.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1382_9x1560_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... . 719 patterns found. (out of a total of 1560 sites) . 822 sites without polymorphism (52.69%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12292.3622] [ 1507] [depth= 2] . ( 1 sec) [ -12289.1883] [ 1503] [depth= 1] . ( 2 sec) [ -12261.1167] [ 1498] [depth= 2] . ( 2 sec) [ -12255.1677] [ 1491] [depth= 1] . ( 2 sec) [ -12253.9049] [ 1492] [depth= 1] . ( 3 sec) [ -12253.3564] [ 1491] [depth= 1] . ( 5 sec) [ -12236.1455] [Branch lengths ] . ( 9 sec) [ -12235.3333] [Branch lengths ] . ( 9 sec) [ -12235.3333] [Topology ] . ( 10 sec) [ -12235.2944] [Topology ] . ( 11 sec) [ -12235.2855] [Topology ] . ( 12 sec) [ -12235.2824] [Topology ] . ( 13 sec) [ -12235.2813] [Topology ] . ( 14 sec) [ -12235.2809] [Topology ] . ( 14 sec) [ -12235.2809] [Topology ] . ( 15 sec) [ -12235.2807] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12235.280736. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 485.248568 1.000000 0.229847 57 13.052533 0.635000 0.038020 61 19.926490 0.906000 0.019419 64 44.020101 0.993000 0.027488 66 36.121391 0.872000 0.029711 41 4.606724 0.381000 0.012054 . Printing the most likely tree in file 'proteic_M1382_9x1560_2003.phy_phyml_tree.txt'... . Time used 0h39m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo