.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1989_18x173_2004.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 7 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 139 patterns found. (out of a total of 173 sites) . 46 sites without polymorphism (26.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 0 sec) [ -3205.9405] [Topology ] . ( 1 sec) [ -3185.8438] [Topology ] . ( 2 sec) [ -3182.6057] [Topology ] . ( 2 sec) [ -3180.8613] [Topology ] . ( 3 sec) [ -3180.4036] [Topology ] . ( 4 sec) [ -3180.3247] [Topology ] . ( 5 sec) [ -3180.2902] [Topology ] . ( 6 sec) [ -3180.2719] [Topology ] . ( 7 sec) [ -3180.2615] [Topology ] . ( 7 sec) [ -3180.2554] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -3179.9529] [Alpha ][ 0.791776] . ( 12 sec) [ -3179.9529] [Topology ] . ( 12 sec) [ -3179.9261] [Topology ] . ( 13 sec) [ -3179.9145] [Topology ] . ( 13 sec) [ -3179.9081] [Topology ] . ( 14 sec) [ -3179.9046] [Topology ] . ( 14 sec) [ -3179.9026] [Topology ] . ( 15 sec) [ -3179.9014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -3179.8991] [Alpha ][ 0.798974] . ( 19 sec) [ -3179.8991] [Topology ] . ( 20 sec) [ -3179.8981] [Topology ] . ( 21 sec) [ -3179.8975] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -3179.8975] [Alpha ][ 0.799773] . ( 28 sec) [ -3179.8975] [Topology ] . ( 29 sec) [ -3179.8971] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897122. . Printing the most likely tree in file 'proteic_M1989_18x173_2004.phy_phyml_tree.txt'... . Time used 0h0m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 31.27user 0.00system 0:38.17elapsed 81%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps