.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -26079.2058] [GTR parameters ] . ( 4 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 5 sec) [ -25726.2013] [ 6340] [depth= 1] . ( 5 sec) [ -25715.3178] [ 6339] [depth= 1] . ( 5 sec) [ -25709.8673] [ 6334] [depth= 1] . ( 6 sec) [ -25700.1364] [ 6331] [depth= 1] . ( 6 sec) [ -25697.8262] [ 6329] [depth= 1] . ( 7 sec) [ -25678.9271] [ 6330] [depth= 1] . ( 7 sec) [ -25677.4132] [ 6335] [depth= 1] . ( 8 sec) [ -25672.7438] [ 6340] [depth= 1] . ( 8 sec) [ -25664.0873] [ 6336] [depth= 1] . ( 9 sec) [ -25661.1875] [ 6340] [depth= 1] . ( 9 sec) [ -25660.3347] [ 6336] [depth= 1] . ( 9 sec) [ -25654.4833] [ 6336] [depth= 1] . ( 9 sec) [ -25654.0909] [ 6336] [depth= 1] . ( 9 sec) [ -25650.7217] [ 6336] [depth= 1] . ( 9 sec) [ -25635.2378] [ 6337] [depth= 1] . ( 10 sec) [ -25633.9748] [ 6347] [depth= 1] . ( 10 sec) [ -25615.1165] [ 6342] [depth= 1] . ( 10 sec) [ -25607.2855] [ 6358] [depth= 1] . ( 10 sec) [ -25586.3386] [ 6342] [depth= 1] . ( 10 sec) [ -25568.6618] [ 6342] [depth= 1] . ( 10 sec) [ -25555.9237] [ 6344] [depth= 1] . ( 10 sec) [ -25555.3437] [ 6347] [depth= 1] . ( 10 sec) [ -25551.3918] [ 6345] [depth= 1] . ( 11 sec) [ -25550.3380] [ 6347] [depth= 1] . ( 11 sec) [ -25539.7391] [ 6343] [depth= 2] . ( 11 sec) [ -25536.7494] [ 6348] [depth= 1] . ( 11 sec) [ -25534.7573] [ 6352] [depth= 2] . ( 11 sec) [ -25522.8402] [ 6348] [depth= 1] . ( 11 sec) [ -25497.0749] [ 6348] [depth= 2] . ( 12 sec) [ -25474.4437] [ 6348] [depth= 3] . ( 12 sec) [ -25463.4150] [ 6347] [depth= 1] . ( 12 sec) [ -25444.1727] [ 6341] [depth= 2] . ( 12 sec) [ -25426.0305] [ 6345] [depth= 1] . ( 12 sec) [ -25415.3203] [ 6341] [depth= 1] . ( 12 sec) [ -25409.5889] [ 6352] [depth= 1] . ( 13 sec) [ -25408.5906] [ 6350] [depth= 1] . ( 13 sec) [ -25404.1584] [ 6349] [depth= 2] . ( 13 sec) [ -25402.3502] [ 6349] [depth= 1] . ( 13 sec) [ -25396.8801] [ 6350] [depth= 7] . ( 13 sec) [ -25396.8363] [ 6352] [depth= 1] . ( 13 sec) [ -25394.5274] [ 6342] [depth= 1] . ( 14 sec) [ -25387.4347] [ 6342] [depth= 1] . ( 14 sec) [ -25383.8752] [ 6341] [depth= 1] . ( 14 sec) [ -25382.8464] [ 6345] [depth= 1] . ( 15 sec) [ -25238.5790] [Branch lengths ] . ( 18 sec) [ -25209.0270] [GTR parameters ] . ( 18 sec) [ -25195.0487] [Alpha ][ 0.417333] . ( 20 sec) [ -25194.7839] [ 6345] [depth= 1] . ( 20 sec) [ -25194.7272] [ 6345] [depth= 1] . ( 21 sec) [ -25193.3147] [ 6343] [depth= 2] . ( 22 sec) [ -25176.8516] [ 6333] [depth= 1] . ( 22 sec) [ -25174.5477] [ 6329] [depth= 1] . ( 24 sec) [ -25171.9010] [ 6329] [depth= 2] . ( 25 sec) [ -25170.5836] [ 6325] [depth= 2] . ( 27 sec) [ -25169.6058] [ 6320] [depth= 1] . ( 27 sec) [ -25144.8505] [Branch lengths ] . ( 30 sec) [ -25142.1541] [GTR parameters ] . ( 30 sec) [ -25142.1434] [Alpha ][ 0.419417] . ( 39 sec) [ -25133.3244] [Branch lengths ] . ( 102 sec) [ -25130.5216] [Branch lengths ] . ( 102 sec) [ -25130.5216] [Topology ] . ( 104 sec) [ -25129.6511] [Topology ] . ( 106 sec) [ -25129.3000] [Topology ] . ( 109 sec) [ -25129.1283] [Topology ] . ( 112 sec) [ -25129.0207] [Topology ] . ( 115 sec) [ -25128.9482] [Topology ] . ( 118 sec) [ -25128.8980] [Topology ] . ( 121 sec) [ -25128.8642] [Topology ] . ( 125 sec) [ -25125.8538] [GTR parameters ] . ( 125 sec) [ -25125.7653] [Alpha ][ 0.425428] . ( 125 sec) [ -25125.7653] [Topology ] . ( 128 sec) [ -25125.0595] [Topology ] . ( 130 sec) [ -25124.6522] [Topology ] . ( 133 sec) [ -25124.3839] [Topology ] . ( 137 sec) [ -25124.2033] [Topology ] . ( 140 sec) [ -25124.0806] [Topology ] . ( 142 sec) [ -25123.9964] [Topology ] . ( 145 sec) [ -25123.6449] [GTR parameters ] . ( 146 sec) [ -25123.6443] [Alpha ][ 0.424924] . ( 146 sec) [ -25123.6443] [Topology ] . ( 148 sec) [ -25123.4320] [Topology ] . ( 151 sec) [ -25123.2972] [Topology ] . ( 154 sec) [ -25123.2054] [Topology ] . ( 156 sec) [ -25123.1421] [Topology ] . ( 159 sec) [ -25123.0983] [Topology ] . ( 161 sec) [ -25123.0678] [Topology ] . ( 164 sec) [ -25122.9467] [GTR parameters ] . ( 165 sec) [ -25122.9455] [Alpha ][ 0.424175] . ( 165 sec) [ -25122.9455] [Topology ] . ( 168 sec) [ -25122.8709] [Topology ] . ( 171 sec) [ -25122.8226] [Topology ] . ( 174 sec) [ -25122.7892] [Topology ] . ( 177 sec) [ -25122.7659] [Topology ] . ( 180 sec) [ -25122.7495] [Topology ] . ( 183 sec) [ -25122.7378] [Topology ] . ( 185 sec) [ -25122.6958] [GTR parameters ] . ( 185 sec) [ -25122.6951] [Alpha ][ 0.423610] . ( 185 sec) [ -25122.6951] [Topology ] . ( 188 sec) [ -25122.6685] [Topology ] . ( 191 sec) [ -25122.6510] [Topology ] . ( 194 sec) [ -25122.6387] [Topology ] . ( 197 sec) [ -25122.6300] [Topology ] . ( 199 sec) [ -25122.6238] [Topology ] . ( 202 sec) [ -25122.6194] [Topology ] . ( 203 sec) [ -25122.6055] [GTR parameters ] . ( 204 sec) [ -25122.6053] [Alpha ][ 0.423186] . ( 204 sec) [ -25122.6053] [Topology ] . ( 206 sec) [ -25122.5961] [Topology ] . ( 209 sec) [ -25122.5901] [Topology ] . ( 211 sec) [ -25122.5859] [Topology ] . ( 214 sec) [ -25122.5828] [Topology ] . ( 217 sec) [ -25122.5806] [Topology ] . ( 219 sec) [ -25122.5791] [Topology ] . ( 221 sec) [ -25122.5693] [GTR parameters ] . ( 221 sec) [ -25122.5693] [Alpha ][ 0.423186] . ( 221 sec) [ -25122.5693] [Topology ] . ( 223 sec) [ -25122.5653] [Topology ] . ( 226 sec) [ -25122.5626] [Topology ] . ( 229 sec) [ -25122.5607] [Topology ] . ( 231 sec) [ -25122.5593] [Topology ] . ( 234 sec) [ -25122.5583] [Topology ] . ( 236 sec) [ -25122.5563] [GTR parameters ] . ( 236 sec) [ -25122.5561] [Alpha ][ 0.422763] . ( 236 sec) [ -25122.5561] [Topology ] . ( 239 sec) [ -25122.5546] [Topology ] . ( 241 sec) [ -25122.5536] [Topology ] . ( 243 sec) [ -25122.5529] [Topology ] . ( 245 sec) [ -25122.5519] [GTR parameters ] . ( 246 sec) [ -25122.5519] [Alpha ][ 0.422763] . ( 246 sec) [ -25122.5519] [Topology ] . ( 248 sec) [ -25122.5509] [Topology ] . ( 251 sec) [ -25122.5502] [Topology ] . ( 251 sec) [ -25122.5500] [GTR parameters ] . ( 252 sec) [ -25122.5500] [Alpha ][ 0.422763] . ( 252 sec) [ -25122.5500] [Topology ] . ( 254 sec) [ -25122.5493] [Topology ] . ( 255 sec) [ -25122.5492] [GTR parameters ] . ( 256 sec) [ -25122.5492] [Alpha ][ 0.422763] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25122.549250. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 0h4m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 213.52user 0.00system 4:39.70elapsed 76%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps