.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2845_68x1715_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 649 patterns found. (out of a total of 1715 sites) . 1119 sites without polymorphism (65.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11707.1211] [Ts/ts ratio ][ 3.452387] . ( 0 sec) [ -11705.2467] [ 1610] [depth= 1] . ( 1 sec) [ -11705.1925] [ 1610] [depth= 1] . ( 1 sec) [ -11704.9991] [ 1610] [depth= 1] . ( 1 sec) [ -11704.9104] [ 1610] [depth= 1] . ( 1 sec) [ -11704.8976] [ 1611] [depth= 2] . ( 1 sec) [ -11703.6190] [ 1611] [depth= 1] . ( 2 sec) [ -11702.7502] [ 1611] [depth= 1] . ( 2 sec) [ -11702.2292] [ 1611] [depth= 1] . ( 3 sec) [ -11702.2134] [ 1613] [depth= 1] . ( 3 sec) [ -11700.2834] [ 1611] [depth= 1] . ( 3 sec) [ -11694.3109] [ 1610] [depth= 1] . ( 4 sec) [ -11688.5742] [ 1609] [depth= 1] . ( 4 sec) [ -11688.2854] [ 1609] [depth= 1] . ( 5 sec) [ -11685.9942] [ 1609] [depth= 1] . ( 5 sec) [ -11680.5633] [ 1603] [depth= 2] . ( 5 sec) [ -11672.0227] [ 1601] [depth= 3] . ( 5 sec) [ -11668.9983] [ 1600] [depth= 1] . ( 6 sec) [ -11668.4128] [ 1598] [depth= 2] . ( 6 sec) [ -11666.4300] [ 1597] [depth= 1] . ( 6 sec) [ -11658.9241] [ 1597] [depth= 1] . ( 6 sec) [ -11646.0840] [ 1596] [depth= 1] . ( 7 sec) [ -11645.4431] [ 1596] [depth= 1] . ( 7 sec) [ -11639.9433] [ 1596] [depth= 2] . ( 8 sec) [ -11639.6807] [ 1595] [depth= 1] . ( 8 sec) [ -11638.6966] [ 1596] [depth= 1] . ( 8 sec) [ -11638.6305] [ 1596] [depth= 1] . ( 8 sec) [ -11634.9048] [ 1596] [depth= 1] . ( 8 sec) [ -11634.3472] [ 1595] [depth= 1] . ( 9 sec) [ -11634.0005] [ 1596] [depth= 1] . ( 9 sec) [ -11633.5401] [ 1599] [depth= 1] . ( 9 sec) [ -11630.5470] [ 1600] [depth= 1] . ( 10 sec) [ -11625.6880] [ 1599] [depth= 1] . ( 10 sec) [ -11625.4342] [ 1601] [depth= 1] . ( 11 sec) [ -11617.9842] [ 1599] [depth= 1] . ( 11 sec) [ -11616.8735] [ 1600] [depth= 1] . ( 12 sec) [ -11613.9413] [ 1599] [depth= 1] . ( 12 sec) [ -11613.6179] [ 1600] [depth= 2] . ( 12 sec) [ -11602.4343] [ 1596] [depth= 2] . ( 12 sec) [ -11602.3226] [ 1598] [depth= 1] . ( 13 sec) [ -11595.6523] [ 1598] [depth= 1] . ( 13 sec) [ -11590.0179] [ 1599] [depth= 2] . ( 13 sec) [ -11583.6785] [ 1597] [depth= 1] . ( 13 sec) [ -11583.6448] [ 1596] [depth= 1] . ( 14 sec) [ -11581.3740] [ 1597] [depth= 3] . ( 14 sec) [ -11581.0912] [ 1597] [depth= 2] . ( 14 sec) [ -11580.1314] [ 1599] [depth= 1] . ( 14 sec) [ -11573.2233] [ 1596] [depth= 2] . ( 14 sec) [ -11572.7448] [ 1595] [depth= 1] . ( 15 sec) [ -11572.5425] [ 1596] [depth= 1] . ( 15 sec) [ -11572.2477] [ 1596] [depth= 2] . ( 16 sec) [ -11569.6983] [ 1596] [depth= 1] . ( 16 sec) [ -11567.5063] [ 1595] [depth= 1] . ( 16 sec) [ -11563.6033] [ 1595] [depth= 1] . ( 18 sec) [ -11500.4200] [Branch lengths ] . ( 18 sec) [ -11500.2059] [Ts/ts ratio ][ 3.572492] . ( 20 sec) [ -11500.0663] [ 1595] [depth= 1] . ( 22 sec) [ -11499.5770] [ 1596] [depth= 1] . ( 22 sec) [ -11497.7509] [ 1595] [depth= 1] . ( 29 sec) [ -11497.0821] [ 1592] [depth= 2] . ( 32 sec) [ -11496.6938] [ 1592] [depth= 1] . ( 35 sec) [ -11494.5865] [ 1591] [depth= 3] . ( 35 sec) [ -11493.7784] [ 1592] [depth= 1] . ( 37 sec) [ -11491.5696] [ 1592] [depth= 2] . ( 40 sec) [ -11491.3455] [ 1592] [depth= 1] . ( 41 sec) [ -11484.4114] [Branch lengths ] . ( 41 sec) [ -11484.4114] [Ts/ts ratio ][ 3.572492] . ( 64 sec) [ -11483.9293] [Branch lengths ] . ( 141 sec) [ -11483.8651] [Branch lengths ] . ( 141 sec) [ -11483.8651] [Topology ] . ( 143 sec) [ -11483.8597] [Topology ] . ( 145 sec) [ -11483.8580] [Topology ] . ( 147 sec) [ -11483.8573] [Topology ] . ( 147 sec) [ -11483.8565] [Ts/ts ratio ][ 3.578863] . ( 147 sec) [ -11483.8565] [Topology ] . ( 149 sec) [ -11483.8561] [Topology ] . ( 149 sec) [ -11483.8561] [Ts/ts ratio ][ 3.578863] . Checking for NNIs, optimizing five branches... . ( 163 sec) [ -11483.8196] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11483.819587. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 58 6.878035 0.387000 0.008785 97 28.164734 0.956000 0.013686 100 139.169741 1.000000 0.033504 100 131.874373 1.000000 0.035749 14 3.294730 0.680000 0.002961 17 2.975530 0.467000 0.004371 20 10.129484 0.803000 0.004138 75 24.189362 0.947000 0.007330 34 0.073070 0.000000 0.002915 98 54.482903 0.978000 0.008985 90 26.499921 0.939000 0.004811 58 6.732447 0.836000 0.003138 74 10.238649 0.865000 0.002736 18 0.271576 0.093000 0.001645 100 313.451164 1.000000 0.062286 91 39.419116 0.985000 0.020215 88 33.012375 0.949000 0.010834 100 62.913937 0.997000 0.013547 92 15.686232 0.899000 0.006114 42 0.618621 0.077000 0.004240 100 117.396147 1.000000 0.023987 91 32.879643 0.966000 0.010980 64 4.453328 0.813000 0.002106 85 36.897304 0.968000 0.006014 78 18.351974 0.916000 0.003664 65 2.669954 0.764000 0.001848 92 29.897450 0.959000 0.007094 58 15.199239 0.869000 0.002052 30 7.590061 0.756000 0.001118 35 4.081080 0.746000 0.000926 76 15.053100 0.922000 0.007212 8 4.156269 0.581000 0.002003 100 141.354993 1.000000 0.031249 96 29.340136 0.966000 0.011822 13 -1.000000 0.000000 0.000000 52 10.315519 0.847000 0.001839 86 26.606220 0.968000 0.012860 63 13.234314 0.816000 0.008815 29 0.649325 0.069000 0.003089 98 58.587515 0.997000 0.011826 40 16.544739 0.937000 0.005997 100 333.505551 1.000000 0.046462 50 4.164962 0.805000 0.002529 17 14.952273 0.920000 0.005273 28 9.314580 0.836000 0.004410 89 48.230360 0.984000 0.007756 62 5.890608 0.774000 0.005196 100 47.785118 0.985000 0.018103 49 9.142501 0.871000 0.005897 38 16.912241 0.925000 0.004658 67 27.304968 0.966000 0.006774 23 1.229079 0.460000 0.000928 100 185.170322 1.000000 0.023252 33 -1.000000 0.000000 0.000000 48 17.659186 0.913000 0.004187 100 98.553966 1.000000 0.014990 94 20.053940 0.933000 0.004405 65 7.871684 0.744000 0.002601 34 0.313114 0.063000 0.001347 55 2.855137 0.757000 0.002094 100 77.230312 0.997000 0.017150 94 27.381507 0.951000 0.007118 19 1.695299 0.314000 0.002083 85 24.305491 0.950000 0.006480 98 23.277719 0.952000 0.005394 . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Time used 4h14m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo