.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_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 . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -5607.7521] [GTR parameters ] . ( 3 sec) [ -5527.3790] [Alpha ][ 0.500960] . ( 3 sec) [ -5525.4341] [ 850] [depth= 1] . ( 3 sec) [ -5523.1508] [ 853] [depth= 1] . ( 3 sec) [ -5519.7480] [ 850] [depth= 1] . ( 3 sec) [ -5507.5690] [ 851] [depth= 1] . ( 3 sec) [ -5504.6039] [ 850] [depth= 1] . ( 4 sec) [ -5504.2033] [ 851] [depth= 1] . ( 4 sec) [ -5499.4790] [ 853] [depth= 2] . ( 4 sec) [ -5496.3204] [ 853] [depth= 1] . ( 4 sec) [ -5494.9652] [ 853] [depth= 1] . ( 4 sec) [ -5491.9958] [ 853] [depth= 1] . ( 4 sec) [ -5491.9336] [ 854] [depth= 1] . ( 4 sec) [ -5491.5124] [ 853] [depth= 1] . ( 5 sec) [ -5484.3297] [ 850] [depth= 2] . ( 5 sec) [ -5484.0153] [ 854] [depth= 1] . ( 5 sec) [ -5483.7437] [ 852] [depth= 3] . ( 5 sec) [ -5482.7273] [ 852] [depth= 1] . ( 5 sec) [ -5476.9810] [ 853] [depth= 1] . ( 5 sec) [ -5476.1077] [ 856] [depth= 1] . ( 6 sec) [ -5475.9828] [ 856] [depth= 1] . ( 6 sec) [ -5475.6959] [ 856] [depth= 1] . ( 6 sec) [ -5475.6531] [ 856] [depth= 1] . ( 6 sec) [ -5475.6184] [ 856] [depth= 1] . ( 6 sec) [ -5472.8772] [ 856] [depth= 7] . ( 6 sec) [ -5471.5922] [ 856] [depth= 1] . ( 6 sec) [ -5470.8353] [ 856] [depth= 1] . ( 6 sec) [ -5470.4251] [ 856] [depth= 1] . ( 7 sec) [ -5470.2628] [ 856] [depth= 1] . ( 7 sec) [ -5470.2514] [ 856] [depth= 1] . ( 7 sec) [ -5470.0594] [ 856] [depth= 1] . ( 7 sec) [ -5469.7286] [ 856] [depth= 1] . ( 7 sec) [ -5469.3775] [ 856] [depth= 2] . ( 7 sec) [ -5469.2834] [ 856] [depth= 2] . ( 7 sec) [ -5469.2086] [ 856] [depth= 2] . ( 8 sec) [ -5442.1144] [Branch lengths ] . ( 9 sec) [ -5440.8970] [GTR parameters ] . ( 9 sec) [ -5399.8619] [Alpha ][ 0.250961] . ( 9 sec) [ -5399.6744] [ 856] [depth= 1] . ( 9 sec) [ -5398.5605] [ 853] [depth= 1] . ( 9 sec) [ -5397.7832] [ 853] [depth= 1] . ( 9 sec) [ -5394.5503] [ 849] [depth= 2] . ( 10 sec) [ -5394.3475] [ 851] [depth= 1] . ( 11 sec) [ -5394.0742] [ 851] [depth= 1] . ( 12 sec) [ -5393.1795] [ 851] [depth= 7] . ( 12 sec) [ -5393.1435] [ 851] [depth= 1] . ( 13 sec) [ -5393.1125] [ 851] [depth= 1] . ( 14 sec) [ -5388.3440] [Branch lengths ] . ( 15 sec) [ -5387.5167] [GTR parameters ] . ( 15 sec) [ -5387.3715] [Alpha ][ 0.241643] . ( 20 sec) [ -5386.9382] [Branch lengths ] . ( 23 sec) [ -5385.2478] [ 854] [depth= 9] . ( 48 sec) [ -5385.2227] [ 854] [depth= 1] . ( 57 sec) [ -5382.8930] [Branch lengths ] . ( 59 sec) [ -5382.6673] [GTR parameters ] . ( 59 sec) [ -5382.6555] [Alpha ][ 0.239178] . ( 94 sec) [ -5382.3816] [Branch lengths ] . ( 94 sec) [ -5382.3816] [Topology ] . ( 95 sec) [ -5382.3693] [Topology ] . ( 96 sec) [ -5382.3660] [Topology ] . ( 97 sec) [ -5382.3646] [Topology ] . ( 98 sec) [ -5382.3639] [Topology ] . ( 99 sec) [ -5382.3618] [GTR parameters ] . ( 99 sec) [ -5382.3616] [Alpha ][ 0.238879] . ( 99 sec) [ -5382.3616] [Topology ] . ( 100 sec) [ -5382.3611] [Topology ] . ( 100 sec) [ -5382.3611] [GTR parameters ] . ( 100 sec) [ -5382.3611] [Alpha ][ 0.238879] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.361105. . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Time used 0h1m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 103.02user 0.00system 1:46.55elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps