.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2696_50x1472_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... . 617 patterns found. (out of a total of 1472 sites) . 982 sites without polymorphism (66.71%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6212.4460] [Ts/ts ratio ][ 2.670832] . ( 1 sec) [ -6208.0485] [ 694] [depth= 1] . ( 1 sec) [ -6207.1947] [ 694] [depth= 2] . ( 1 sec) [ -6206.5150] [ 694] [depth= 1] . ( 1 sec) [ -6204.5785] [ 689] [depth= 2] . ( 2 sec) [ -6204.4732] [ 693] [depth= 1] . ( 2 sec) [ -6204.4123] [ 693] [depth= 1] . ( 3 sec) [ -6203.9491] [ 693] [depth= 1] . ( 3 sec) [ -6199.9231] [ 692] [depth= 1] . ( 3 sec) [ -6199.3060] [ 692] [depth= 1] . ( 3 sec) [ -6199.2560] [ 692] [depth= 1] . ( 3 sec) [ -6199.1998] [ 692] [depth= 1] . ( 4 sec) [ -6199.1522] [ 692] [depth= 1] . ( 5 sec) [ -6198.9712] [ 692] [depth= 1] . ( 5 sec) [ -6198.6956] [ 692] [depth= 1] . ( 5 sec) [ -6198.6778] [ 692] [depth= 1] . ( 7 sec) [ -6197.9437] [ 692] [depth= 1] . ( 7 sec) [ -6197.9247] [ 692] [depth= 1] . ( 7 sec) [ -6197.8914] [ 692] [depth= 1] . ( 8 sec) [ -6197.8631] [ 692] [depth= 1] . ( 8 sec) [ -6197.7378] [ 692] [depth= 1] . ( 8 sec) [ -6197.6441] [ 692] [depth= 1] . ( 8 sec) [ -6196.5715] [ 692] [depth= 1] . ( 9 sec) [ -6196.2568] [ 692] [depth= 1] . ( 9 sec) [ -6192.6873] [ 692] [depth= 1] . ( 10 sec) [ -6191.6571] [ 692] [depth= 1] . ( 10 sec) [ -6191.6015] [ 692] [depth= 1] . ( 13 sec) [ -6191.5663] [ 692] [depth= 1] . ( 19 sec) [ -6191.2340] [ 692] [depth= 1] . ( 19 sec) [ -6191.0869] [ 692] [depth= 1] . ( 20 sec) [ -6190.8750] [ 692] [depth= 1] . ( 20 sec) [ -6190.2369] [ 692] [depth= 1] . ( 20 sec) [ -6184.5475] [ 691] [depth= 2] . ( 21 sec) [ -6184.2122] [ 691] [depth= 3] . ( 21 sec) [ -6184.0918] [ 691] [depth= 3] . ( 21 sec) [ -6184.0731] [ 691] [depth= 2] . ( 21 sec) [ -6183.9684] [ 691] [depth= 3] . ( 22 sec) [ -6183.9149] [ 691] [depth= 2] . ( 22 sec) [ -6183.8726] [ 691] [depth= 1] . ( 23 sec) [ -6183.8308] [ 691] [depth= 2] . ( 26 sec) [ -6179.2296] [Branch lengths ] . ( 27 sec) [ -6179.2209] [Ts/ts ratio ][ 2.699192] . ( 63 sec) [ -6179.1414] [Branch lengths ] . ( 114 sec) [ -6179.1409] [Branch lengths ] . ( 114 sec) [ -6179.1409] [Topology ] . ( 116 sec) [ -6179.1409] [Topology ] . ( 116 sec) [ -6179.1409] [Ts/ts ratio ][ 2.699192] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6179.140889. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 80 6.827307 0.808000 0.002918 56 5.778659 0.551000 0.003093 100 101.513855 0.995000 0.013798 76 13.833314 0.815000 0.004476 100 29.969541 0.979000 0.010868 95 27.321931 0.950000 0.004303 75 7.766198 0.861000 0.003449 39 0.756171 0.129000 0.001269 58 0.317705 0.078000 0.000930 99 16.682048 0.945000 0.006798 100 84.128887 0.996000 0.010550 99 55.339056 0.986000 0.004898 77 18.138270 0.897000 0.001371 18 -1.000000 0.000000 0.000000 75 11.033884 0.842000 0.000687 47 -1.000000 0.000000 0.000000 76 28.094371 0.897000 0.001429 18 2.856670 0.770000 0.000636 28 -1.000000 0.000000 0.000000 37 5.916398 0.709000 0.000693 63 11.189262 0.865000 0.001357 29 2.003717 0.747000 0.000594 100 73.824787 0.993000 0.005595 39 13.631907 0.912000 0.002027 89 34.679209 0.963000 0.002755 16 -1.000000 0.000000 0.000000 67 8.944245 0.781000 0.000687 51 0.001791 0.000000 0.000293 65 20.544801 0.891000 0.002003 72 6.644666 0.745000 0.000759 63 11.034630 0.780000 0.000687 31 -1.000000 0.000000 0.000000 56 12.117139 0.723000 0.002274 66 6.938424 0.774000 0.001249 4 -1.000000 0.000000 0.000000 60 37.961654 0.949000 0.002060 25 -1.000000 0.000000 0.000000 17 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 49 10.887731 0.869000 0.000686 2 -1.000000 0.000000 0.000000 85 25.380270 0.922000 0.001832 77 8.331666 0.776000 0.000915 5 -1.000000 0.000000 0.000000 77 33.020403 0.931000 0.002071 81 17.970988 0.864000 0.001375 24 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2696_50x1472_2006.phy_phyml_tree.txt'... . Time used 3h20m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo