.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_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 . Compressing sequences... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14390.2378] [Ts/ts ratio ][ 6.022232] . ( 1 sec) [ -14370.1272] [ 2324] [depth= 1] . ( 1 sec) [ -14368.8113] [ 2324] [depth= 1] . ( 1 sec) [ -14368.1864] [ 2324] [depth= 1] . ( 2 sec) [ -14365.2725] [ 2324] [depth= 1] . ( 3 sec) [ -14362.0385] [ 2324] [depth= 1] . ( 3 sec) [ -14356.8109] [ 2324] [depth= 1] . ( 3 sec) [ -14355.7864] [ 2326] [depth= 2] . ( 3 sec) [ -14353.2644] [ 2326] [depth= 1] . ( 4 sec) [ -14352.3358] [ 2330] [depth= 1] . ( 4 sec) [ -14351.1438] [ 2326] [depth= 1] . ( 4 sec) [ -14350.6917] [ 2325] [depth= 1] . ( 5 sec) [ -14347.3818] [ 2319] [depth= 1] . ( 5 sec) [ -14341.4976] [ 2319] [depth= 2] . ( 5 sec) [ -14339.5111] [ 2317] [depth= 2] . ( 6 sec) [ -14338.6374] [ 2320] [depth= 1] . ( 6 sec) [ -14333.3532] [ 2317] [depth= 1] . ( 6 sec) [ -14330.8880] [ 2313] [depth= 6] . ( 7 sec) [ -14324.9612] [ 2312] [depth= 1] . ( 7 sec) [ -14317.6972] [ 2313] [depth= 1] . ( 8 sec) [ -14310.1839] [ 2312] [depth= 1] . ( 8 sec) [ -14292.1248] [ 2314] [depth= 2] . ( 9 sec) [ -14278.7471] [ 2319] [depth= 2] . ( 9 sec) [ -14272.9584] [ 2312] [depth= 2] . ( 9 sec) [ -14268.5234] [ 2312] [depth= 1] . ( 9 sec) [ -14268.0749] [ 2312] [depth= 1] . ( 10 sec) [ -14267.9478] [ 2313] [depth= 1] . ( 10 sec) [ -14262.0646] [ 2314] [depth= 1] . ( 10 sec) [ -14260.3232] [ 2313] [depth= 1] . ( 10 sec) [ -14259.7050] [ 2312] [depth= 1] . ( 11 sec) [ -14258.1275] [ 2319] [depth= 6] . ( 11 sec) [ -14257.9954] [ 2323] [depth= 1] . ( 11 sec) [ -14256.7387] [ 2319] [depth= 1] . ( 12 sec) [ -14253.7441] [ 2318] [depth= 3] . ( 12 sec) [ -14253.5600] [ 2320] [depth= 1] . ( 12 sec) [ -14250.4200] [ 2318] [depth= 2] . ( 13 sec) [ -14246.8724] [ 2312] [depth= 6] . ( 13 sec) [ -14243.5313] [ 2315] [depth= 1] . ( 13 sec) [ -14242.5070] [ 2314] [depth= 2] . ( 14 sec) [ -14242.0344] [ 2316] [depth= 2] . ( 15 sec) [ -14181.2027] [Branch lengths ] . ( 15 sec) [ -14180.4881] [Ts/ts ratio ][ 6.378695] . ( 16 sec) [ -14179.7708] [ 2315] [depth= 1] . ( 18 sec) [ -14179.7591] [ 2316] [depth= 1] . ( 23 sec) [ -14176.4312] [ 2319] [depth= 8] . ( 25 sec) [ -14175.8852] [ 2319] [depth= 3] . ( 32 sec) [ -14175.7803] [ 2318] [depth= 4] . ( 35 sec) [ -14168.8663] [Branch lengths ] . ( 35 sec) [ -14168.8298] [Ts/ts ratio ][ 6.464146] . ( 53 sec) [ -14167.8978] [ 2317] [depth= 2] . ( 54 sec) [ -14164.8739] [ 2316] [depth= 1] . ( 56 sec) [ -14164.0559] [Branch lengths ] . ( 56 sec) [ -14164.0462] [Ts/ts ratio ][ 6.508857] . ( 77 sec) [ -14163.9839] [Branch lengths ] . ( 153 sec) [ -14163.9787] [Branch lengths ] . ( 153 sec) [ -14163.9787] [Topology ] . ( 155 sec) [ -14163.9286] [Topology ] . ( 157 sec) [ -14162.9894] [Topology ] . ( 158 sec) [ -14162.6976] [Topology ] . ( 160 sec) [ -14162.6783] [Topology ] . ( 162 sec) [ -14162.6765] [Topology ] . ( 164 sec) [ -14162.6763] [Topology ] . ( 165 sec) [ -14162.6727] [Ts/ts ratio ][ 6.536360] . ( 165 sec) [ -14162.6727] [Topology ] . ( 167 sec) [ -14162.6726] [Topology ] . ( 167 sec) [ -14162.6726] [Ts/ts ratio ][ 6.536360] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14162.672606. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 108.277041 0.999000 0.024500 100 115.447116 1.000000 0.032275 100 65.283287 0.998000 0.017938 91 37.535911 0.963000 0.011038 55 1.234670 0.584000 0.002431 80 20.931252 0.918000 0.015924 100 206.218663 1.000000 0.057575 100 66.045361 0.999000 0.027572 65 4.644147 0.838000 0.006471 33 5.460283 0.563000 0.010857 82 45.041454 0.990000 0.015489 98 51.354528 0.984000 0.014095 34 7.530053 0.842000 0.004220 23 5.623054 0.809000 0.003080 19 0.696490 0.067000 0.001649 45 4.768719 0.646000 0.002599 96 60.058961 0.998000 0.014896 70 4.621606 0.598000 0.004702 57 11.817584 0.846000 0.005588 89 29.976813 0.974000 0.015221 43 5.767146 0.715000 0.007624 35 12.143345 0.880000 0.008521 13 2.399085 0.218000 0.006266 97 33.520887 0.967000 0.009401 10 5.412251 0.827000 0.006433 100 98.319523 0.999000 0.061424 15 2.545633 0.378000 0.005535 100 75.069307 0.998000 0.018668 11 3.963187 0.633000 0.005273 8 8.736262 0.904000 0.004403 19 4.951912 0.721000 0.002352 38 13.521119 0.909000 0.004161 47 25.846100 0.943000 0.006029 93 45.006893 0.979000 0.008155 98 11.158530 0.867000 0.003022 71 13.898185 0.875000 0.004424 59 8.839606 0.820000 0.002544 77 20.880954 0.941000 0.007252 21 0.572465 0.286000 0.000691 100 86.495176 0.996000 0.012242 99 54.274609 0.991000 0.012949 100 107.841781 1.000000 0.022119 62 1.714202 0.724000 0.000883 21 21.254763 0.963000 0.010445 5 6.146071 0.673000 0.005361 100 226.866457 1.000000 0.042324 23 2.795299 0.657000 0.003689 38 6.101250 0.772000 0.008040 16 1.290116 0.418000 0.006438 . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Time used 4h29m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo