.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2627_54x1915_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... . 1299 patterns found. (out of a total of 1915 sites) . 625 sites without polymorphism (32.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -36710.7724] [GTR parameters ] . ( 2 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 8 sec) [ -36464.9677] [ 8258] [depth= 1] . ( 8 sec) [ -36460.8603] [ 8291] [depth= 2] . ( 8 sec) [ -36413.8896] [ 8255] [depth= 2] . ( 8 sec) [ -36411.3454] [ 8249] [depth= 1] . ( 9 sec) [ -36399.1307] [ 8268] [depth= 1] . ( 10 sec) [ -36378.9510] [ 8249] [depth= 1] . ( 10 sec) [ -36376.2148] [ 8248] [depth= 1] . ( 10 sec) [ -36359.2113] [ 8249] [depth= 1] . ( 11 sec) [ -36357.1179] [ 8252] [depth= 1] . ( 11 sec) [ -36342.5478] [ 8249] [depth= 1] . ( 12 sec) [ -36341.3053] [ 8246] [depth= 1] . ( 12 sec) [ -36341.1909] [ 8245] [depth= 1] . ( 13 sec) [ -36335.1502] [ 8241] [depth= 1] . ( 14 sec) [ -36321.6304] [ 8240] [depth= 1] . ( 16 sec) [ -36319.6389] [ 8239] [depth= 1] . ( 18 sec) [ -36192.9441] [Branch lengths ] . ( 24 sec) [ -35342.1676] [GTR parameters ] . ( 24 sec) [ -35338.8540] [Alpha ][ 0.461044] . ( 27 sec) [ -35336.0126] [ 8235] [depth= 1] . ( 29 sec) [ -35335.4131] [ 8235] [depth= 2] . ( 30 sec) [ -35332.0186] [ 8233] [depth= 1] . ( 30 sec) [ -35330.9355] [ 8231] [depth= 1] . ( 36 sec) [ -35288.4984] [Branch lengths ] . ( 40 sec) [ -35284.1495] [GTR parameters ] . ( 40 sec) [ -35283.4896] [Alpha ][ 0.478254] . ( 52 sec) [ -35267.3775] [Branch lengths ] . ( 134 sec) [ -35262.6685] [Branch lengths ] . ( 134 sec) [ -35262.6685] [Topology ] . ( 137 sec) [ -35261.7680] [Topology ] . ( 139 sec) [ -35261.3430] [Topology ] . ( 142 sec) [ -35261.0603] [Topology ] . ( 145 sec) [ -35260.8643] [Topology ] . ( 148 sec) [ -35260.7259] [Topology ] . ( 151 sec) [ -35260.6267] [Topology ] . ( 157 sec) [ -35257.3767] [GTR parameters ] . ( 157 sec) [ -35256.5494] [Alpha ][ 0.497328] . ( 157 sec) [ -35256.5494] [Topology ] . ( 160 sec) [ -35255.7357] [Topology ] . ( 163 sec) [ -35255.2056] [Topology ] . ( 166 sec) [ -35254.8332] [Topology ] . ( 169 sec) [ -35254.5674] [Topology ] . ( 172 sec) [ -35254.3760] [Topology ] . ( 175 sec) [ -35254.2368] [Topology ] . ( 178 sec) [ -35254.1006] [GTR parameters ] . ( 178 sec) [ -35254.0896] [Alpha ][ 0.499566] . ( 178 sec) [ -35254.0896] [Topology ] . ( 181 sec) [ -35253.9042] [Topology ] . ( 184 sec) [ -35253.7711] [Topology ] . ( 187 sec) [ -35253.6730] [Topology ] . ( 190 sec) [ -35253.6008] [Topology ] . ( 193 sec) [ -35253.5474] [Topology ] . ( 196 sec) [ -35253.5076] [Topology ] . ( 198 sec) [ -35253.4470] [GTR parameters ] . ( 198 sec) [ -35253.4470] [Alpha ][ 0.499566] . ( 198 sec) [ -35253.4470] [Topology ] . ( 201 sec) [ -35253.3886] [Topology ] . ( 204 sec) [ -35253.3466] [Topology ] . ( 209 sec) [ -35253.3153] [Topology ] . ( 214 sec) [ -35253.2919] [Topology ] . ( 218 sec) [ -35253.2743] [Topology ] . ( 223 sec) [ -35253.2611] [Topology ] . ( 226 sec) [ -35253.2381] [GTR parameters ] . ( 226 sec) [ -35253.2381] [Alpha ][ 0.499566] . ( 226 sec) [ -35253.2381] [Topology ] . ( 232 sec) [ -35253.2176] [Topology ] . ( 237 sec) [ -35253.2027] [Topology ] . ( 242 sec) [ -35253.1916] [Topology ] . ( 247 sec) [ -35253.1832] [Topology ] . ( 252 sec) [ -35253.1768] [Topology ] . ( 257 sec) [ -35253.1720] [Topology ] . ( 262 sec) [ -35253.1645] [GTR parameters ] . ( 262 sec) [ -35253.1644] [Alpha ][ 0.499066] . ( 262 sec) [ -35253.1644] [Topology ] . ( 267 sec) [ -35253.1572] [Topology ] . ( 272 sec) [ -35253.1520] [Topology ] . ( 277 sec) [ -35253.1481] [Topology ] . ( 282 sec) [ -35253.1452] [Topology ] . ( 287 sec) [ -35253.1429] [Topology ] . ( 292 sec) [ -35253.1412] [Topology ] . ( 295 sec) [ -35253.1382] [GTR parameters ] . ( 295 sec) [ -35253.1382] [Alpha ][ 0.499066] . ( 295 sec) [ -35253.1382] [Topology ] . ( 301 sec) [ -35253.1355] [Topology ] . ( 306 sec) [ -35253.1335] [Topology ] . ( 311 sec) [ -35253.1320] [Topology ] . ( 316 sec) [ -35253.1309] [Topology ] . ( 321 sec) [ -35253.1300] [Topology ] . ( 324 sec) [ -35253.1294] [GTR parameters ] . ( 324 sec) [ -35253.1294] [Alpha ][ 0.499066] . ( 324 sec) [ -35253.1294] [Topology ] . ( 329 sec) [ -35253.1283] [Topology ] . ( 334 sec) [ -35253.1275] [Topology ] . ( 340 sec) [ -35253.1274] [GTR parameters ] . ( 341 sec) [ -35253.1274] [Alpha ][ 0.499066] . ( 341 sec) [ -35253.1274] [Topology ] . ( 346 sec) [ -35253.1266] [Topology ] . ( 347 sec) [ -35253.1266] [GTR parameters ] . ( 348 sec) [ -35253.1266] [Alpha ][ 0.499066] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.126644. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 0h6m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 304.60user 0.00system 6:28.23elapsed 78%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps