.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1384_11x391_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... . 195 patterns found. (out of a total of 391 sites) . 216 sites without polymorphism (55.24%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -2867.8537] [ 341] [depth= 1] . ( 5 sec) [ -2866.1392] [ 341] [depth= 1] . ( 5 sec) [ -2865.2694] [ 340] [depth= 1] . ( 5 sec) [ -2863.6668] [ 340] [depth= 1] . ( 9 sec) [ -2863.6249] [ 340] [depth= 1] . ( 10 sec) [ -2858.9668] [Branch lengths ] . ( 15 sec) [ -2858.9213] [ 340] [depth= 1] . ( 22 sec) [ -2858.5611] [Branch lengths ] . ( 22 sec) [ -2858.5611] [Topology ] . ( 22 sec) [ -2858.5483] [Topology ] . ( 23 sec) [ -2858.5462] [Topology ] . ( 23 sec) [ -2858.5457] [Topology ] . ( 23 sec) [ -2858.5457] [Topology ] . ( 24 sec) [ -2858.5455] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2858.545546. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 40.089403 0.991000 0.114532 87 15.187203 0.913000 0.060680 57 4.870854 0.592000 0.022643 32 8.540829 0.861000 0.010689 28 3.299512 0.751000 0.004572 56 15.762716 0.906000 0.010675 29 3.228012 0.614000 0.002710 23 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'proteic_M1384_11x391_2003.phy_phyml_tree.txt'... . Time used 0h36m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo