.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1383_11x1561_2003.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... . 753 patterns found. (out of a total of 1561 sites) . 798 sites without polymorphism (51.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 17Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13668.1351] [ 1759] [depth= 5] . ( 2 sec) [ -13635.1571] [ 1756] [depth= 4] . ( 3 sec) [ -13634.6695] [ 1754] [depth= 1] . ( 4 sec) [ -13631.4597] [ 1756] [depth= 1] . ( 4 sec) [ -13623.2993] [ 1754] [depth= 1] . ( 5 sec) [ -13619.3364] [ 1752] [depth= 4] . ( 6 sec) [ -13615.3982] [ 1748] [depth= 1] . ( 7 sec) [ -13613.7128] [ 1753] [depth= 2] . ( 7 sec) [ -13613.3049] [ 1753] [depth= 1] . ( 8 sec) [ -13594.9388] [Branch lengths ] . ( 11 sec) [ -13593.8723] [ 1758] [depth= 2] . ( 23 sec) [ -13592.7271] [Branch lengths ] . ( 41 sec) [ -13592.6767] [Branch lengths ] . ( 42 sec) [ -13592.6767] [Topology ] . ( 43 sec) [ -13592.6720] [Topology ] . ( 44 sec) [ -13592.6707] [Topology ] . ( 46 sec) [ -13592.6702] [Topology ] . ( 46 sec) [ -13592.6702] [Topology ] . ( 47 sec) [ -13592.6700] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13592.670034. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 507.395493 1.000000 0.239105 39 34.448087 0.981000 0.041448 10 5.620036 0.420000 0.010202 71 42.465125 0.991000 0.025647 72 62.893789 0.979000 0.033404 11 11.877060 0.708000 0.013329 57 8.024449 0.715000 0.010789 20 0.284322 0.009000 0.010274 . Printing the most likely tree in file 'proteic_M1383_11x1561_2003.phy_phyml_tree.txt'... . Time used 1h12m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo