.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_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 . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5586.0029] [Ts/ts ratio ][ 4.203089] . ( 1 sec) [ -5583.3883] [ 850] [depth= 1] . ( 1 sec) [ -5580.8539] [ 853] [depth= 1] . ( 1 sec) [ -5578.4804] [ 850] [depth= 1] . ( 1 sec) [ -5578.3430] [ 853] [depth= 1] . ( 1 sec) [ -5567.5066] [ 853] [depth= 1] . ( 1 sec) [ -5563.2596] [ 853] [depth= 1] . ( 1 sec) [ -5555.0809] [ 856] [depth= 2] . ( 2 sec) [ -5553.8100] [ 856] [depth= 1] . ( 2 sec) [ -5550.7388] [ 856] [depth= 1] . ( 2 sec) [ -5550.4802] [ 857] [depth= 1] . ( 2 sec) [ -5550.2839] [ 856] [depth= 1] . ( 3 sec) [ -5548.8412] [ 859] [depth= 1] . ( 3 sec) [ -5547.7860] [ 855] [depth= 2] . ( 3 sec) [ -5545.7819] [ 855] [depth= 1] . ( 3 sec) [ -5542.3554] [ 855] [depth= 1] . ( 3 sec) [ -5541.2980] [ 857] [depth= 1] . ( 3 sec) [ -5537.6249] [ 858] [depth= 2] . ( 4 sec) [ -5537.5222] [ 859] [depth= 1] . ( 4 sec) [ -5535.1659] [ 856] [depth= 1] . ( 4 sec) [ -5533.9768] [ 854] [depth= 1] . ( 5 sec) [ -5533.9326] [ 856] [depth= 1] . ( 6 sec) [ -5533.7980] [ 856] [depth= 1] . ( 6 sec) [ -5533.5086] [ 856] [depth= 1] . ( 6 sec) [ -5533.4471] [ 856] [depth= 1] . ( 6 sec) [ -5533.4144] [ 856] [depth= 1] . ( 7 sec) [ -5527.9397] [ 857] [depth= 7] . ( 7 sec) [ -5527.1104] [ 857] [depth= 1] . ( 7 sec) [ -5525.6084] [ 857] [depth= 1] . ( 8 sec) [ -5525.2151] [ 857] [depth= 1] . ( 8 sec) [ -5525.0087] [ 857] [depth= 1] . ( 8 sec) [ -5524.9892] [ 857] [depth= 1] . ( 10 sec) [ -5524.7785] [ 857] [depth= 1] . ( 10 sec) [ -5524.4508] [ 857] [depth= 1] . ( 11 sec) [ -5524.0707] [ 857] [depth= 2] . ( 11 sec) [ -5524.0415] [ 857] [depth= 2] . ( 11 sec) [ -5523.9084] [ 857] [depth= 1] . ( 12 sec) [ -5523.8956] [ 857] [depth= 1] . ( 13 sec) [ -5493.5181] [Branch lengths ] . ( 13 sec) [ -5492.9573] [Ts/ts ratio ][ 4.546484] . ( 13 sec) [ -5492.0536] [ 855] [depth= 1] . ( 14 sec) [ -5492.0395] [ 855] [depth= 1] . ( 15 sec) [ -5492.0125] [ 855] [depth= 1] . ( 17 sec) [ -5489.0536] [ 853] [depth= 1] . ( 17 sec) [ -5488.0453] [ 852] [depth= 1] . ( 20 sec) [ -5488.0352] [ 852] [depth= 2] . ( 21 sec) [ -5487.9818] [ 852] [depth= 1] . ( 22 sec) [ -5487.9601] [ 852] [depth= 1] . ( 28 sec) [ -5485.5654] [Branch lengths ] . ( 28 sec) [ -5485.5654] [Ts/ts ratio ][ 4.546484] . ( 43 sec) [ -5485.4699] [Branch lengths ] . ( 77 sec) [ -5485.4638] [Branch lengths ] . ( 77 sec) [ -5485.4638] [Topology ] . ( 78 sec) [ -5485.4634] [Topology ] . ( 78 sec) [ -5485.4620] [Ts/ts ratio ][ 4.564865] . ( 78 sec) [ -5485.4620] [Topology ] . ( 79 sec) [ -5485.4617] [Topology ] . ( 79 sec) [ -5485.4617] [Ts/ts ratio ][ 4.564865] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -5485.2865] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5485.286454. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 91 2.304055 0.719000 0.004593 100 83.388615 0.999000 0.072176 55 0.350581 0.027000 0.022294 92 13.005760 0.899000 0.027605 44 0.206052 0.000000 0.040458 100 76.494762 1.000000 0.095674 100 55.463176 0.997000 0.076746 100 48.280805 0.992000 0.038842 18 1.800123 0.226000 0.018485 97 18.325528 0.938000 0.019260 16 6.677791 0.732000 0.009758 100 104.773243 1.000000 0.050079 81 6.237216 0.826000 0.006862 95 21.939349 0.948000 0.008200 23 13.505585 0.859000 0.017073 92 43.889830 0.996000 0.030376 90 23.842877 0.952000 0.014224 18 0.387751 0.057000 0.006266 88 28.608916 0.980000 0.030995 34 7.944003 0.865000 0.008217 98 40.314430 0.984000 0.019615 16 -1.000000 0.000000 0.000000 76 30.007414 0.959000 0.004847 39 -1.000000 0.000000 0.000000 64 9.295478 0.826000 0.001611 13 6.711753 0.856000 0.006867 68 20.486868 0.931000 0.014678 64 13.247682 0.872000 0.007627 52 5.096231 0.522000 0.003586 52 4.825422 0.776000 0.006056 40 2.725989 0.717000 0.005824 49 37.558056 0.990000 0.019355 36 -1.000000 0.000000 0.000000 61 13.666346 0.887000 0.004805 63 7.355218 0.741000 0.003444 98 24.433202 0.924000 0.006413 35 29.905716 0.954000 0.006525 92 45.013915 0.977000 0.008158 85 18.111405 0.888000 0.003259 14 -1.000000 0.000000 0.000000 73 9.754070 0.850000 0.001611 10 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 70 10.890959 0.834000 0.001771 8 6.882990 0.783000 0.001646 12 15.845051 0.889000 0.003300 20 22.394846 0.921000 0.003301 19 9.852339 0.834000 0.001644 9 -1.000000 0.000000 0.000000 22 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Time used 2h16m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo