.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2599_66x1137_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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 . Compressing sequences... . 131 patterns found. (out of a total of 1137 sites) . 1062 sites without polymorphism (93.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -2167.7777] [GTR parameters ] . ( 1 sec) [ -2167.7484] [Alpha ][ 0.762192] . ( 1 sec) [ -2167.7484] [Topology ] . ( 1 sec) [ -2164.8151] [Topology ] . ( 2 sec) [ -2164.1354] [Topology ] . ( 2 sec) [ -2163.7186] [Topology ] . ( 2 sec) [ -2163.5431] [Topology ] . ( 3 sec) [ -2163.5011] [Topology ] . ( 3 sec) [ -2163.4908] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5 sec) [ -2163.4906] [GTR parameters ] . ( 5 sec) [ -2163.4906] [Alpha ][ 0.759129] . ( 5 sec) [ -2163.4906] [Topology ] . ( 5 sec) [ -2163.4878] [Topology ] . ( 5 sec) [ -2163.4872] [Topology ] . Checking for NNIs, optimizing five branches... . ( 7 sec) [ -2163.4872] [GTR parameters ] . ( 7 sec) [ -2163.4872] [Alpha ][ 0.759129] . ( 7 sec) [ -2163.4872] [Topology ] . ( 7 sec) [ -2163.4870] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 11 sec) [ -2167.7777] [GTR parameters ] . ( 11 sec) [ -2167.7484] [Alpha ][ 0.762192] . ( 11 sec) [ -2167.5690] [ 80] [depth= 5] . ( 11 sec) [ -2167.5255] [ 80] [depth= 1] . ( 11 sec) [ -2167.4612] [ 80] [depth= 1] . ( 11 sec) [ -2167.4301] [ 80] [depth= 2] . ( 11 sec) [ -2167.3835] [ 80] [depth= 2] . ( 11 sec) [ -2167.2964] [ 80] [depth= 1] . ( 11 sec) [ -2167.2521] [ 80] [depth= 1] . ( 13 sec) [ -2167.2139] [ 80] [depth= 3] . ( 13 sec) [ -2167.1975] [ 80] [depth= 3] . ( 13 sec) [ -2167.1458] [ 80] [depth= 1] . ( 13 sec) [ -2166.6462] [ 80] [depth= 5] . ( 13 sec) [ -2166.6336] [ 80] [depth= 5] . ( 13 sec) [ -2166.5335] [ 80] [depth= 3] . ( 13 sec) [ -2166.5235] [ 80] [depth= 3] . ( 13 sec) [ -2166.5082] [ 80] [depth= 1] . ( 13 sec) [ -2166.4108] [ 80] [depth= 2] . ( 14 sec) [ -2165.9948] [ 80] [depth= 2] . ( 14 sec) [ -2165.9793] [ 80] [depth= 1] . ( 14 sec) [ -2165.8827] [ 80] [depth= 3] . ( 14 sec) [ -2165.7892] [ 80] [depth= 4] . ( 15 sec) [ -2165.6397] [ 80] [depth= 4] . ( 15 sec) [ -2165.6014] [ 80] [depth= 4] . ( 15 sec) [ -2165.5608] [ 80] [depth= 3] . ( 15 sec) [ -2165.5485] [ 80] [depth= 5] . ( 18 sec) [ -2165.5263] [ 80] [depth= 1] . ( 20 sec) [ -2165.4871] [ 80] [depth= 2] . ( 20 sec) [ -2165.4203] [ 80] [depth= 2] . ( 20 sec) [ -2165.3554] [ 80] [depth= 1] . ( 22 sec) [ -2165.3401] [ 80] [depth= 1] . ( 22 sec) [ -2164.9097] [ 80] [depth= 1] . ( 22 sec) [ -2164.8711] [ 80] [depth= 3] . ( 22 sec) [ -2164.8555] [ 80] [depth= 2] . ( 22 sec) [ -2164.8322] [ 80] [depth= 3] . ( 22 sec) [ -2164.7953] [ 80] [depth= 1] . ( 23 sec) [ -2164.7507] [ 80] [depth= 2] . ( 23 sec) [ -2164.7201] [ 80] [depth= 1] . ( 24 sec) [ -2164.6756] [ 80] [depth= 4] . ( 24 sec) [ -2164.5015] [ 80] [depth= 5] . ( 24 sec) [ -2164.4504] [ 80] [depth= 6] . ( 24 sec) [ -2164.3594] [ 80] [depth= 2] . ( 24 sec) [ -2164.1632] [ 80] [depth= 1] . ( 25 sec) [ -2164.0895] [ 80] [depth= 1] . ( 31 sec) [ -2163.8452] [ 80] [depth= 1] . ( 35 sec) [ -2163.7936] [ 80] [depth= 6] . ( 35 sec) [ -2163.7456] [ 80] [depth= 5] . ( 43 sec) [ -2163.4890] [Branch lengths ] . ( 43 sec) [ -2163.4889] [GTR parameters ] . ( 43 sec) [ -2163.4888] [Alpha ][ 0.759420] . ( 87 sec) [ -2163.4873] [Branch lengths ] . ( 105 sec) [ -2163.4873] [Branch lengths ] . ( 105 sec) [ -2163.4873] [Topology ] . ( 105 sec) [ -2163.4873] [Topology ] . ( 105 sec) [ -2163.4873] [GTR parameters ] . ( 105 sec) [ -2163.4873] [Alpha ][ 0.759420] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2163.487012 . Log likelihood obtained after SPR moves : -2163.487251 . Log likelihood of the current tree: -2163.487012. . Printing the most likely tree in file 'nucleic_M2599_66x1137_2006.phy_phyml_tree.txt'... . Time used 0h1m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 103.69user 0.00system 1:47.63elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps