.......................... 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 : 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... . 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 NNI moves)... . ( 2 sec) [ -5728.9072] [GTR parameters ] . ( 2 sec) [ -5606.6718] [Alpha ][ 0.500960] . ( 2 sec) [ -5606.6718] [Topology ] . ( 3 sec) [ -5510.2825] [Topology ] . ( 4 sec) [ -5499.3079] [Topology ] . ( 5 sec) [ -5491.5808] [Topology ] . ( 5 sec) [ -5489.3486] [Topology ] . ( 6 sec) [ -5488.5977] [Topology ] . ( 7 sec) [ -5488.4658] [Topology ] . ( 8 sec) [ -5488.4264] [Topology ] . ( 8 sec) [ -5488.4137] [Topology ] . ( 9 sec) [ -5488.4094] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -5488.3977] [Topology ] . ( 16 sec) [ -5487.6246] [GTR parameters ] . ( 16 sec) [ -5400.5669] [Alpha ][ 0.250961] . ( 16 sec) [ -5400.5669] [Topology ] . ( 17 sec) [ -5400.1158] [Topology ] . ( 18 sec) [ -5400.0577] [Topology ] . ( 19 sec) [ -5400.0430] [Topology ] . ( 19 sec) [ -5400.0386] [Topology ] . ( 20 sec) [ -5400.0372] [Topology ] . ( 21 sec) [ -5400.0368] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -5399.3839] [GTR parameters ] . ( 27 sec) [ -5384.6965] [Alpha ][ 0.172277] . ( 27 sec) [ -5384.6965] [Topology ] . ( 28 sec) [ -5384.4114] [Topology ] . ( 29 sec) [ -5384.3536] [Topology ] . ( 29 sec) [ -5384.3367] [Topology ] . ( 30 sec) [ -5384.3312] [Topology ] . ( 31 sec) [ -5384.3293] [Topology ] . ( 32 sec) [ -5384.3287] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5384.2239] [GTR parameters ] . ( 38 sec) [ -5384.1911] [Alpha ][ 0.169387] . ( 38 sec) [ -5384.1911] [Topology ] . ( 38 sec) [ -5384.1899] [Topology ] . ( 39 sec) [ -5384.1896] [Topology ] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -5384.1893] [GTR parameters ] . ( 45 sec) [ -5384.1892] [Alpha ][ 0.169217] . ( 45 sec) [ -5384.1892] [Topology ] . ( 46 sec) [ -5384.1891] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 58 sec) [ -5728.9072] [GTR parameters ] . ( 58 sec) [ -5606.6718] [Alpha ][ 0.500960] . ( 58 sec) [ -5604.1549] [ 870] [depth= 1] . ( 59 sec) [ -5603.7101] [ 873] [depth= 1] . ( 59 sec) [ -5602.5602] [ 873] [depth= 1] . ( 60 sec) [ -5602.5495] [ 873] [depth= 1] . ( 60 sec) [ -5602.1653] [ 873] [depth= 1] . ( 60 sec) [ -5601.1809] [ 873] [depth= 1] . ( 60 sec) [ -5596.0814] [ 873] [depth= 1] . ( 60 sec) [ -5588.1092] [ 872] [depth= 1] . ( 60 sec) [ -5586.4381] [ 873] [depth= 1] . ( 60 sec) [ -5578.9807] [ 870] [depth= 1] . ( 60 sec) [ -5573.6518] [ 873] [depth= 3] . ( 60 sec) [ -5571.2321] [ 874] [depth= 1] . ( 60 sec) [ -5565.9621] [ 873] [depth= 1] . ( 61 sec) [ -5564.0713] [ 873] [depth= 2] . ( 61 sec) [ -5562.6399] [ 870] [depth= 1] . ( 61 sec) [ -5553.6603] [ 867] [depth= 1] . ( 61 sec) [ -5552.7440] [ 870] [depth= 1] . ( 61 sec) [ -5552.4439] [ 870] [depth= 1] . ( 61 sec) [ -5551.1027] [ 871] [depth= 1] . ( 61 sec) [ -5549.8428] [ 870] [depth= 1] . ( 62 sec) [ -5549.6923] [ 870] [depth= 1] . ( 62 sec) [ -5546.1460] [ 869] [depth= 2] . ( 62 sec) [ -5545.4896] [ 869] [depth= 1] . ( 62 sec) [ -5543.9660] [ 869] [depth= 1] . ( 62 sec) [ -5543.9544] [ 869] [depth= 1] . ( 62 sec) [ -5543.9115] [ 869] [depth= 1] . ( 63 sec) [ -5542.3207] [ 870] [depth= 1] . ( 63 sec) [ -5540.4171] [ 869] [depth= 1] . ( 63 sec) [ -5539.8329] [ 870] [depth= 2] . ( 63 sec) [ -5538.0824] [ 870] [depth= 1] . ( 63 sec) [ -5536.9322] [ 870] [depth= 1] . ( 63 sec) [ -5535.8431] [ 870] [depth= 1] . ( 63 sec) [ -5535.6406] [ 869] [depth= 3] . ( 63 sec) [ -5533.2370] [ 868] [depth= 1] . ( 64 sec) [ -5532.7731] [ 869] [depth= 2] . ( 64 sec) [ -5532.7105] [ 869] [depth= 1] . ( 64 sec) [ -5532.6955] [ 869] [depth= 2] . ( 65 sec) [ -5493.7044] [Branch lengths ] . ( 66 sec) [ -5492.9840] [GTR parameters ] . ( 66 sec) [ -5405.5034] [Alpha ][ 0.250961] . ( 67 sec) [ -5402.9994] [ 866] [depth= 1] . ( 70 sec) [ -5398.3249] [ 868] [depth= 8] . ( 72 sec) [ -5398.3115] [ 868] [depth= 1] . ( 73 sec) [ -5398.0718] [ 868] [depth= 1] . ( 74 sec) [ -5398.0072] [ 868] [depth= 2] . ( 76 sec) [ -5395.1170] [Branch lengths ] . ( 77 sec) [ -5394.6346] [GTR parameters ] . ( 77 sec) [ -5380.1976] [Alpha ][ 0.172872] . ( 81 sec) [ -5380.0177] [ 866] [depth= 2] . ( 85 sec) [ -5379.9978] [ 866] [depth= 4] . ( 86 sec) [ -5378.8965] [Branch lengths ] . ( 87 sec) [ -5378.7548] [GTR parameters ] . ( 87 sec) [ -5378.7207] [Alpha ][ 0.169912] . ( 96 sec) [ -5378.6658] [Branch lengths ] . ( 128 sec) [ -5378.6613] [Branch lengths ] . ( 128 sec) [ -5378.6613] [Topology ] . ( 129 sec) [ -5378.6611] [Topology ] . ( 129 sec) [ -5378.6608] [GTR parameters ] . ( 129 sec) [ -5378.6592] [Alpha ][ 0.169218] . ( 129 sec) [ -5378.6592] [Topology ] . ( 130 sec) [ -5378.6589] [Topology ] . ( 130 sec) [ -5378.6589] [GTR parameters ] . ( 130 sec) [ -5378.6589] [Alpha ][ 0.169218] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5384.189132 . Log likelihood obtained after SPR moves : -5378.658910 . Log likelihood of the current tree: -5378.658910. . Printing the most likely tree in file 'nucleic_M2974_56x827_2006.phy_phyml_tree.txt'... . Time used 0h2m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 134.97user 0.00system 2:15.83elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps