.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M3862_362x1207_2008.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 : NNIs . 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... . 1028 patterns found. (out of a total of 1207 sites) . 273 sites without polymorphism (22.62%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 199Mo of memory space... . Maximizing likelihood (using NNI moves)... . ( 32 sec) [ -99137.4102] [GTR parameters ] . ( 35 sec) [ -97876.2894] [Alpha ][ 0.500960] . ( 35 sec) [ -97876.2894] [Topology ] . ( 59 sec) [ -95938.9156] [Topology ] . ( 83 sec) [ -95511.8217] [Topology ] . ( 108 sec) [ -95327.6079] [Topology ] . ( 133 sec) [ -95255.6109] [Topology ] . ( 157 sec) [ -95207.1076] [Topology ] . ( 182 sec) [ -95168.0332] [Topology ] . ( 207 sec) [ -95131.0759] [Topology ] . ( 232 sec) [ -95111.5856] [Topology ] . ( 256 sec) [ -95092.8440] [Topology ] . ( 293 sec) [ -95004.7862] [GTR parameters ] . ( 294 sec) [ -94997.8648] [Alpha ][ 0.530442] . ( 295 sec) [ -94997.8648] [Topology ] . ( 320 sec) [ -94978.3446] [Topology ] . ( 345 sec) [ -94957.6816] [Topology ] . ( 369 sec) [ -94942.4318] [Topology ] . ( 394 sec) [ -94931.7119] [Topology ] . ( 419 sec) [ -94926.9954] [Topology ] . ( 443 sec) [ -94923.6731] [Topology ] . ( 469 sec) [ -94920.5980] [Topology ] . ( 493 sec) [ -94919.4428] [Topology ] . ( 518 sec) [ -94917.6062] [Topology ] . Checking for NNIs, optimizing five branches... . ( 667 sec) [ -94916.5556] [Topology ] . ( 679 sec) [ -94913.2996] [GTR parameters ] . ( 680 sec) [ -94913.0283] [Alpha ][ 0.524647] . ( 681 sec) [ -94913.0283] [Topology ] . ( 705 sec) [ -94912.3533] [Topology ] . ( 730 sec) [ -94912.1147] [Topology ] . ( 755 sec) [ -94912.0107] [Topology ] . ( 780 sec) [ -94911.9631] [Topology ] . ( 805 sec) [ -94911.9406] [Topology ] . ( 830 sec) [ -94911.9299] [Topology ] . Checking for NNIs, optimizing five branches... . ( 954 sec) [ -94911.8724] [Topology ] . ( 963 sec) [ -94911.7863] [GTR parameters ] . ( 965 sec) [ -94911.7713] [Alpha ][ 0.523226] . ( 965 sec) [ -94911.7713] [Topology ] . ( 990 sec) [ -94911.7435] [Topology ] . ( 1015 sec) [ -94911.7341] [Topology ] . ( 1040 sec) [ -94911.7297] [Topology ] . ( 1064 sec) [ -94911.7276] [Topology ] . ( 1089 sec) [ -94911.7265] [Topology ] . ( 1114 sec) [ -94911.7260] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1237 sec) [ -94911.6794] [Topology ] . ( 1244 sec) [ -94911.6702] [GTR parameters ] . ( 1246 sec) [ -94911.6577] [Alpha ][ 0.521910] . ( 1246 sec) [ -94911.6577] [Topology ] . ( 1271 sec) [ -94911.5909] [Topology ] . ( 1296 sec) [ -94911.5816] [Topology ] . ( 1320 sec) [ -94911.5796] [Topology ] . ( 1345 sec) [ -94911.5790] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1468 sec) [ -94911.5747] [Topology ] . ( 1470 sec) [ -94911.5742] [GTR parameters ] . ( 1472 sec) [ -94911.5742] [Alpha ][ 0.521910] . ( 1472 sec) [ -94911.5742] [Topology ] . ( 1497 sec) [ -94910.9244] [Topology ] . ( 1522 sec) [ -94910.8097] [Topology ] . ( 1546 sec) [ -94910.7909] [Topology ] . ( 1571 sec) [ -94910.7852] [Topology ] . ( 1596 sec) [ -94910.7833] [Topology ] . ( 1621 sec) [ -94910.7827] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1747 sec) [ -94910.7826] [GTR parameters ] . ( 1748 sec) [ -94910.7826] [Alpha ][ 0.521910] . ( 1749 sec) [ -94910.7826] [Topology ] . ( 1774 sec) [ -94910.7824] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -94910.782403. . Printing the most likely tree in file 'nucleic_M3862_362x1207_2008.phy_phyml_tree.txt'... . Time used 0h33m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2002.37user 0.00system 33:57.71elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps