.......................... 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] . ( 7 sec) [ -36464.9677] [ 8258] [depth= 1] . ( 7 sec) [ -36460.8603] [ 8291] [depth= 2] . ( 7 sec) [ -36413.8896] [ 8255] [depth= 2] . ( 8 sec) [ -36411.3454] [ 8249] [depth= 1] . ( 8 sec) [ -36397.3331] [ 8254] [depth= 1] . ( 8 sec) [ -36396.4495] [ 8264] [depth= 1] . ( 9 sec) [ -36396.4283] [ 8268] [depth= 1] . ( 9 sec) [ -36393.2290] [ 8263] [depth= 2] . ( 9 sec) [ -36391.5326] [ 8259] [depth= 1] . ( 10 sec) [ -36388.9751] [ 8260] [depth= 1] . ( 10 sec) [ -36362.6353] [ 8249] [depth= 5] . ( 10 sec) [ -36359.1347] [ 8255] [depth= 1] . ( 11 sec) [ -36350.2260] [ 8249] [depth= 1] . ( 12 sec) [ -36349.7371] [ 8242] [depth= 1] . ( 12 sec) [ -36349.4200] [ 8246] [depth= 1] . ( 13 sec) [ -36343.2807] [ 8241] [depth= 1] . ( 13 sec) [ -36329.9012] [ 8240] [depth= 1] . ( 17 sec) [ -36327.9565] [ 8239] [depth= 1] . ( 19 sec) [ -36197.4375] [Branch lengths ] . ( 26 sec) [ -35337.0661] [GTR parameters ] . ( 26 sec) [ -35334.1525] [Alpha ][ 0.463557] . ( 29 sec) [ -35331.7797] [ 8231] [depth= 1] . ( 31 sec) [ -35326.9401] [ 8235] [depth= 1] . ( 31 sec) [ -35323.2659] [ 8231] [depth= 1] . ( 40 sec) [ -35284.2968] [Branch lengths ] . ( 44 sec) [ -35280.5360] [GTR parameters ] . ( 44 sec) [ -35279.7293] [Alpha ][ 0.482446] . ( 58 sec) [ -35265.7588] [Branch lengths ] . ( 139 sec) [ -35261.5709] [Branch lengths ] . ( 139 sec) [ -35261.5709] [Topology ] . ( 142 sec) [ -35260.7430] [Topology ] . ( 145 sec) [ -35260.3509] [Topology ] . ( 148 sec) [ -35260.0876] [Topology ] . ( 150 sec) [ -35259.9043] [Topology ] . ( 153 sec) [ -35259.7739] [Topology ] . ( 156 sec) [ -35259.6805] [Topology ] . ( 159 sec) [ -35256.7278] [GTR parameters ] . ( 160 sec) [ -35256.1861] [Alpha ][ 0.497802] . ( 160 sec) [ -35256.1861] [Topology ] . ( 163 sec) [ -35255.4758] [Topology ] . ( 165 sec) [ -35255.0131] [Topology ] . ( 168 sec) [ -35254.6866] [Topology ] . ( 171 sec) [ -35254.4527] [Topology ] . ( 174 sec) [ -35254.2838] [Topology ] . ( 177 sec) [ -35254.1601] [Topology ] . ( 178 sec) [ -35254.0202] [GTR parameters ] . ( 179 sec) [ -35254.0124] [Alpha ][ 0.499682] . ( 179 sec) [ -35254.0124] [Topology ] . ( 182 sec) [ -35253.8451] [Topology ] . ( 185 sec) [ -35253.7249] [Topology ] . ( 187 sec) [ -35253.6364] [Topology ] . ( 190 sec) [ -35253.5712] [Topology ] . ( 193 sec) [ -35253.5228] [Topology ] . ( 196 sec) [ -35253.4868] [Topology ] . ( 197 sec) [ -35253.4261] [GTR parameters ] . ( 198 sec) [ -35253.4261] [Alpha ][ 0.499682] . ( 198 sec) [ -35253.4261] [Topology ] . ( 201 sec) [ -35253.3725] [Topology ] . ( 204 sec) [ -35253.3340] [Topology ] . ( 206 sec) [ -35253.3053] [Topology ] . ( 209 sec) [ -35253.2838] [Topology ] . ( 212 sec) [ -35253.2676] [Topology ] . ( 215 sec) [ -35253.2554] [Topology ] . ( 216 sec) [ -35253.2326] [GTR parameters ] . ( 216 sec) [ -35253.2326] [Alpha ][ 0.499682] . ( 216 sec) [ -35253.2326] [Topology ] . ( 219 sec) [ -35253.2134] [Topology ] . ( 222 sec) [ -35253.1996] [Topology ] . ( 225 sec) [ -35253.1893] [Topology ] . ( 228 sec) [ -35253.1815] [Topology ] . ( 231 sec) [ -35253.1756] [Topology ] . ( 234 sec) [ -35253.1711] [Topology ] . ( 235 sec) [ -35253.1631] [GTR parameters ] . ( 236 sec) [ -35253.1629] [Alpha ][ 0.499183] . ( 236 sec) [ -35253.1629] [Topology ] . ( 239 sec) [ -35253.1561] [Topology ] . ( 241 sec) [ -35253.1513] [Topology ] . ( 244 sec) [ -35253.1476] [Topology ] . ( 247 sec) [ -35253.1448] [Topology ] . ( 250 sec) [ -35253.1427] [Topology ] . ( 253 sec) [ -35253.1412] [Topology ] . ( 255 sec) [ -35253.1379] [GTR parameters ] . ( 255 sec) [ -35253.1379] [Alpha ][ 0.499183] . ( 255 sec) [ -35253.1379] [Topology ] . ( 258 sec) [ -35253.1354] [Topology ] . ( 261 sec) [ -35253.1335] [Topology ] . ( 264 sec) [ -35253.1321] [Topology ] . ( 267 sec) [ -35253.1311] [Topology ] . ( 269 sec) [ -35253.1302] [Topology ] . ( 271 sec) [ -35253.1295] [GTR parameters ] . ( 271 sec) [ -35253.1295] [Alpha ][ 0.499183] . ( 271 sec) [ -35253.1295] [Topology ] . ( 274 sec) [ -35253.1285] [Topology ] . ( 275 sec) [ -35253.1284] [GTR parameters ] . ( 275 sec) [ -35253.1284] [Alpha ][ 0.499183] . ( 275 sec) [ -35253.1284] [Topology ] . ( 278 sec) [ -35253.1275] [Topology ] . ( 279 sec) [ -35253.1274] [GTR parameters ] . ( 280 sec) [ -35253.1274] [Alpha ][ 0.499183] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127376. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 0h5m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 302.25user 0.00system 5:04.50elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps