ -7776.9566] [ 1112] [depth= 6] . ( 22 sec) [ -7770.7154] [ 1110] [depth= 4] . ( 22 sec) [ -7770.5479] [ 1110] [depth= 1] . ( 23 sec) [ -7770.2703] [ 1110] [depth= 1] . ( 23 sec) [ -7770.2280] [ 1110] [depth= 3] . ( 23 sec) [ -7765.2448] [ 1109] [depth= 1] . ( 23 sec) [ -7762.6461] [ 1110] [depth= 5] . ( 23 sec) [ -7761.8805] [ 1110] [depth= 1] . ( 23 sec) [ -7757.7349] [ 1109] [depth= 5] . ( 24 sec) [ -7757.3951] [ 1109] [depth= 1] . ( 24 sec) [ -7756.3997] [ 1109] [depth= 3] . ( 24 sec) [ -7755.3507] [ 1109] [depth= 3] . ( 24 sec) [ -7752.5504] [ 1109] [depth= 4] . ( 24 sec) [ -7752.3814] [ 1109] [depth= 1] . ( 24 sec) [ -7751.7259] [ 1109] [depth= 4] . ( 25 sec) [ -7750.6351] [ 1109] [depth= 1] . ( 25 sec) [ -7750.6042] [ 1109] [depth= 2] . ( 25 sec) [ -7749.9088] [ 1109] [depth= 2] . ( 27 sec) [ -7749.6415] [ 1109] [depth= 2] . ( 27 sec) [ -7744.8916] [ 1109] [depth= 1] . ( 27 sec) [ -7739.9541] [ 1107] [depth= 2] . ( 27 sec) [ -7739.9012] [ 1107] [depth= 3] . ( 30 sec) [ -7739.3366] [ 1107] [depth= 1] . ( 32 sec) [ -7738.4894] [ 1107] [depth= 1] . ( 34 sec) [ -7737.8801] [ 1108] [depth= 1] . ( 35 sec) [ -7737.6977] [ 1109] [depth= 1] . ( 36 sec) [ -7737.6118] [ 1111] [depth= 1] . ( 36 sec) [ -7734.6208] [ 1108] [depth= 1] . ( 36 sec) [ -7723.0809] [ 1104] [depth= 5] . ( 39 sec) [ -7720.9315] [ 1104] [depth= 1] . ( 39 sec) [ -7716.7677] [ 1103] [depth= 3] . ( 41 sec) [ -7716.6560] [ 1104] [depth= 1] . ( 41 sec) [ -7716.4297] [ 1104] [depth= 4] . ( 41 sec) [ -7713.4148] [ 1104] [depth= 5] . ( 42 sec) [ -7712.7091] [ 1103] [depth= 2] . ( 43 sec) [ -7707.5255] [ 1102] [depth= 2] . ( 45 sec) [ -7707.2576] [ 1102] [depth= 1] . ( 45 sec) [ -7707.2466] [ 1102] [depth= 1] . ( 45 sec) [ -7707.0588] [ 1102] [depth= 4] . ( 45 sec) [ -7706.7363] [ 1102] [depth= 2] . ( 46 sec) [ -7706.7108] [ 1102] [depth= 2] . ( 46 sec) [ -7706.5214] [ 1102] [depth= 3] . ( 46 sec) [ -7706.4482] [ 1102] [depth= 1] . ( 46 sec) [ -7706.4208] [ 1102] [depth= 1] . ( 47 sec) [ -7705.9652] [ 1102] [depth= 1] . ( 48 sec) [ -7705.8729] [ 1102] [depth= 1] . ( 50 sec) [ -7705.6466] [ 1102] [depth= 2] . ( 52 sec) [ -7703.9811] [ 1102] [depth= 1] . ( 53 sec) [ -7703.9539] [ 1102] [depth= 1] . ( 53 sec) [ -7703.9118] [ 1102] [depth= 1] . ( 53 sec) [ -7703.3662] [ 1102] [depth= 2] . ( 54 sec) [ -7703.2576] [ 1102] [depth= 1] . ( 55 sec) [ -7703.1129] [ 1102] [depth= 1] . ( 56 sec) [ -7703.0624] [ 1102] [depth= 2] . ( 56 sec) [ -7703.0425] [ 1102] [depth= 3] . ( 59 sec) [ -7703.0180] [ 1102] [depth= 4] . ( 59 sec) [ -7702.9907] [ 1102] [depth= 1] . ( 60 sec) [ -7702.9532] [ 1102] [depth= 1] . ( 72 sec) [ -7666.9237] [Branch lengths ] . ( 72 sec) [ -7665.1974] [Ts/ts ratio ][ 3.631074] . ( 73 sec) [ -7664.5361] [ 1104] [depth= 4] . ( 74 sec) [ -7664.5259] [ 1104] [depth= 1] . ( 84 sec) [ -7664.4521] [ 1107] [depth= 1] . ( 86 sec) [ -7664.4356] [ 1109] [depth= 1] . ( 89 sec) [ -7664.4222] [ 1109] [depth= 1] . ( 91 sec) [ -7656.6572] [ 1102] [depth= 4] . ( 93 sec) [ -7651.4492] [ 1100] [depth= 4] . ( 95 sec) [ -7651.3989] [ 1100] [depth= 1] . ( 118 sec) [ -7651.3201] [ 1100] [depth= 1] . ( 127 sec) [ -7651.2386] [ 1100] [depth= 1] . ( 128 sec) [ -7649.4547] [ 1100] [depth= 4] . ( 131 sec) [ -7649.0698] [ 1100] [depth= 1] . ( 131 sec) [ -7648.8565] [ 1100] [depth= 3] . ( 134 sec) [ -7648.7674] [ 1100] [depth= 2] . ( 135 sec) [ -7648.5795] [ 1100] [depth= 3] . ( 137 sec) [ -7648.5229] [ 1100] [depth= 3] . ( 138 sec) [ -7648.4991] [ 1100] [depth= 3] . ( 138 sec) [ -7648.4853] [ 1100] [depth= 1] . ( 145 sec) [ -7648.4748] [ 1100] [depth= 1] . ( 145 sec) [ -7648.4517] [ 1100] [depth= 1] . ( 158 sec) [ -7648.4407] [ 1100] [depth= 12] . ( 180 sec) [ -7641.4259] [Branch lengths ] . ( 180 sec) [ -7641.4184] [Ts/ts ratio ][ 3.661526] . ( 181 sec) [ -7641.2348] [ 1098] [depth= 3] . ( 189 sec) [ -7641.1989] [ 1099] [depth= 1] . ( 250 sec) [ -7641.1798] [ 1099] [depth= 4] . ( 250 sec) [ -7640.9607] [ 1099] [depth= 1] . ( 257 sec) [ -7638.1962] [ 1098] [depth= 1] . ( 261 sec) [ -7638.1493] [ 1098] [depth= 1] . ( 267 sec) [ -7638.1370] [ 1098] [depth= 1] . ( 270 sec) [ -7638.0732] [ 1098] [depth= 3] . ( 294 sec) [ -7636.7305] [Branch lengths ] . ( 294 sec) [ -7636.7298] [Ts/ts ratio ][ 3.650323] . ( 295 sec) [ -7636.6272] [ 1098] [depth= 2] . ( 387 sec) [ -7635.5789] [ 1099] [depth= 10] . ( 388 sec) [ -7635.4625] [ 1099] [depth= 1] . ( 391 sec) [ -7635.0363] [ 1099] [depth= 1] . ( 391 sec) [ -7635.0238] [ 1099] [depth= 17] . ( 408 sec) [ -7634.6269] [Branch lengths ] . ( 408 sec) [ -7634.6199] [Ts/ts ratio ][ 3.679954] . ( 478 sec) [ -7630.3539] [ 1098] [depth= 9] . ( 479 sec) [ -7630.3027] [ 1098] [depth= 1] . ( 479 sec) [ -7630.1147] [ 1098] [depth= 4] . ( 479 sec) [ -7630.1010] [ 1098] [depth= 1] . ( 480 sec) [ -7630.0260] [ 1098] [depth= 3] . ( 480 sec) [ -7629.9547] [ 1098] [depth= 2] . ( 481 sec) [ -7629.8832] [ 1098] [depth= 2] . ( 487 sec) [ -7629.8571] [ 1098] [depth= 1] . ( 496 sec) [ -7629.4216] [ 1098] [depth= 2] . ( 498 sec) [ -7629.4078] [ 1098] [depth= 3] . ( 502 sec) [ -7629.3809] [ 1098] [depth= 16] . ( 506 sec) [ -7629.2807] [ 1098] [depth= 1] . ( 517 sec) [ -7629.0430] [Branch lengths ] . ( 518 sec) [ -7629.0428] [Ts/ts ratio ][ 3.672631] . ( 584 sec) [ -7629.0289] [ 1098] [depth= 3] . ( 631 sec) [ -7629.0184] [Branch lengths ] . ( 632 sec) [ -7629.0184] [Ts/ts ratio ][ 3.672631] . ( 751 sec) [ -7629.0165] [Branch lengths ] . ( 751 sec) [ -7629.0165] [Topology ] . ( 754 sec) [ -7628.6388] [Topology ] . ( 756 sec) [ -7628.5855] [Topology ] . ( 758 sec) [ -7628.5803] [Topology ] . ( 760 sec) [ -7628.5793] [Topology ] . ( 763 sec) [ -7628.5789] [Topology ] . ( 763 sec) [ -7628.5789] [Ts/ts ratio ][ 3.672631] . ( 763 sec) [ -7628.5789] [Topology ] . ( 765 sec) [ -7628.5788] [Topology ] . ( 766 sec) [ -7628.5788] [Ts/ts ratio ][ 3.672631] . Checking for NNIs, optimizing five branches... . ( 782 sec) [ -7628.5726] [Topology ] . Checking for NNIs, optimizing five branches... . ( 797 sec) [ -7628.5725] [Topology ] . Checking for NNIs, optimizing five branches... . ( 813 sec) [ -7628.5672] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7628.567152. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 419.412710 1.000000 1.328429 16 -1.000000 0.000000 0.000006 29 6.606483 0.782000 0.001920 83 12.083950 0.849000 0.001633 30 19.762974 0.920000 0.004074 27 6.363661 0.698000 0.004861 31 14.953670 0.937000 0.013617 92 35.038296 0.981000 0.022089 96 37.975954 0.996000 0.022998 41 -1.000000 0.000000 0.000000 97 20.333059 0.935000 0.013653 25 1.494949 0.339000 0.005706 63 6.252181 0.770000 0.009262 68 8.762723 0.782000 0.005917 51 6.107693 0.519000 0.004065 13 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 84 13.494149 0.929000 0.006235 40 0.617279 0.097000 0.004038 69 2.921149 0.355000 0.007136 48 33.582009 0.960000 0.027066 16 5.560518 0.849000 0.013347 41 14.674868 0.906000 0.021735 93 34.986669 0.975000 0.022991 66 4.441243 0.795000 0.004189 62 7.555483 0.793000 0.001954 29 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 67 14.198084 0.901000 0.003748 21 8.438206 0.698000 0.017304 100 44.592508 0.992000 0.029187 14 2.068919 0.340000 0.005755 75 35.942075 0.980000 0.025451 50 0.927289 0.253000 0.005173 21 5.235376 0.820000 0.005630 21 3.738085 0.643000 0.005130 87 60.900720 0.998000 0.047206 66 14.827361 0.925000 0.017184 38 4.425800 0.509000 0.007857 63 10.645776 0.809000 0.009864 10 8.063761 0.783000 0.003140 17 3.897484 0.760000 0.003286 21 0.304376 0.038000 0.002690 0 -1.000000 0.000000 0.000000 24 3.945924 0.738000 0.001888 6 16.401474 0.903000 0.003707 14 21.784322 0.899000 0.004319 4 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 37 12.148004 0.871000 0.004343 1 -1.000000 0.000000 0.000000 32 8.557849 0.754000 0.001861 36 0.012726 0.000000 0.001831 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000001 32 8.956446 0.734000 0.007643 92 21.263525 0.931000 0.018602 96 17.588660 0.939000 0.013757 43 2.547611 0.757000 0.004155 59 5.122714 0.719000 0.004283 98 29.936973 0.975000 0.026565 12 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 2 35.016345 0.947000 0.007890 2 7.582143 0.754000 0.001979 3 11.187315 0.849000 0.003925 2 -1.000000 0.000000 0.000000 2 5.401015 0.768000 0.001948 1 8.465067 0.828000 0.004427 1 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 45 8.599147 0.751000 0.004010 46 0.516330 0.633000 0.003929 10 12.346250 0.863000 0.003986 22 12.000947 0.880000 0.003994 18 4.621450 0.744000 0.001952 14 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 5 42.957251 0.982000 0.009044 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 23 4.792294 0.858000 0.017693 67 13.390161 0.905000 0.027785 72 3.079960 0.788000 0.029840 100 79.861126 1.000000 0.140842 99 93.293594 1.000000 0.157977 97 18.261914 0.908000 0.008575 . Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'... . Time used 14h7m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo