.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2696_50x1472_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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1472 sites) . 982 sites without polymorphism (66.71%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -6200.7052] [GTR parameters ] . ( 2 sec) [ -6200.4585] [Alpha ][ 0.888648] . ( 13 sec) [ -6195.9714] [ 694] [depth= 1] . ( 13 sec) [ -6194.9058] [ 694] [depth= 2] . ( 14 sec) [ -6194.2719] [ 694] [depth= 1] . ( 14 sec) [ -6191.7026] [ 689] [depth= 2] . ( 23 sec) [ -6191.6456] [ 689] [depth= 1] . ( 24 sec) [ -6191.1332] [ 689] [depth= 1] . ( 25 sec) [ -6187.2019] [ 688] [depth= 1] . ( 25 sec) [ -6186.5973] [ 688] [depth= 1] . ( 25 sec) [ -6186.5564] [ 688] [depth= 1] . ( 25 sec) [ -6186.4915] [ 688] [depth= 1] . ( 26 sec) [ -6186.4566] [ 688] [depth= 1] . ( 28 sec) [ -6186.2611] [ 688] [depth= 1] . ( 29 sec) [ -6186.0197] [ 688] [depth= 1] . ( 29 sec) [ -6186.0009] [ 688] [depth= 1] . ( 35 sec) [ -6185.2512] [ 688] [depth= 1] . ( 35 sec) [ -6185.2308] [ 688] [depth= 1] . ( 35 sec) [ -6185.2025] [ 688] [depth= 1] . ( 35 sec) [ -6185.1748] [ 688] [depth= 1] . ( 36 sec) [ -6185.0588] [ 688] [depth= 1] . ( 36 sec) [ -6184.9805] [ 688] [depth= 1] . ( 36 sec) [ -6183.1945] [ 688] [depth= 1] . ( 38 sec) [ -6182.9011] [ 688] [depth= 1] . ( 38 sec) [ -6179.7585] [ 688] [depth= 1] . ( 46 sec) [ -6178.7250] [ 688] [depth= 1] . ( 46 sec) [ -6178.6783] [ 688] [depth= 1] . ( 57 sec) [ -6178.6440] [ 688] [depth= 1] . ( 73 sec) [ -6178.6081] [ 688] [depth= 1] . ( 73 sec) [ -6177.9620] [ 688] [depth= 1] . ( 73 sec) [ -6177.8896] [ 688] [depth= 1] . ( 73 sec) [ -6177.2200] [ 688] [depth= 1] . ( 74 sec) [ -6171.3743] [ 687] [depth= 2] . ( 77 sec) [ -6171.0396] [ 687] [depth= 3] . ( 77 sec) [ -6170.9276] [ 687] [depth= 3] . ( 77 sec) [ -6170.9170] [ 687] [depth= 2] . ( 77 sec) [ -6170.8169] [ 687] [depth= 3] . ( 79 sec) [ -6170.7633] [ 687] [depth= 2] . ( 79 sec) [ -6170.7197] [ 687] [depth= 1] . ( 79 sec) [ -6170.6773] [ 687] [depth= 2] . ( 86 sec) [ -6165.5609] [Branch lengths ] . ( 87 sec) [ -6165.5176] [GTR parameters ] . ( 87 sec) [ -6165.4624] [Alpha ][ 0.937895] . ( 205 sec) [ -6165.3852] [Branch lengths ] . ( 257 sec) [ -6165.3848] [Branch lengths ] . ( 257 sec) [ -6165.3848] [Topology ] . ( 258 sec) [ -6165.3848] [Topology ] . ( 259 sec) [ -6165.3846] [GTR parameters ] . ( 259 sec) [ -6165.3846] [Alpha ][ 0.938833] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.384557. . Printing the most likely tree in file 'nucleic_M2696_50x1472_2006.phy_phyml_tree.txt'... . Time used 0h4m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 266.74user 0.00system 4:28.36elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps