.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2638_18x378_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... . 75 patterns found. (out of a total of 378 sites) . 321 sites without polymorphism (84.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -1688.2708] [ 82] [depth= 1] . ( 6 sec) [ -1687.6180] [ 82] [depth= 1] . ( 9 sec) [ -1687.2898] [ 81] [depth= 3] . ( 10 sec) [ -1685.4621] [ 81] [depth= 2] . ( 11 sec) [ -1684.1127] [ 81] [depth= 1] . ( 14 sec) [ -1683.9495] [ 81] [depth= 3] . ( 14 sec) [ -1683.8562] [ 81] [depth= 2] . ( 15 sec) [ -1683.8415] [ 81] [depth= 2] . ( 20 sec) [ -1682.9347] [Branch lengths ] . ( 44 sec) [ -1682.9255] [Branch lengths ] . ( 44 sec) [ -1682.9255] [Topology ] . ( 45 sec) [ -1682.9254] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1682.925414. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 98 34.952822 0.958000 0.015735 89 25.840365 0.946000 0.013146 93 25.117694 0.950000 0.015225 44 14.552771 0.921000 0.010299 1 -1.000000 0.000000 0.000000 16 9.438844 0.843000 0.005615 46 4.136921 0.404000 0.005513 64 3.951839 0.740000 0.002821 98 54.407017 0.965000 0.016159 77 5.398881 0.777000 0.002675 54 1.787833 0.758000 0.002482 10 -1.000000 0.000000 0.000000 78 8.391989 0.761000 0.002698 1 -1.000000 0.000000 0.000000 99 60.748100 0.993000 0.016528 . Printing the most likely tree in file 'proteic_M2638_18x378_2006.phy_phyml_tree.txt'... . Time used 1h20m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo