.......................... 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 : 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 . 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 NNI moves)... . ( 1 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 1 sec) [ -2496.1543] [Topology ] . ( 2 sec) [ -2426.2101] [Topology ] . ( 3 sec) [ -2408.7866] [Topology ] . ( 4 sec) [ -2399.9867] [Topology ] . ( 5 sec) [ -2397.8601] [Topology ] . ( 6 sec) [ -2397.4479] [Topology ] . ( 7 sec) [ -2397.3036] [Topology ] . ( 8 sec) [ -2397.2430] [Topology ] . ( 9 sec) [ -2397.2138] [Topology ] . ( 10 sec) [ -2397.1983] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -2395.8503] [Topology ] . ( 17 sec) [ -2394.5012] [Alpha ][ 1.313066] . ( 18 sec) [ -2394.5012] [Topology ] . ( 19 sec) [ -2394.4118] [Topology ] . ( 20 sec) [ -2394.3864] [Topology ] . ( 20 sec) [ -2394.3757] [Topology ] . ( 21 sec) [ -2394.3709] [Topology ] . ( 22 sec) [ -2394.3686] [Topology ] . ( 23 sec) [ -2394.3674] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -2394.1201] [Topology ] . ( 31 sec) [ -2394.1162] [Alpha ][ 1.291508] . ( 31 sec) [ -2394.1162] [Topology ] . ( 32 sec) [ -2394.1143] [Topology ] . ( 33 sec) [ -2394.1136] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -2394.1136] [Alpha ][ 1.289494] . ( 40 sec) [ -2394.1136] [Topology ] . ( 41 sec) [ -2394.1132] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 54 sec) [ -2496.1543] [Alpha ][ 1.825144] . ( 54 sec) [ -2494.7867] [ 428] [depth= 1] . ( 54 sec) [ -2494.7532] [ 428] [depth= 1] . ( 54 sec) [ -2494.6570] [ 428] [depth= 1] . ( 55 sec) [ -2492.7817] [ 428] [depth= 1] . ( 55 sec) [ -2478.1770] [ 425] [depth= 2] . ( 55 sec) [ -2478.0286] [ 425] [depth= 1] . ( 55 sec) [ -2472.2849] [ 424] [depth= 1] . ( 56 sec) [ -2467.8608] [ 423] [depth= 1] . ( 59 sec) [ -2467.8396] [ 424] [depth= 1] . ( 59 sec) [ -2466.6043] [ 424] [depth= 1] . ( 59 sec) [ -2466.5595] [ 423] [depth= 1] . ( 60 sec) [ -2466.0622] [ 423] [depth= 2] . ( 60 sec) [ -2464.9704] [ 424] [depth= 1] . ( 60 sec) [ -2464.9498] [ 424] [depth= 1] . ( 61 sec) [ -2461.7771] [ 421] [depth= 1] . ( 62 sec) [ -2418.2926] [ 422] [depth= 1] . ( 64 sec) [ -2418.0150] [ 421] [depth= 1] . ( 66 sec) [ -2416.6167] [ 425] [depth= 1] . ( 67 sec) [ -2415.7755] [ 425] [depth= 1] . ( 68 sec) [ -2415.4146] [ 422] [depth= 2] . ( 68 sec) [ -2412.8793] [ 427] [depth= 5] . ( 68 sec) [ -2412.5181] [ 430] [depth= 1] . ( 68 sec) [ -2410.3918] [ 428] [depth= 1] . ( 69 sec) [ -2408.9820] [ 431] [depth= 2] . ( 70 sec) [ -2408.0823] [ 428] [depth= 2] . ( 70 sec) [ -2407.4660] [ 429] [depth= 1] . ( 72 sec) [ -2405.1994] [ 428] [depth= 2] . ( 72 sec) [ -2405.1753] [ 427] [depth= 1] . ( 73 sec) [ -2402.6960] [ 425] [depth= 1] . ( 75 sec) [ -2402.1954] [ 424] [depth= 1] . ( 76 sec) [ -2401.8737] [ 424] [depth= 1] . ( 76 sec) [ -2399.8426] [ 424] [depth= 2] . ( 76 sec) [ -2399.6347] [ 424] [depth= 1] . ( 80 sec) [ -2399.3996] [ 424] [depth= 2] . ( 82 sec) [ -2390.3633] [Branch lengths ] . ( 83 sec) [ -2389.3200] [Alpha ][ 1.355713] . ( 99 sec) [ -2389.2749] [ 425] [depth= 1] . ( 101 sec) [ -2389.2330] [ 421] [depth= 2] . ( 101 sec) [ -2388.0985] [ 425] [depth= 2] . ( 113 sec) [ -2387.9053] [ 423] [depth= 4] . ( 116 sec) [ -2387.5581] [ 424] [depth= 1] . ( 120 sec) [ -2386.4682] [ 424] [depth= 2] . ( 121 sec) [ -2385.9907] [ 424] [depth= 2] . ( 122 sec) [ -2385.6290] [ 424] [depth= 2] . ( 123 sec) [ -2385.3606] [ 424] [depth= 2] . ( 123 sec) [ -2384.6288] [Branch lengths ] . ( 123 sec) [ -2384.6282] [Alpha ][ 1.346040] . ( 142 sec) [ -2384.6100] [ 427] [depth= 1] . ( 142 sec) [ -2384.5969] [ 424] [depth= 1] . ( 172 sec) [ -2384.4898] [Branch lengths ] . ( 172 sec) [ -2384.4898] [Alpha ][ 1.346040] . ( 172 sec) [ -2384.4898] [Topology ] . ( 173 sec) [ -2384.4753] [Topology ] . ( 174 sec) [ -2384.4686] [Topology ] . ( 175 sec) [ -2384.4652] [Topology ] . ( 176 sec) [ -2384.4635] [Topology ] . ( 177 sec) [ -2384.4626] [Topology ] . ( 178 sec) [ -2384.4625] [Alpha ][ 1.342407] . ( 178 sec) [ -2384.4625] [Topology ] . ( 179 sec) [ -2384.4620] [Topology ] . ( 179 sec) [ -2384.4620] [Alpha ][ 1.342407] . Checking for NNIs, optimizing five branches... . ( 186 sec) [ -2384.4617] [Topology ] . Checking for NNIs, optimizing five branches... . ( 192 sec) [ -2384.4616] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2394.113150 . Log likelihood obtained after SPR moves : -2384.461583 . Log likelihood of the current tree: -2384.461583. . Printing the most likely tree in file 'proteic_M1991_32x129_2004.phy_phyml_tree.txt'... . Time used 0h3m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 198.31user 0.00system 3:18.98elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps