.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2640_18x243_2006.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... . 160 patterns found. (out of a total of 243 sites) . 99 sites without polymorphism (40.74%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2510.4732] [ 328] [depth= 1] . ( 1 sec) [ -2510.4294] [ 328] [depth= 1] . ( 13 sec) [ -2504.6533] [Branch lengths ] . ( 26 sec) [ -2504.5713] [Branch lengths ] . ( 26 sec) [ -2504.5713] [Topology ] . ( 26 sec) [ -2504.5699] [Topology ] . ( 27 sec) [ -2504.5696] [Topology ] . ( 27 sec) [ -2504.5696] [Topology ] . ( 28 sec) [ -2504.5696] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2504.569560. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 96 48.164780 0.985000 0.062452 100 43.386243 0.981000 0.055336 81 15.854584 0.917000 0.027446 65 7.773046 0.716000 0.016884 100 27.248473 0.952000 0.032383 52 4.555848 0.538000 0.012218 97 48.259785 0.991000 0.045414 96 5.923463 0.826000 0.011744 86 17.648587 0.931000 0.025691 100 63.931390 0.996000 0.057811 99 34.649712 0.973000 0.035159 64 -1.000000 0.000000 0.000000 89 8.777701 0.882000 0.014341 54 3.140329 0.424000 0.010644 81 17.198417 0.919000 0.018557 . Printing the most likely tree in file 'proteic_M2640_18x243_2006.phy_phyml_tree.txt'... . Time used 0h48m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo