.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2565_51x1951_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 763 patterns found. (out of a total of 1951 sites) . 1244 sites without polymorphism (63.76%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15219.6216] [Ts/ts ratio ][ 3.667398] . ( 1 sec) [ -15219.5766] [ 2401] [depth= 1] . ( 1 sec) [ -15219.5625] [ 2401] [depth= 1] . ( 1 sec) [ -15216.8657] [ 2400] [depth= 1] . ( 2 sec) [ -15211.4314] [ 2399] [depth= 1] . ( 3 sec) [ -15208.3704] [ 2404] [depth= 1] . ( 3 sec) [ -15196.2378] [ 2405] [depth= 1] . ( 3 sec) [ -15195.4844] [ 2404] [depth= 1] . ( 4 sec) [ -15193.6383] [ 2405] [depth= 1] . ( 4 sec) [ -15191.0569] [ 2407] [depth= 2] . ( 4 sec) [ -15181.3405] [ 2403] [depth= 2] . ( 4 sec) [ -15181.2130] [ 2405] [depth= 1] . ( 4 sec) [ -15160.2442] [ 2407] [depth= 1] . ( 4 sec) [ -15157.1989] [ 2405] [depth= 1] . ( 4 sec) [ -15151.8955] [ 2411] [depth= 2] . ( 4 sec) [ -15148.8569] [ 2403] [depth= 2] . ( 5 sec) [ -15148.0672] [ 2405] [depth= 1] . ( 5 sec) [ -15147.3719] [ 2410] [depth= 1] . ( 5 sec) [ -15138.4595] [ 2405] [depth= 1] . ( 5 sec) [ -15137.0779] [ 2408] [depth= 1] . ( 5 sec) [ -15136.8210] [ 2405] [depth= 1] . ( 6 sec) [ -15125.0342] [ 2402] [depth= 1] . ( 6 sec) [ -15123.7411] [ 2400] [depth= 1] . ( 6 sec) [ -15118.4793] [ 2402] [depth= 1] . ( 7 sec) [ -15106.0241] [ 2405] [depth= 1] . ( 7 sec) [ -15105.3015] [ 2402] [depth= 2] . ( 7 sec) [ -15099.1334] [ 2399] [depth= 2] . ( 7 sec) [ -15081.6680] [ 2400] [depth= 1] . ( 7 sec) [ -15076.8239] [ 2402] [depth= 1] . ( 8 sec) [ -15064.9892] [ 2406] [depth= 2] . ( 8 sec) [ -15064.7989] [ 2406] [depth= 1] . ( 8 sec) [ -15063.7478] [ 2407] [depth= 1] . ( 8 sec) [ -15057.0480] [ 2405] [depth= 1] . ( 9 sec) [ -15049.7371] [ 2405] [depth= 1] . ( 9 sec) [ -15048.9025] [ 2406] [depth= 1] . ( 9 sec) [ -15047.9792] [ 2407] [depth= 1] . ( 9 sec) [ -15046.7702] [ 2406] [depth= 1] . ( 9 sec) [ -15046.0092] [ 2407] [depth= 1] . ( 10 sec) [ -15044.1925] [ 2408] [depth= 3] . ( 10 sec) [ -15043.4132] [ 2408] [depth= 1] . ( 10 sec) [ -15043.3566] [ 2408] [depth= 1] . ( 11 sec) [ -15043.2700] [ 2408] [depth= 1] . ( 11 sec) [ -15041.1188] [ 2408] [depth= 1] . ( 11 sec) [ -15040.4442] [ 2408] [depth= 1] . ( 11 sec) [ -15037.9717] [ 2408] [depth= 1] . ( 11 sec) [ -15037.7839] [ 2409] [depth= 1] . ( 12 sec) [ -14938.2627] [Branch lengths ] . ( 12 sec) [ -14937.2697] [Ts/ts ratio ][ 3.900815] . ( 13 sec) [ -14934.4017] [ 2404] [depth= 1] . ( 16 sec) [ -14932.3915] [ 2407] [depth= 1] . ( 16 sec) [ -14931.5971] [ 2407] [depth= 1] . ( 18 sec) [ -14931.2742] [ 2401] [depth= 1] . ( 19 sec) [ -14930.7324] [ 2407] [depth= 1] . ( 19 sec) [ -14930.3456] [ 2410] [depth= 1] . ( 21 sec) [ -14928.6797] [ 2406] [depth= 3] . ( 22 sec) [ -14928.4908] [ 2406] [depth= 1] . ( 24 sec) [ -14917.7127] [Branch lengths ] . ( 24 sec) [ -14917.6824] [Ts/ts ratio ][ 3.942822] . ( 31 sec) [ -14917.1227] [ 2403] [depth= 1] . ( 34 sec) [ -14917.1089] [ 2403] [depth= 1] . ( 35 sec) [ -14916.3367] [Branch lengths ] . ( 36 sec) [ -14916.3333] [Ts/ts ratio ][ 3.957243] . ( 47 sec) [ -14916.2581] [Branch lengths ] . ( 81 sec) [ -14916.0744] [ 2401] [depth= 1] . ( 95 sec) [ -14915.9768] [Branch lengths ] . ( 96 sec) [ -14915.9766] [Ts/ts ratio ][ 3.961200] . ( 96 sec) [ -14915.9766] [Topology ] . ( 97 sec) [ -14915.9258] [Topology ] . ( 99 sec) [ -14915.6094] [Topology ] . ( 100 sec) [ -14914.1047] [Topology ] . ( 102 sec) [ -14911.8155] [Topology ] . ( 104 sec) [ -14911.4628] [Topology ] . ( 105 sec) [ -14911.3870] [Topology ] . ( 105 sec) [ -14911.3865] [Ts/ts ratio ][ 3.955972] . ( 105 sec) [ -14911.3865] [Topology ] . ( 107 sec) [ -14911.3684] [Topology ] . ( 109 sec) [ -14911.3639] [Topology ] . ( 110 sec) [ -14911.3628] [Topology ] . ( 112 sec) [ -14911.3625] [Topology ] . ( 112 sec) [ -14911.3625] [Ts/ts ratio ][ 3.955972] . ( 112 sec) [ -14911.3625] [Topology ] . ( 114 sec) [ -14911.3624] [Topology ] . ( 114 sec) [ -14911.3624] [Ts/ts ratio ][ 3.955972] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14911.362432. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 153.739423 1.000000 0.046361 96 14.782740 0.917000 0.012515 100 71.737237 1.000000 0.028188 99 60.978893 0.997000 0.027334 60 8.638269 0.563000 0.015056 73 15.537718 0.916000 0.011494 97 47.499148 0.995000 0.022302 69 14.175837 0.897000 0.007043 48 2.811739 0.428000 0.003959 100 141.812150 1.000000 0.041283 70 8.430883 0.662000 0.016154 100 73.069393 0.999000 0.023338 100 57.497232 0.995000 0.023992 82 11.123018 0.894000 0.005755 68 6.385528 0.653000 0.005528 51 2.777053 0.363000 0.005898 78 35.518831 0.956000 0.012167 36 0.580221 0.160000 0.003432 100 260.488034 1.000000 0.062060 60 4.261860 0.520000 0.007654 100 168.728755 1.000000 0.034588 100 108.580125 1.000000 0.034712 100 70.608647 0.999000 0.023399 95 102.320829 0.999000 0.025398 70 21.819066 0.867000 0.017037 100 129.005220 0.999000 0.032894 97 80.987174 1.000000 0.034279 68 6.426216 0.561000 0.009617 100 138.949717 1.000000 0.025590 33 -1.000000 0.000000 0.000000 100 78.971195 0.997000 0.018526 79 9.005601 0.828000 0.002681 54 13.853103 0.898000 0.002450 47 2.580540 0.738000 0.000768 51 1.658031 0.699000 0.002884 89 67.435961 0.999000 0.019103 75 5.019867 0.528000 0.003536 75 26.109140 0.933000 0.011008 60 14.664055 0.777000 0.006710 70 20.109946 0.871000 0.003005 43 -1.000000 0.000000 0.000000 37 5.566582 0.779000 0.001892 34 2.940745 0.717000 0.000894 49 2.960573 0.335000 0.011017 61 0.905065 0.489000 0.005006 100 231.351877 1.000000 0.085949 100 55.994693 0.995000 0.031456 66 6.849589 0.703000 0.008501 . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Time used 2h52m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo