.......................... 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)... . ( 3 sec) [ -6773.7497] [GTR parameters ] . ( 3 sec) [ -6662.0020] [Alpha ][ 0.500960] . ( 3 sec) [ -6661.2176] [ 1015] [depth= 1] . ( 4 sec) [ -6657.6560] [ 1017] [depth= 1] . ( 4 sec) [ -6643.6053] [ 1021] [depth= 3] . ( 4 sec) [ -6641.0309] [ 1021] [depth= 1] . ( 4 sec) [ -6638.5305] [ 1021] [depth= 1] . ( 4 sec) [ -6633.4998] [ 1021] [depth= 1] . ( 4 sec) [ -6630.8745] [ 1021] [depth= 1] . ( 4 sec) [ -6629.9916] [ 1021] [depth= 1] . ( 4 sec) [ -6622.7123] [ 1018] [depth= 2] . ( 5 sec) [ -6620.8611] [ 1019] [depth= 1] . ( 5 sec) [ -6618.3075] [ 1018] [depth= 1] . ( 5 sec) [ -6617.4845] [ 1018] [depth= 1] . ( 5 sec) [ -6608.1318] [ 1014] [depth= 1] . ( 5 sec) [ -6605.4512] [ 1016] [depth= 1] . ( 5 sec) [ -6601.3304] [ 1016] [depth= 2] . ( 6 sec) [ -6598.9046] [ 1016] [depth= 1] . ( 6 sec) [ -6592.5119] [ 1016] [depth= 1] . ( 6 sec) [ -6592.0810] [ 1016] [depth= 1] . ( 6 sec) [ -6590.3886] [ 1016] [depth= 1] . ( 6 sec) [ -6588.5375] [ 1016] [depth= 1] . ( 6 sec) [ -6588.3462] [ 1016] [depth= 1] . ( 6 sec) [ -6586.9839] [ 1016] [depth= 1] . ( 6 sec) [ -6586.1409] [ 1016] [depth= 1] . ( 6 sec) [ -6583.5917] [ 1015] [depth= 1] . ( 7 sec) [ -6581.9287] [ 1015] [depth= 1] . ( 7 sec) [ -6578.6323] [ 1014] [depth= 2] . ( 7 sec) [ -6577.1582] [ 1018] [depth= 2] . ( 7 sec) [ -6576.8376] [ 1018] [depth= 1] . ( 7 sec) [ -6576.6075] [ 1015] [depth= 2] . ( 7 sec) [ -6575.9342] [ 1015] [depth= 1] . ( 8 sec) [ -6574.3204] [ 1016] [depth= 1] . ( 8 sec) [ -6572.1022] [ 1017] [depth= 1] . ( 9 sec) [ -6568.5239] [ 1020] [depth= 2] . ( 9 sec) [ -6566.9919] [ 1019] [depth= 6] . ( 9 sec) [ -6565.9826] [ 1019] [depth= 1] . ( 9 sec) [ -6565.1147] [ 1019] [depth= 1] . ( 9 sec) [ -6563.3709] [ 1019] [depth= 1] . ( 9 sec) [ -6561.3762] [ 1017] [depth= 1] . ( 9 sec) [ -6521.1650] [Branch lengths ] . ( 11 sec) [ -6520.5787] [GTR parameters ] . ( 11 sec) [ -6459.1866] [Alpha ][ 0.250961] . ( 11 sec) [ -6458.9328] [ 1017] [depth= 1] . ( 11 sec) [ -6458.9152] [ 1017] [depth= 1] . ( 12 sec) [ -6454.4210] [ 1015] [depth= 2] . ( 13 sec) [ -6452.4718] [ 1012] [depth= 4] . ( 14 sec) [ -6451.8967] [ 1008] [depth= 8] . ( 14 sec) [ -6451.7592] [ 1008] [depth= 1] . ( 15 sec) [ -6444.1466] [Branch lengths ] . ( 16 sec) [ -6442.6926] [GTR parameters ] . ( 16 sec) [ -6441.1439] [Alpha ][ 0.222742] . ( 16 sec) [ -6440.8479] [ 1008] [depth= 1] . ( 16 sec) [ -6439.5164] [ 1008] [depth= 1] . ( 21 sec) [ -6438.6139] [Branch lengths ] . ( 22 sec) [ -6438.5431] [GTR parameters ] . ( 22 sec) [ -6438.5388] [Alpha ][ 0.221280] . ( 27 sec) [ -6438.5143] [Branch lengths ] . ( 68 sec) [ -6438.5130] [Branch lengths ] . ( 68 sec) [ -6438.5130] [Topology ] . ( 69 sec) [ -6438.5129] [Topology ] . ( 70 sec) [ -6438.5127] [GTR parameters ] . ( 70 sec) [ -6438.5126] [Alpha ][ 0.221043] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -6438.3474] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6438.347406. . Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'... . Time used 0h1m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 80.52user 0.00system 1:26.42elapsed 93%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps