.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2479_30x627_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 521 patterns found. (out of a total of 627 sites) . 123 sites without polymorphism (19.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 37Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18035.2389] [ 3274] [depth= 1] . ( 3 sec) [ -18034.9431] [ 3272] [depth= 1] . ( 7 sec) [ -18032.2996] [ 3277] [depth= 1] . ( 9 sec) [ -18030.9925] [ 3272] [depth= 1] . ( 14 sec) [ -18029.5046] [ 3274] [depth= 1] . ( 15 sec) [ -18026.8629] [ 3273] [depth= 1] . ( 16 sec) [ -18026.8067] [ 3273] [depth= 1] . ( 16 sec) [ -18025.9751] [ 3274] [depth= 1] . ( 17 sec) [ -18023.5495] [ 3273] [depth= 1] . ( 20 sec) [ -18023.1390] [ 3277] [depth= 2] . ( 21 sec) [ -18012.9612] [ 3269] [depth= 2] . ( 22 sec) [ -18011.5166] [ 3274] [depth= 1] . ( 25 sec) [ -18009.9800] [ 3278] [depth= 1] . ( 25 sec) [ -18004.3735] [ 3271] [depth= 2] . ( 26 sec) [ -17997.3330] [ 3272] [depth= 1] . ( 26 sec) [ -17983.7362] [ 3267] [depth= 3] . ( 27 sec) [ -17975.3653] [ 3265] [depth= 1] . ( 29 sec) [ -17974.9520] [ 3273] [depth= 1] . ( 31 sec) [ -17974.7169] [ 3268] [depth= 1] . ( 35 sec) [ -17940.6261] [Branch lengths ] . ( 37 sec) [ -17940.4353] [ 3265] [depth= 1] . ( 40 sec) [ -17940.1090] [ 3262] [depth= 1] . ( 49 sec) [ -17939.9551] [ 3263] [depth= 1] . ( 56 sec) [ -17938.8797] [ 3263] [depth= 4] . ( 60 sec) [ -17938.2283] [ 3263] [depth= 1] . ( 61 sec) [ -17934.2825] [ 3265] [depth= 2] . ( 67 sec) [ -17933.8900] [ 3267] [depth= 1] . ( 81 sec) [ -17926.8495] [Branch lengths ] . ( 133 sec) [ -17926.5987] [Branch lengths ] . ( 133 sec) [ -17926.5987] [Topology ] . ( 136 sec) [ -17926.5927] [Topology ] . ( 139 sec) [ -17926.5916] [Topology ] . ( 142 sec) [ -17926.5911] [Topology ] . ( 142 sec) [ -17926.5911] [Topology ] . ( 145 sec) [ -17926.5909] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -17926.590910. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 95 39.822350 0.980000 0.047574 63 6.443117 0.530000 0.037638 100 54.773490 0.991000 0.065788 100 128.463264 1.000000 0.120503 48 2.455214 0.166000 0.025280 100 66.278495 0.997000 0.074815 100 81.950763 0.999000 0.097351 45 14.331389 0.852000 0.037529 10 1.056851 0.112000 0.016958 86 44.560983 0.991000 0.081166 23 12.510840 0.889000 0.026417 54 15.257858 0.844000 0.033752 98 74.240100 0.997000 0.085632 99 43.536520 0.983000 0.067863 35 0.043750 0.000000 0.018596 33 25.779285 0.949000 0.038705 63 6.012261 0.634000 0.034339 6 5.954052 0.725000 0.020901 84 32.415109 0.966000 0.046732 100 141.765437 1.000000 0.108584 100 63.024482 0.997000 0.041340 46 2.645415 0.203000 0.019327 52 3.106701 0.257000 0.022320 100 116.920702 0.999000 0.087014 77 20.398351 0.923000 0.038549 82 11.229520 0.691000 0.026607 27 10.543502 0.868000 0.026812 . Printing the most likely tree in file 'proteic_M2479_30x627_2005.phy_phyml_tree.txt'... . Time used 4h29m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo