.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2655_50x872_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... . 374 patterns found. (out of a total of 872 sites) . 550 sites without polymorphism (63.07%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -6841.6794] [GTR parameters ] . ( 2 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 2 sec) [ -6719.2727] [ 1115] [depth= 1] . ( 2 sec) [ -6718.1728] [ 1115] [depth= 1] . ( 2 sec) [ -6713.9543] [ 1115] [depth= 1] . ( 2 sec) [ -6713.8010] [ 1115] [depth= 1] . ( 2 sec) [ -6709.1247] [ 1118] [depth= 1] . ( 3 sec) [ -6708.8321] [ 1121] [depth= 1] . ( 3 sec) [ -6705.1067] [ 1118] [depth= 1] . ( 3 sec) [ -6700.9852] [ 1118] [depth= 1] . ( 3 sec) [ -6699.3761] [ 1116] [depth= 1] . ( 4 sec) [ -6693.9948] [ 1117] [depth= 1] . ( 4 sec) [ -6691.2533] [ 1116] [depth= 1] . ( 4 sec) [ -6690.7609] [ 1118] [depth= 1] . ( 4 sec) [ -6686.6861] [ 1116] [depth= 1] . ( 4 sec) [ -6686.4973] [ 1115] [depth= 1] . ( 4 sec) [ -6677.1250] [ 1115] [depth= 1] . ( 4 sec) [ -6674.3542] [ 1114] [depth= 3] . ( 4 sec) [ -6670.8009] [ 1117] [depth= 2] . ( 4 sec) [ -6670.3706] [ 1117] [depth= 1] . ( 4 sec) [ -6666.4555] [ 1115] [depth= 2] . ( 4 sec) [ -6663.4851] [ 1112] [depth= 1] . ( 5 sec) [ -6655.1382] [ 1122] [depth= 1] . ( 5 sec) [ -6653.6844] [ 1122] [depth= 3] . ( 5 sec) [ -6652.7442] [ 1128] [depth= 1] . ( 5 sec) [ -6652.3698] [ 1130] [depth= 1] . ( 5 sec) [ -6648.6509] [ 1124] [depth= 1] . ( 5 sec) [ -6643.6118] [ 1123] [depth= 1] . ( 5 sec) [ -6638.0482] [ 1121] [depth= 1] . ( 6 sec) [ -6637.1228] [ 1120] [depth= 1] . ( 6 sec) [ -6634.6754] [ 1121] [depth= 1] . ( 6 sec) [ -6633.1658] [ 1120] [depth= 1] . ( 6 sec) [ -6591.1814] [Branch lengths ] . ( 8 sec) [ -6589.2336] [GTR parameters ] . ( 8 sec) [ -6531.2897] [Alpha ][ 0.250961] . ( 8 sec) [ -6530.9858] [ 1120] [depth= 1] . ( 8 sec) [ -6529.8800] [ 1119] [depth= 3] . ( 9 sec) [ -6528.0571] [ 1119] [depth= 1] . ( 9 sec) [ -6523.0532] [ 1108] [depth= 1] . ( 9 sec) [ -6523.0427] [ 1108] [depth= 1] . ( 9 sec) [ -6522.8295] [ 1108] [depth= 3] . ( 9 sec) [ -6522.8108] [ 1108] [depth= 1] . ( 9 sec) [ -6520.2146] [ 1111] [depth= 1] . ( 11 sec) [ -6513.9369] [Branch lengths ] . ( 12 sec) [ -6512.5851] [GTR parameters ] . ( 12 sec) [ -6511.9285] [Alpha ][ 0.233204] . ( 12 sec) [ -6511.8615] [ 1111] [depth= 1] . ( 13 sec) [ -6511.7794] [ 1111] [depth= 1] . ( 16 sec) [ -6511.5420] [Branch lengths ] . ( 17 sec) [ -6511.5291] [GTR parameters ] . ( 17 sec) [ -6511.5285] [Alpha ][ 0.232662] . ( 48 sec) [ -6511.5228] [Branch lengths ] . ( 48 sec) [ -6511.5228] [Topology ] . ( 48 sec) [ -6511.5225] [Topology ] . ( 49 sec) [ -6511.5225] [GTR parameters ] . ( 49 sec) [ -6511.5225] [Alpha ][ 0.232662] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6511.522530. . Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'... . Time used 0h0m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 53.67user 0.00system 0:55.48elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps