.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2655_50x872_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... . 374 patterns found. (out of a total of 872 sites) . 550 sites without polymorphism (63.07%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6795.9258] [Ts/ts ratio ][ 4.401381] . ( 0 sec) [ -6793.3896] [ 1115] [depth= 1] . ( 0 sec) [ -6792.4236] [ 1115] [depth= 1] . ( 0 sec) [ -6788.2414] [ 1115] [depth= 1] . ( 0 sec) [ -6788.2282] [ 1115] [depth= 1] . ( 0 sec) [ -6782.8498] [ 1118] [depth= 1] . ( 0 sec) [ -6781.2326] [ 1121] [depth= 1] . ( 0 sec) [ -6778.6444] [ 1118] [depth= 1] . ( 0 sec) [ -6773.7305] [ 1118] [depth= 1] . ( 1 sec) [ -6772.2288] [ 1116] [depth= 1] . ( 1 sec) [ -6772.0656] [ 1120] [depth= 2] . ( 1 sec) [ -6766.9251] [ 1116] [depth= 1] . ( 1 sec) [ -6763.7604] [ 1115] [depth= 1] . ( 2 sec) [ -6757.5591] [ 1116] [depth= 1] . ( 2 sec) [ -6752.9773] [ 1119] [depth= 2] . ( 2 sec) [ -6751.1137] [ 1120] [depth= 2] . ( 2 sec) [ -6746.2775] [ 1122] [depth= 1] . ( 2 sec) [ -6745.6104] [ 1126] [depth= 1] . ( 2 sec) [ -6743.2995] [ 1128] [depth= 2] . ( 2 sec) [ -6739.6172] [ 1125] [depth= 2] . ( 2 sec) [ -6734.5425] [ 1121] [depth= 1] . ( 2 sec) [ -6734.2746] [ 1121] [depth= 1] . ( 2 sec) [ -6728.1131] [ 1116] [depth= 2] . ( 2 sec) [ -6727.0248] [ 1119] [depth= 1] . ( 3 sec) [ -6726.8317] [ 1118] [depth= 1] . ( 3 sec) [ -6724.7193] [ 1121] [depth= 1] . ( 3 sec) [ -6715.3977] [ 1118] [depth= 1] . ( 3 sec) [ -6710.2674] [ 1117] [depth= 1] . ( 4 sec) [ -6708.4220] [ 1121] [depth= 1] . ( 4 sec) [ -6701.9246] [ 1117] [depth= 1] . ( 4 sec) [ -6701.3398] [ 1117] [depth= 1] . ( 4 sec) [ -6695.1187] [ 1116] [depth= 1] . ( 5 sec) [ -6644.3079] [Branch lengths ] . ( 5 sec) [ -6642.8155] [Ts/ts ratio ][ 4.932020] . ( 5 sec) [ -6642.7832] [ 1115] [depth= 1] . ( 7 sec) [ -6642.0497] [ 1113] [depth= 1] . ( 7 sec) [ -6640.6199] [ 1110] [depth= 1] . ( 8 sec) [ -6640.4682] [ 1111] [depth= 1] . ( 12 sec) [ -6637.0080] [Branch lengths ] . ( 12 sec) [ -6636.9780] [Ts/ts ratio ][ 5.014827] . ( 12 sec) [ -6636.9263] [ 1110] [depth= 1] . ( 12 sec) [ -6636.9150] [ 1108] [depth= 1] . ( 18 sec) [ -6636.5383] [Branch lengths ] . ( 18 sec) [ -6636.5360] [Ts/ts ratio ][ 5.035237] . ( 32 sec) [ -6636.5215] [ 1113] [depth= 2] . ( 46 sec) [ -6635.1628] [Branch lengths ] . ( 46 sec) [ -6635.1462] [Ts/ts ratio ][ 5.097862] . ( 48 sec) [ -6634.6367] [ 1115] [depth= 1] . ( 48 sec) [ -6634.6226] [ 1117] [depth= 1] . ( 49 sec) [ -6634.4316] [ 1115] [depth= 1] . ( 59 sec) [ -6632.5711] [ 1117] [depth= 5] . ( 74 sec) [ -6630.3845] [Branch lengths ] . ( 74 sec) [ -6630.3027] [Ts/ts ratio ][ 4.961630] . ( 87 sec) [ -6629.6977] [ 1116] [depth= 1] . ( 102 sec) [ -6629.4172] [Branch lengths ] . ( 102 sec) [ -6629.4170] [Ts/ts ratio ][ 4.971561] . ( 102 sec) [ -6629.4170] [Topology ] . ( 103 sec) [ -6629.4089] [Topology ] . ( 104 sec) [ -6629.4076] [Topology ] . ( 105 sec) [ -6629.4072] [Topology ] . ( 105 sec) [ -6629.4071] [Ts/ts ratio ][ 4.966589] . ( 105 sec) [ -6629.4071] [Topology ] . ( 105 sec) [ -6629.4070] [Topology ] . ( 106 sec) [ -6629.4070] [Ts/ts ratio ][ 4.966589] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6629.406955. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 89.904447 0.997000 0.027936 34 3.595112 0.249000 0.006602 39 0.019434 0.000000 0.000749 100 306.603992 1.000000 0.170937 33 4.199369 0.354000 0.019398 12 1.822683 0.455000 0.009202 41 87.340578 0.999000 0.046197 58 4.097412 0.794000 0.005112 67 7.101991 0.864000 0.009369 12 1.356312 0.295000 0.008686 100 244.224059 1.000000 0.203709 62 4.714054 0.816000 0.009769 100 205.136345 1.000000 0.083898 67 3.239943 0.437000 0.009337 27 1.137779 0.599000 0.006705 100 157.008486 1.000000 0.094095 17 10.289949 0.864000 0.013633 100 251.359328 1.000000 0.147147 76 1.685353 0.735000 0.004561 46 2.008368 0.580000 0.007891 94 36.378465 0.986000 0.034649 100 87.017393 1.000000 0.047957 40 3.424546 0.767000 0.006048 34 4.419610 0.804000 0.004585 79 38.746905 0.981000 0.009834 95 38.893014 0.969000 0.013891 100 41.903371 0.991000 0.015026 25 0.582815 0.632000 0.001384 100 166.686417 1.000000 0.093060 87 9.519634 0.862000 0.012983 99 35.675512 0.970000 0.026939 100 36.716950 0.994000 0.028417 97 17.494930 0.925000 0.019806 62 13.347545 0.914000 0.013818 70 14.325118 0.932000 0.014675 74 47.287296 0.984000 0.024772 91 20.950134 0.941000 0.011614 74 4.199097 0.756000 0.001621 89 9.674201 0.880000 0.010838 68 13.468686 0.878000 0.006621 54 5.603849 0.761000 0.003212 88 22.189829 0.945000 0.015999 96 45.928255 0.993000 0.019471 59 5.704793 0.810000 0.003991 74 17.281898 0.914000 0.012964 94 13.489527 0.911000 0.008409 62 4.615162 0.810000 0.001649 . Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'... . Time used 1h29m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo