.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2928_81x1651_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... . 507 patterns found. (out of a total of 1651 sites) . 1189 sites without polymorphism (72.02%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7271.1166] [GTR parameters ] . ( 1 sec) [ -7211.7409] [Alpha ][ 0.500960] . ( 1 sec) [ -7211.1362] [ 888] [depth= 1] . ( 2 sec) [ -7210.8001] [ 888] [depth= 1] . ( 2 sec) [ -7210.5133] [ 888] [depth= 3] . ( 2 sec) [ -7210.3174] [ 888] [depth= 2] . ( 2 sec) [ -7209.9139] [ 888] [depth= 2] . ( 3 sec) [ -7209.8287] [ 888] [depth= 3] . ( 3 sec) [ -7209.7725] [ 888] [depth= 1] . ( 3 sec) [ -7209.7412] [ 888] [depth= 3] . ( 3 sec) [ -7209.7265] [ 888] [depth= 1] . ( 4 sec) [ -7209.7034] [ 888] [depth= 2] . ( 5 sec) [ -7208.7158] [ 888] [depth= 1] . ( 5 sec) [ -7208.6945] [ 888] [depth= 1] . ( 5 sec) [ -7208.5133] [ 888] [depth= 1] . ( 5 sec) [ -7208.4151] [ 888] [depth= 1] . ( 6 sec) [ -7208.3997] [ 888] [depth= 1] . ( 6 sec) [ -7208.2465] [ 888] [depth= 2] . ( 7 sec) [ -7207.2513] [ 886] [depth= 1] . ( 7 sec) [ -7206.4792] [ 888] [depth= 1] . ( 7 sec) [ -7204.3768] [ 886] [depth= 1] . ( 7 sec) [ -7190.8764] [ 883] [depth= 1] . ( 8 sec) [ -7190.8428] [ 883] [depth= 1] . ( 8 sec) [ -7190.8300] [ 883] [depth= 1] . ( 8 sec) [ -7190.6890] [ 883] [depth= 1] . ( 8 sec) [ -7189.0839] [ 883] [depth= 2] . ( 8 sec) [ -7189.0599] [ 883] [depth= 1] . ( 9 sec) [ -7184.6932] [ 883] [depth= 1] . ( 9 sec) [ -7184.6670] [ 883] [depth= 3] . ( 9 sec) [ -7183.2709] [ 883] [depth= 1] . ( 9 sec) [ -7183.1314] [ 883] [depth= 1] . ( 9 sec) [ -7182.8239] [ 883] [depth= 1] . ( 9 sec) [ -7182.7625] [ 883] [depth= 7] . ( 9 sec) [ -7182.5927] [ 883] [depth= 6] . ( 9 sec) [ -7181.8481] [ 883] [depth= 2] . ( 10 sec) [ -7181.6056] [ 883] [depth= 6] . ( 10 sec) [ -7181.4232] [ 883] [depth= 5] . ( 10 sec) [ -7181.3420] [ 883] [depth= 4] . ( 10 sec) [ -7181.2230] [ 883] [depth= 4] . ( 10 sec) [ -7181.1390] [ 883] [depth= 1] . ( 11 sec) [ -7180.8160] [ 883] [depth= 1] . ( 11 sec) [ -7180.5654] [ 883] [depth= 1] . ( 12 sec) [ -7180.3242] [ 883] [depth= 2] . ( 12 sec) [ -7180.3130] [ 883] [depth= 4] . ( 13 sec) [ -7180.1583] [ 883] [depth= 2] . ( 13 sec) [ -7173.9857] [ 883] [depth= 1] . ( 14 sec) [ -7173.5099] [ 883] [depth= 1] . ( 14 sec) [ -7172.8175] [ 883] [depth= 1] . ( 14 sec) [ -7172.8067] [ 883] [depth= 2] . ( 15 sec) [ -7172.1141] [ 883] [depth= 1] . ( 15 sec) [ -7171.4101] [ 882] [depth= 3] . ( 15 sec) [ -7171.3947] [ 882] [depth= 1] . ( 15 sec) [ -7171.3811] [ 882] [depth= 1] . ( 15 sec) [ -7171.3362] [ 882] [depth= 2] . ( 15 sec) [ -7171.3224] [ 882] [depth= 1] . ( 16 sec) [ -7171.2366] [ 883] [depth= 1] . ( 16 sec) [ -7171.1725] [ 883] [depth= 1] . ( 16 sec) [ -7171.1620] [ 883] [depth= 1] . ( 21 sec) [ -7154.0244] [Branch lengths ] . ( 22 sec) [ -6759.5350] [GTR parameters ] . ( 22 sec) [ -6722.6522] [Alpha ][ 0.250961] . ( 26 sec) [ -6722.5434] [ 883] [depth= 2] . ( 27 sec) [ -6722.3984] [ 885] [depth= 1] . ( 28 sec) [ -6721.1796] [ 889] [depth= 1] . ( 43 sec) [ -6716.1115] [Branch lengths ] . ( 47 sec) [ -6694.5554] [GTR parameters ] . ( 47 sec) [ -6692.1406] [Alpha ][ 0.206695] . ( 52 sec) [ -6692.1280] [ 889] [depth= 2] . ( 68 sec) [ -6690.9786] [Branch lengths ] . ( 70 sec) [ -6690.8418] [GTR parameters ] . ( 70 sec) [ -6690.8405] [Alpha ][ 0.205750] . ( 75 sec) [ -6690.2545] [ 889] [depth= 1] . ( 90 sec) [ -6689.8212] [Branch lengths ] . ( 93 sec) [ -6689.7902] [GTR parameters ] . ( 93 sec) [ -6689.7901] [Alpha ][ 0.205987] . ( 107 sec) [ -6689.7734] [ 888] [depth= 1] . ( 111 sec) [ -6689.6798] [Branch lengths ] . ( 112 sec) [ -6689.6798] [GTR parameters ] . ( 112 sec) [ -6689.6797] [Alpha ][ 0.206193] . ( 179 sec) [ -6689.6656] [Branch lengths ] . ( 179 sec) [ -6689.6656] [Topology ] . ( 180 sec) [ -6689.6643] [Topology ] . ( 182 sec) [ -6689.6640] [Topology ] . ( 183 sec) [ -6689.6621] [GTR parameters ] . ( 183 sec) [ -6689.6621] [Alpha ][ 0.206193] . ( 183 sec) [ -6689.6621] [Topology ] . ( 185 sec) [ -6689.6619] [Topology ] . ( 186 sec) [ -6689.6609] [GTR parameters ] . ( 186 sec) [ -6689.6609] [Alpha ][ 0.206193] . ( 186 sec) [ -6689.6609] [Topology ] . ( 187 sec) [ -6689.6608] [Topology ] . ( 190 sec) [ -6689.6584] [GTR parameters ] . ( 190 sec) [ -6689.6583] [Alpha ][ 0.205930] . ( 190 sec) [ -6689.6583] [Topology ] . ( 191 sec) [ -6689.6582] [Topology ] . ( 192 sec) [ -6689.6582] [GTR parameters ] . ( 192 sec) [ -6689.6582] [Alpha ][ 0.205930] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.658164. . Printing the most likely tree in file 'nucleic_M2928_81x1651_2006.phy_phyml_tree.txt'... . Time used 0h3m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 199.56user 0.00system 3:21.94elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps