.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1373_23x392_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... . 206 patterns found. (out of a total of 392 sites) . 200 sites without polymorphism (51.02%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -3521.8854] [ 459] [depth= 1] . ( 4 sec) [ -3520.6054] [ 455] [depth= 8] . ( 8 sec) [ -3515.5397] [ 456] [depth= 1] . ( 8 sec) [ -3513.8551] [ 456] [depth= 1] . ( 10 sec) [ -3510.6035] [ 455] [depth= 2] . ( 25 sec) [ -3509.9361] [ 455] [depth= 1] . ( 30 sec) [ -3509.7386] [ 455] [depth= 1] . ( 42 sec) [ -3509.4923] [ 455] [depth= 1] . ( 45 sec) [ -3509.4773] [ 455] [depth= 1] . ( 50 sec) [ -3509.3895] [ 455] [depth= 1] . ( 53 sec) [ -3509.3766] [ 455] [depth= 1] . ( 64 sec) [ -3503.5334] [Branch lengths ] . ( 65 sec) [ -3503.1938] [ 453] [depth= 8] . ( 69 sec) [ -3502.9461] [ 455] [depth= 5] . ( 73 sec) [ -3501.9861] [ 453] [depth= 5] . ( 91 sec) [ -3501.8039] [ 453] [depth= 1] . ( 92 sec) [ -3501.7929] [ 453] [depth= 1] . ( 140 sec) [ -3500.9135] [Branch lengths ] . ( 154 sec) [ -3499.3569] [ 455] [depth= 5] . ( 196 sec) [ -3499.3346] [ 455] [depth= 1] . ( 222 sec) [ -3499.2237] [Branch lengths ] . ( 306 sec) [ -3499.2191] [Branch lengths ] . ( 306 sec) [ -3499.2191] [Topology ] . ( 307 sec) [ -3499.2188] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3499.218836. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 81 11.109608 0.887000 0.041094 99 53.430070 0.992000 0.080651 89 17.596920 0.962000 0.045630 43 3.428814 0.761000 0.015283 22 8.537251 0.781000 0.009689 12 6.923045 0.748000 0.003754 19 6.594434 0.748000 0.003687 3 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 11 5.262666 0.682000 0.003429 86 26.487727 0.936000 0.013364 4 13.541414 0.859000 0.002713 33 3.453467 0.476000 0.002701 2 -1.000000 0.000000 0.000000 12 6.627530 0.791000 0.002700 74 22.943578 0.940000 0.033061 100 43.226491 0.989000 0.047040 31 -1.000000 0.000000 0.000000 37 10.012712 0.855000 0.002702 18 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'proteic_M1373_23x392_2003.phy_phyml_tree.txt'... . Time used 5h13m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo