.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2974_56x827_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 . Compressing sequences... . 330 patterns found. (out of a total of 827 sites) . 592 sites without polymorphism (71.58%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -5728.9072] [GTR parameters ] . ( 2 sec) [ -5606.6718] [Alpha ][ 0.500960] . ( 3 sec) [ -5604.1549] [ 870] [depth= 1] . ( 3 sec) [ -5603.7101] [ 873] [depth= 1] . ( 4 sec) [ -5602.5602] [ 873] [depth= 1] . ( 4 sec) [ -5602.5495] [ 873] [depth= 1] . ( 4 sec) [ -5602.1653] [ 873] [depth= 1] . ( 4 sec) [ -5601.1809] [ 873] [depth= 1] . ( 4 sec) [ -5596.0814] [ 873] [depth= 1] . ( 4 sec) [ -5588.1092] [ 872] [depth= 1] . ( 4 sec) [ -5586.4381] [ 873] [depth= 1] . ( 4 sec) [ -5578.9807] [ 870] [depth= 1] . ( 4 sec) [ -5573.6518] [ 873] [depth= 3] . ( 4 sec) [ -5571.2321] [ 874] [depth= 1] . ( 5 sec) [ -5565.9621] [ 873] [depth= 1] . ( 5 sec) [ -5564.0713] [ 873] [depth= 2] . ( 5 sec) [ -5562.6399] [ 870] [depth= 1] . ( 5 sec) [ -5553.6603] [ 867] [depth= 1] . ( 5 sec) [ -5552.7440] [ 870] [depth= 1] . ( 5 sec) [ -5552.4439] [ 870] [depth= 1] . ( 5 sec) [ -5551.1027] [ 871] [depth= 1] . ( 5 sec) [ -5549.8428] [ 870] [depth= 1] . ( 5 sec) [ -5549.6923] [ 870] [depth= 1] . ( 5 sec) [ -5546.1460] [ 869] [depth= 2] . ( 5 sec) [ -5545.4896] [ 869] [depth= 1] . ( 5 sec) [ -5543.9660] [ 869] [depth= 1] . ( 5 sec) [ -5543.9544] [ 869] [depth= 1] . ( 6 sec) [ -5543.9115] [ 869] [depth= 1] . ( 6 sec) [ -5542.3207] [ 870] [depth= 1] . ( 6 sec) [ -5540.4171] [ 869] [depth= 1] . ( 6 sec) [ -5539.8329] [ 870] [depth= 2] . ( 6 sec) [ -5538.0824] [ 870] [depth= 1] . ( 6 sec) [ -5536.9322] [ 870] [depth= 1] . ( 6 sec) [ -5535.8431] [ 870] [depth= 1] . ( 6 sec) [ -5535.6406] [ 869] [depth= 3] . ( 6 sec) [ -5533.2370] [ 868] [depth= 1] . ( 6 sec) [ -5532.7731] [ 869] [depth= 2] . ( 6 sec) [ -5532.7105] [ 869] [depth= 1] . ( 6 sec) [ -5532.6955] [ 869] [depth= 2] . ( 7 sec) [ -5493.7044] [Branch lengths ] . ( 8 sec) [ -5492.9840] [GTR parameters ] . ( 8 sec) [ -5405.5034] [Alpha ][ 0.250961] . ( 9 sec) [ -5402.9994] [ 866] [depth= 1] . ( 11 sec) [ -5402.9596] [ 867] [depth= 1] . ( 11 sec) [ -5402.8874] [ 867] [depth= 2] . ( 12 sec) [ -5400.2484] [Branch lengths ] . ( 13 sec) [ -5399.6176] [GTR parameters ] . ( 14 sec) [ -5384.6010] [Alpha ][ 0.171159] . ( 18 sec) [ -5384.3078] [Branch lengths ] . ( 34 sec) [ -5381.8447] [ 870] [depth= 5] . ( 44 sec) [ -5381.5771] [ 869] [depth= 1] . ( 44 sec) [ -5381.3512] [ 868] [depth= 1] . ( 45 sec) [ -5381.3343] [ 872] [depth= 1] . ( 46 sec) [ -5381.3177] [ 872] [depth= 1] . ( 47 sec) [ -5381.2170] [ 868] [depth= 1] . ( 50 sec) [ -5380.3420] [Branch lengths ] . ( 51 sec) [ -5380.2424] [GTR parameters ] . ( 51 sec) [ -5380.2291] [Alpha ][ 0.169203] . ( 68 sec) [ -5380.0504] [ 868] [depth= 3] . ( 85 sec) [ -5379.9726] [Branch lengths ] . ( 86 sec) [ -5379.9647] [GTR parameters ] . ( 87 sec) [ -5379.9636] [Alpha ][ 0.169740] . ( 87 sec) [ -5379.9636] [Topology ] . ( 88 sec) [ -5379.9572] [Topology ] . ( 88 sec) [ -5379.9556] [Topology ] . ( 89 sec) [ -5379.9549] [Topology ] . ( 89 sec) [ -5379.9549] [GTR parameters ] . ( 89 sec) [ -5379.9549] [Alpha ][ 0.169740] . ( 89 sec) [ -5379.9549] [Topology ] . ( 91 sec) [ -5379.9546] [Topology ] . ( 91 sec) [ -5379.9546] [GTR parameters ] . ( 91 sec) [ -5379.9546] [Alpha ][ 0.169740] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -5379.8814] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5379.881357. . Printing the most likely tree in file 'nucleic_M2974_56x827_2006.phy_phyml_tree.txt'... . Time used 0h1m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 96.32user 0.00system 1:50.49elapsed 87%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps