.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2304_31x429_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 35 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 305 patterns found. (out of a total of 429 sites) . 122 sites without polymorphism (28.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -5525.2178] [Alpha ][ 1.019870] . ( 0 sec) [ -5525.2178] [Topology ] . ( 3 sec) [ -5509.1416] [Topology ] . ( 6 sec) [ -5506.8771] [Topology ] . ( 9 sec) [ -5506.3210] [Topology ] . ( 11 sec) [ -5506.1448] [Topology ] . ( 14 sec) [ -5506.0815] [Topology ] . ( 16 sec) [ -5506.0573] [Topology ] . ( 19 sec) [ -5506.0478] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -5506.0474] [Alpha ][ 1.016286] . ( 34 sec) [ -5506.0474] [Topology ] . ( 37 sec) [ -5506.0435] [Topology ] . ( 39 sec) [ -5506.0420] [Topology ] . ( 41 sec) [ -5506.0414] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -5506.0414] [Alpha ][ 1.017303] . ( 57 sec) [ -5506.0414] [Topology ] . ( 60 sec) [ -5506.0411] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 90 sec) [ -5525.2178] [Alpha ][ 1.019870] . ( 92 sec) [ -5523.7723] [ 799] [depth= 1] . ( 92 sec) [ -5518.4228] [ 794] [depth= 1] . ( 95 sec) [ -5517.8227] [ 795] [depth= 1] . ( 96 sec) [ -5517.6086] [ 794] [depth= 1] . ( 97 sec) [ -5517.0146] [ 794] [depth= 1] . ( 98 sec) [ -5516.7583] [ 794] [depth= 1] . ( 98 sec) [ -5514.9515] [ 794] [depth= 1] . ( 107 sec) [ -5514.9117] [ 794] [depth= 1] . ( 110 sec) [ -5514.7584] [ 794] [depth= 1] . ( 142 sec) [ -5514.1524] [ 794] [depth= 1] . ( 143 sec) [ -5513.7654] [ 794] [depth= 1] . ( 145 sec) [ -5513.6489] [ 794] [depth= 2] . ( 147 sec) [ -5513.5736] [ 794] [depth= 1] . ( 153 sec) [ -5513.3028] [ 794] [depth= 1] . ( 153 sec) [ -5512.9288] [ 794] [depth= 1] . ( 155 sec) [ -5512.9169] [ 794] [depth= 2] . ( 155 sec) [ -5507.5579] [Branch lengths ] . ( 156 sec) [ -5507.5577] [Alpha ][ 1.017255] . ( 160 sec) [ -5506.6049] [ 795] [depth= 1] . ( 239 sec) [ -5506.0668] [Branch lengths ] . ( 240 sec) [ -5506.0668] [Alpha ][ 1.018272] . ( 324 sec) [ -5506.0415] [Branch lengths ] . ( 324 sec) [ -5506.0415] [Topology ] . ( 327 sec) [ -5506.0411] [Topology ] . ( 327 sec) [ -5506.0410] [Alpha ][ 1.016884] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5506.041091 . Log likelihood obtained after SPR moves : -5506.041042 . Log likelihood of the current tree: -5506.041042. . Printing the most likely tree in file 'proteic_M2304_31x429_2005.phy_phyml_tree.txt'... . Time used 0h5m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 340.22user 0.00system 5:42.83elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps