.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1991_32x129_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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 9 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 113 patterns found. (out of a total of 129 sites) . 25 sites without polymorphism (19.38%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 0 sec) [ -2494.7867] [ 428] [depth= 1] . ( 0 sec) [ -2494.7532] [ 428] [depth= 1] . ( 0 sec) [ -2494.6570] [ 428] [depth= 1] . ( 1 sec) [ -2492.7817] [ 428] [depth= 1] . ( 1 sec) [ -2478.1770] [ 425] [depth= 2] . ( 1 sec) [ -2478.0286] [ 425] [depth= 1] . ( 1 sec) [ -2472.2849] [ 424] [depth= 1] . ( 2 sec) [ -2467.8608] [ 423] [depth= 1] . ( 2 sec) [ -2466.7332] [ 423] [depth= 1] . ( 2 sec) [ -2466.1534] [ 424] [depth= 1] . ( 3 sec) [ -2465.3705] [ 424] [depth= 2] . ( 3 sec) [ -2462.3314] [ 421] [depth= 1] . ( 3 sec) [ -2418.8571] [ 422] [depth= 1] . ( 4 sec) [ -2418.5786] [ 421] [depth= 1] . ( 5 sec) [ -2417.6442] [ 421] [depth= 1] . ( 6 sec) [ -2415.6942] [ 419] [depth= 1] . ( 6 sec) [ -2412.1650] [ 417] [depth= 1] . ( 6 sec) [ -2410.5892] [ 418] [depth= 2] . ( 6 sec) [ -2410.1065] [ 419] [depth= 1] . ( 7 sec) [ -2409.5098] [ 418] [depth= 1] . ( 8 sec) [ -2407.1663] [ 418] [depth= 3] . ( 8 sec) [ -2407.0469] [ 418] [depth= 1] . ( 9 sec) [ -2406.5871] [ 418] [depth= 1] . ( 9 sec) [ -2406.5017] [ 418] [depth= 1] . ( 10 sec) [ -2393.2587] [Branch lengths ] . ( 10 sec) [ -2391.8650] [Alpha ][ 1.301684] . ( 13 sec) [ -2391.7857] [ 419] [depth= 1] . ( 13 sec) [ -2391.7054] [ 419] [depth= 1] . ( 14 sec) [ -2391.1798] [ 418] [depth= 1] . ( 15 sec) [ -2390.6670] [ 416] [depth= 1] . ( 18 sec) [ -2389.4108] [Branch lengths ] . ( 18 sec) [ -2389.3972] [Alpha ][ 1.261574] . ( 21 sec) [ -2389.3645] [ 415] [depth= 1] . ( 26 sec) [ -2389.3365] [Branch lengths ] . ( 26 sec) [ -2389.3362] [Alpha ][ 1.267170] . ( 26 sec) [ -2389.3362] [Topology ] . ( 27 sec) [ -2389.3300] [Topology ] . ( 28 sec) [ -2389.3275] [Topology ] . ( 30 sec) [ -2389.3260] [Topology ] . ( 31 sec) [ -2389.3251] [Topology ] . ( 31 sec) [ -2389.3250] [Alpha ][ 1.270642] . ( 31 sec) [ -2389.3250] [Topology ] . ( 32 sec) [ -2389.3244] [Topology ] . ( 32 sec) [ -2389.3244] [Alpha ][ 1.271912] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -2389.3243] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2389.324285. . Printing the most likely tree in file 'proteic_M1991_32x129_2004.phy_phyml_tree.txt'... . Time used 0h0m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 45.70user 0.00system 0:57.72elapsed 79%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps