.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2738_53x1538_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... . 762 patterns found. (out of a total of 1538 sites) . 828 sites without polymorphism (53.84%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14259.1168] [Ts/ts ratio ][ 4.223348] . ( 0 sec) [ -14252.3321] [ 2609] [depth= 1] . ( 0 sec) [ -14244.4800] [ 2603] [depth= 1] . ( 0 sec) [ -14242.3816] [ 2609] [depth= 1] . ( 1 sec) [ -14232.9501] [ 2616] [depth= 1] . ( 1 sec) [ -14230.4907] [ 2606] [depth= 1] . ( 1 sec) [ -14220.8870] [ 2603] [depth= 1] . ( 1 sec) [ -14210.0714] [ 2606] [depth= 1] . ( 1 sec) [ -14206.2843] [ 2603] [depth= 1] . ( 2 sec) [ -14206.1504] [ 2603] [depth= 1] . ( 2 sec) [ -14205.7692] [ 2603] [depth= 1] . ( 3 sec) [ -14204.6145] [ 2603] [depth= 1] . ( 3 sec) [ -14204.4240] [ 2603] [depth= 1] . ( 5 sec) [ -14196.1025] [ 2605] [depth= 1] . ( 5 sec) [ -14186.4476] [ 2603] [depth= 1] . ( 6 sec) [ -14180.7615] [ 2605] [depth= 1] . ( 6 sec) [ -14176.5518] [ 2611] [depth= 2] . ( 6 sec) [ -14171.5689] [ 2609] [depth= 1] . ( 6 sec) [ -14171.0341] [ 2611] [depth= 1] . ( 6 sec) [ -14170.8099] [ 2609] [depth= 1] . ( 7 sec) [ -14162.6327] [ 2611] [depth= 1] . ( 7 sec) [ -14159.8001] [ 2609] [depth= 1] . ( 7 sec) [ -14153.2115] [ 2610] [depth= 1] . ( 8 sec) [ -14151.0148] [ 2608] [depth= 2] . ( 8 sec) [ -14149.3741] [ 2609] [depth= 2] . ( 8 sec) [ -14141.3070] [ 2612] [depth= 1] . ( 9 sec) [ -14135.3189] [ 2612] [depth= 1] . ( 9 sec) [ -14132.9876] [ 2609] [depth= 2] . ( 9 sec) [ -14132.2664] [ 2609] [depth= 1] . ( 9 sec) [ -14128.0532] [ 2609] [depth= 1] . ( 9 sec) [ -14127.1984] [ 2609] [depth= 1] . ( 9 sec) [ -14127.0516] [ 2606] [depth= 1] . ( 10 sec) [ -14126.6159] [ 2609] [depth= 1] . ( 11 sec) [ -14126.0965] [ 2610] [depth= 2] . ( 11 sec) [ -14119.3328] [ 2608] [depth= 2] . ( 11 sec) [ -14112.0792] [ 2607] [depth= 3] . ( 12 sec) [ -14110.6224] [ 2606] [depth= 1] . ( 12 sec) [ -14110.3995] [ 2609] [depth= 1] . ( 12 sec) [ -14109.7231] [ 2606] [depth= 1] . ( 14 sec) [ -14038.4990] [Branch lengths ] . ( 14 sec) [ -14035.1320] [Ts/ts ratio ][ 4.720125] . ( 15 sec) [ -14034.0576] [ 2604] [depth= 1] . ( 16 sec) [ -14034.0017] [ 2604] [depth= 1] . ( 16 sec) [ -14033.9817] [ 2604] [depth= 1] . ( 17 sec) [ -14033.9487] [ 2604] [depth= 1] . ( 17 sec) [ -14033.7124] [ 2604] [depth= 1] . ( 19 sec) [ -14033.0927] [ 2603] [depth= 1] . ( 23 sec) [ -14032.4381] [ 2601] [depth= 1] . ( 28 sec) [ -14022.2270] [Branch lengths ] . ( 28 sec) [ -14022.0412] [Ts/ts ratio ][ 4.844286] . ( 42 sec) [ -14020.8213] [Branch lengths ] . ( 85 sec) [ -14020.4666] [ 2614] [depth= 4] . ( 106 sec) [ -14019.6660] [Branch lengths ] . ( 106 sec) [ -14019.6411] [Ts/ts ratio ][ 4.892054] . ( 169 sec) [ -14019.5892] [Branch lengths ] . ( 169 sec) [ -14019.5892] [Topology ] . ( 171 sec) [ -14019.4270] [Topology ] . ( 173 sec) [ -14019.4115] [Topology ] . ( 175 sec) [ -14019.4101] [Topology ] . ( 176 sec) [ -14019.4099] [Topology ] . ( 177 sec) [ -14019.4091] [Ts/ts ratio ][ 4.899333] . ( 177 sec) [ -14019.4091] [Topology ] . ( 178 sec) [ -14019.4090] [Topology ] . ( 179 sec) [ -14019.4090] [Ts/ts ratio ][ 4.899333] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14019.408998. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 79.892098 1.000000 0.112198 67 7.361341 0.773000 0.039194 100 142.626543 1.000000 0.148859 62 3.239818 0.657000 0.026672 98 72.866405 0.999000 0.095501 42 2.854736 0.425000 0.014967 100 162.875662 1.000000 0.090237 100 44.247026 0.990000 0.045328 100 42.666779 0.996000 0.052166 85 11.609317 0.865000 0.014777 56 5.124054 0.654000 0.008613 66 8.668283 0.856000 0.007374 100 120.857528 1.000000 0.030284 51 2.129549 0.255000 0.006302 95 13.754738 0.905000 0.010942 100 100.378328 1.000000 0.025536 97 17.965978 0.937000 0.011110 94 27.209345 0.961000 0.012101 90 21.639235 0.963000 0.018838 34 2.665001 0.717000 0.006866 21 2.570705 0.481000 0.006591 27 11.542450 0.880000 0.011624 100 87.342270 1.000000 0.034488 54 2.373465 0.592000 0.005362 100 46.483735 0.991000 0.027502 18 2.668960 0.529000 0.005301 100 84.277134 0.999000 0.036691 100 17.508105 0.918000 0.006558 97 23.399746 0.945000 0.009553 100 46.001766 0.985000 0.012511 79 4.422940 0.789000 0.002242 98 26.517898 0.955000 0.005821 99 28.055349 0.967000 0.009176 51 0.351275 0.090000 0.000773 100 104.994400 0.998000 0.014644 32 -1.000000 0.000000 0.000000 96 38.466046 0.980000 0.016569 100 149.766498 1.000000 0.043408 97 24.730824 0.954000 0.012105 38 4.762829 0.451000 0.004104 42 7.608117 0.833000 0.006998 100 139.794064 1.000000 0.038433 100 65.288219 0.999000 0.023576 100 16.376015 0.934000 0.009230 47 2.072277 0.731000 0.001921 59 9.364434 0.874000 0.006870 100 172.513266 1.000000 0.048008 100 44.429009 0.987000 0.019911 98 18.995310 0.937000 0.008704 100 78.620440 0.994000 0.014178 . Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'... . Time used 3h26m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo