.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -25691.5291] [Ts/ts ratio ][ 3.179105] . ( 2 sec) [ -25689.4105] [ 6342] [depth= 1] . ( 2 sec) [ -25689.3796] [ 6340] [depth= 1] . ( 2 sec) [ -25689.2464] [ 6342] [depth= 1] . ( 2 sec) [ -25678.1197] [ 6341] [depth= 1] . ( 3 sec) [ -25673.2104] [ 6336] [depth= 1] . ( 3 sec) [ -25669.0705] [ 6333] [depth= 1] . ( 3 sec) [ -25651.4198] [ 6334] [depth= 1] . ( 3 sec) [ -25647.9807] [ 6339] [depth= 1] . ( 4 sec) [ -25647.6225] [ 6337] [depth= 1] . ( 4 sec) [ -25643.3950] [ 6335] [depth= 1] . ( 4 sec) [ -25631.4136] [ 6323] [depth= 2] . ( 5 sec) [ -25631.0432] [ 6328] [depth= 1] . ( 6 sec) [ -25612.6290] [ 6323] [depth= 1] . ( 6 sec) [ -25604.1236] [ 6319] [depth= 1] . ( 6 sec) [ -25603.2953] [ 6323] [depth= 1] . ( 6 sec) [ -25601.9609] [ 6319] [depth= 1] . ( 6 sec) [ -25595.7375] [ 6320] [depth= 1] . ( 6 sec) [ -25594.9383] [ 6325] [depth= 1] . ( 7 sec) [ -25593.5231] [ 6319] [depth= 1] . ( 7 sec) [ -25585.6397] [ 6316] [depth= 1] . ( 7 sec) [ -25578.5625] [ 6319] [depth= 1] . ( 7 sec) [ -25577.4227] [ 6324] [depth= 1] . ( 7 sec) [ -25576.6362] [ 6319] [depth= 1] . ( 7 sec) [ -25564.0129] [ 6323] [depth= 1] . ( 8 sec) [ -25561.3669] [ 6328] [depth= 1] . ( 8 sec) [ -25552.5247] [ 6331] [depth= 2] . ( 8 sec) [ -25506.1852] [ 6334] [depth= 2] . ( 8 sec) [ -25503.7871] [ 6328] [depth= 1] . ( 8 sec) [ -25489.3617] [ 6334] [depth= 3] . ( 8 sec) [ -25489.1348] [ 6339] [depth= 1] . ( 8 sec) [ -25488.0640] [ 6350] [depth= 1] . ( 8 sec) [ -25478.5685] [ 6339] [depth= 1] . ( 9 sec) [ -25453.4928] [ 6344] [depth= 3] . ( 9 sec) [ -25452.1793] [ 6337] [depth= 2] . ( 9 sec) [ -25437.1452] [ 6334] [depth= 3] . ( 9 sec) [ -25431.2496] [ 6346] [depth= 1] . ( 9 sec) [ -25423.6222] [ 6334] [depth= 1] . ( 9 sec) [ -25422.6620] [ 6339] [depth= 1] . ( 9 sec) [ -25420.4202] [ 6340] [depth= 1] . ( 9 sec) [ -25408.3043] [ 6330] [depth= 3] . ( 10 sec) [ -25406.3116] [ 6334] [depth= 1] . ( 10 sec) [ -25402.3631] [ 6332] [depth= 1] . ( 10 sec) [ -25398.0704] [ 6328] [depth= 1] . ( 10 sec) [ -25394.4277] [ 6329] [depth= 1] . ( 10 sec) [ -25389.6088] [ 6332] [depth= 1] . ( 11 sec) [ -25388.4738] [ 6332] [depth= 1] . ( 11 sec) [ -25387.1892] [ 6334] [depth= 1] . ( 12 sec) [ -25268.4735] [Branch lengths ] . ( 12 sec) [ -25254.6868] [Ts/ts ratio ][ 3.702919] . ( 14 sec) [ -25254.1237] [ 6334] [depth= 2] . ( 14 sec) [ -25253.3691] [ 6327] [depth= 1] . ( 15 sec) [ -25247.9099] [ 6324] [depth= 1] . ( 17 sec) [ -25247.5806] [ 6322] [depth= 1] . ( 17 sec) [ -25246.0276] [ 6324] [depth= 1] . ( 17 sec) [ -25243.7712] [ 6324] [depth= 1] . ( 17 sec) [ -25242.6771] [ 6326] [depth= 1] . ( 18 sec) [ -25240.5751] [ 6326] [depth= 1] . ( 19 sec) [ -25239.1052] [ 6325] [depth= 1] . ( 20 sec) [ -25238.9230] [ 6324] [depth= 2] . ( 22 sec) [ -25213.6173] [Branch lengths ] . ( 22 sec) [ -25213.1130] [Ts/ts ratio ][ 3.812656] . ( 32 sec) [ -25207.8312] [Branch lengths ] . ( 66 sec) [ -25206.7562] [ 6319] [depth= 1] . ( 91 sec) [ -25205.1921] [Branch lengths ] . ( 92 sec) [ -25204.8020] [Ts/ts ratio ][ 3.912772] . ( 151 sec) [ -25204.0974] [Branch lengths ] . ( 151 sec) [ -25204.0974] [Topology ] . ( 152 sec) [ -25203.1304] [Topology ] . ( 154 sec) [ -25202.9028] [Topology ] . ( 156 sec) [ -25202.8309] [Topology ] . ( 158 sec) [ -25202.7937] [Topology ] . ( 159 sec) [ -25202.7708] [Topology ] . ( 161 sec) [ -25202.7557] [Topology ] . ( 163 sec) [ -25202.7455] [Topology ] . ( 163 sec) [ -25202.6447] [Ts/ts ratio ][ 3.964804] . ( 163 sec) [ -25202.6447] [Topology ] . ( 165 sec) [ -25202.6179] [Topology ] . ( 167 sec) [ -25202.6006] [Topology ] . ( 168 sec) [ -25202.5885] [Topology ] . ( 170 sec) [ -25202.5800] [Topology ] . ( 172 sec) [ -25202.5740] [Topology ] . ( 174 sec) [ -25202.5697] [Topology ] . ( 174 sec) [ -25202.5615] [Ts/ts ratio ][ 3.979820] . ( 174 sec) [ -25202.5615] [Topology ] . ( 176 sec) [ -25202.5554] [Topology ] . ( 177 sec) [ -25202.5512] [Topology ] . ( 179 sec) [ -25202.5483] [Topology ] . ( 181 sec) [ -25202.5461] [Topology ] . ( 182 sec) [ -25202.5446] [Topology ] . ( 184 sec) [ -25202.5435] [Topology ] . ( 184 sec) [ -25202.5417] [Ts/ts ratio ][ 3.988121] . ( 184 sec) [ -25202.5417] [Topology ] . ( 186 sec) [ -25202.5400] [Topology ] . ( 188 sec) [ -25202.5389] [Topology ] . ( 190 sec) [ -25202.5381] [Topology ] . ( 190 sec) [ -25202.5381] [Ts/ts ratio ][ 3.988121] . ( 190 sec) [ -25202.5381] [Topology ] . ( 192 sec) [ -25202.5375] [Topology ] . ( 192 sec) [ -25202.5375] [Ts/ts ratio ][ 3.988121] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25202.537476. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 104.218911 1.000000 0.259238 100 40.116281 0.991000 0.139086 63 6.208752 0.707000 0.035962 100 88.643742 1.000000 0.176528 92 36.785870 0.979000 0.089397 100 54.714317 0.995000 0.146525 100 64.428831 0.993000 0.155969 100 117.442427 1.000000 0.232535 100 39.911388 0.982000 0.113680 100 71.100339 0.999000 0.183197 93 17.227560 0.947000 0.081225 33 1.564940 0.267000 0.049688 97 78.752491 0.998000 0.126449 59 9.385444 0.853000 0.038795 31 3.900584 0.449000 0.039121 99 180.315136 1.000000 0.258691 100 49.536262 0.987000 0.069958 100 57.542149 0.999000 0.073347 60 10.126398 0.855000 0.034681 99 52.362062 0.995000 0.049865 82 32.769105 0.982000 0.017746 60 1.842892 0.397000 0.010673 41 4.057837 0.649000 0.020691 99 35.423439 0.980000 0.042438 99 69.892689 0.997000 0.113972 40 1.891944 0.255000 0.033589 96 37.669302 0.986000 0.095602 100 78.763286 1.000000 0.153528 100 99.192480 1.000000 0.155141 57 13.165018 0.797000 0.062356 100 181.989862 1.000000 0.242272 97 32.609541 0.970000 0.091026 72 19.436192 0.951000 0.051058 38 2.956625 0.459000 0.020095 100 52.872090 0.993000 0.083287 44 18.321943 0.937000 0.080017 100 96.195607 1.000000 0.198677 100 80.266325 1.000000 0.177460 100 51.357762 0.990000 0.109854 100 56.963410 0.991000 0.089460 47 6.873106 0.800000 0.038147 100 277.350151 1.000000 0.313918 44 13.593660 0.922000 0.046856 100 152.082289 1.000000 0.174157 51 0.060852 0.000000 0.001190 96 43.305038 0.977000 0.014158 18 11.455764 0.811000 0.041679 10 2.589433 0.578000 0.017261 23 10.208467 0.883000 0.034679 100 160.519707 1.000000 0.206745 18 5.781823 0.735000 0.038966 100 53.954458 0.993000 0.092503 24 2.133526 0.209000 0.047018 77 23.767165 0.980000 0.076667 100 160.006807 1.000000 0.253694 20 6.654837 0.898000 0.048407 100 247.123844 1.000000 0.326503 99 72.681701 1.000000 0.160292 . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 4h46m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo