.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2921_54x966_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 397 patterns found. (out of a total of 966 sites) . 643 sites without polymorphism (66.56%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -6773.7497] [GTR parameters ] . ( 2 sec) [ -6662.0020] [Alpha ][ 0.500960] . ( 4 sec) [ -6661.2176] [ 1015] [depth= 1] . ( 4 sec) [ -6657.6560] [ 1017] [depth= 1] . ( 4 sec) [ -6643.6053] [ 1021] [depth= 3] . ( 6 sec) [ -6641.0309] [ 1021] [depth= 1] . ( 6 sec) [ -6638.5305] [ 1021] [depth= 1] . ( 6 sec) [ -6633.4998] [ 1021] [depth= 1] . ( 7 sec) [ -6630.8745] [ 1021] [depth= 1] . ( 7 sec) [ -6629.9916] [ 1021] [depth= 1] . ( 7 sec) [ -6622.7123] [ 1018] [depth= 2] . ( 15 sec) [ -6621.7876] [ 1019] [depth= 1] . ( 15 sec) [ -6617.7013] [ 1018] [depth= 1] . ( 16 sec) [ -6608.9048] [ 1016] [depth= 1] . ( 17 sec) [ -6601.3592] [ 1014] [depth= 1] . ( 22 sec) [ -6601.1610] [ 1016] [depth= 1] . ( 23 sec) [ -6598.7269] [ 1016] [depth= 1] . ( 23 sec) [ -6592.3337] [ 1016] [depth= 1] . ( 26 sec) [ -6591.8220] [ 1016] [depth= 1] . ( 26 sec) [ -6590.0681] [ 1016] [depth= 1] . ( 26 sec) [ -6588.2294] [ 1016] [depth= 1] . ( 26 sec) [ -6588.1324] [ 1016] [depth= 1] . ( 27 sec) [ -6586.6852] [ 1016] [depth= 1] . ( 28 sec) [ -6586.5950] [ 1020] [depth= 2] . ( 28 sec) [ -6582.2061] [ 1020] [depth= 2] . ( 28 sec) [ -6581.5121] [ 1020] [depth= 1] . ( 28 sec) [ -6580.0273] [ 1020] [depth= 1] . ( 28 sec) [ -6579.5942] [ 1019] [depth= 1] . ( 28 sec) [ -6577.0371] [ 1018] [depth= 1] . ( 29 sec) [ -6576.6929] [ 1018] [depth= 1] . ( 39 sec) [ -6575.7276] [ 1020] [depth= 1] . ( 41 sec) [ -6574.3250] [ 1020] [depth= 1] . ( 44 sec) [ -6572.4235] [ 1022] [depth= 1] . ( 44 sec) [ -6572.3127] [ 1022] [depth= 1] . ( 44 sec) [ -6572.1131] [ 1022] [depth= 1] . ( 49 sec) [ -6570.5866] [ 1020] [depth= 1] . ( 54 sec) [ -6569.8711] [ 1022] [depth= 2] . ( 54 sec) [ -6563.0274] [ 1018] [depth= 1] . ( 56 sec) [ -6560.2201] [ 1019] [depth= 1] . ( 56 sec) [ -6554.7428] [ 1015] [depth= 3] . ( 59 sec) [ -6551.7431] [ 1015] [depth= 1] . ( 61 sec) [ -6547.0640] [ 1015] [depth= 1] . ( 62 sec) [ -6547.0264] [ 1015] [depth= 1] . ( 62 sec) [ -6545.5836] [ 1015] [depth= 1] . ( 66 sec) [ -6509.9789] [Branch lengths ] . ( 68 sec) [ -6508.8959] [GTR parameters ] . ( 68 sec) [ -6448.6182] [Alpha ][ 0.250961] . ( 78 sec) [ -6448.5987] [ 1015] [depth= 1] . ( 91 sec) [ -6448.2173] [ 1016] [depth= 1] . ( 93 sec) [ -6443.9611] [ 1013] [depth= 2] . ( 109 sec) [ -6443.8114] [ 1012] [depth= 1] . ( 110 sec) [ -6443.5939] [ 1012] [depth= 1] . ( 158 sec) [ -6440.4312] [Branch lengths ] . ( 159 sec) [ -6439.6497] [GTR parameters ] . ( 159 sec) [ -6437.8273] [Alpha ][ 0.220074] . ( 251 sec) [ -6437.7151] [Branch lengths ] . ( 288 sec) [ -6437.7093] [Branch lengths ] . ( 288 sec) [ -6437.7093] [Topology ] . ( 289 sec) [ -6437.7091] [Topology ] . ( 290 sec) [ -6437.6682] [GTR parameters ] . ( 290 sec) [ -6437.6661] [Alpha ][ 0.219041] . ( 290 sec) [ -6437.6661] [Topology ] . ( 291 sec) [ -6437.6657] [Topology ] . ( 291 sec) [ -6437.6656] [GTR parameters ] . ( 291 sec) [ -6437.6656] [Alpha ][ 0.219041] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6437.665605. . Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'... . Time used 0h4m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 292.36user 0.00system 4:58.79elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps