.......................... 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)... . ( 3 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] . ( 5 sec) [ -25700.1364] [ 6331] [depth= 1] . ( 6 sec) [ -25699.7942] [ 6333] [depth= 1] . ( 6 sec) [ -25695.6843] [ 6329] [depth= 1] . ( 6 sec) [ -25682.5744] [ 6317] [depth= 2] . ( 6 sec) [ -25682.3575] [ 6318] [depth= 1] . ( 7 sec) [ -25681.9471] [ 6322] [depth= 1] . ( 7 sec) [ -25667.9534] [ 6328] [depth= 1] . ( 7 sec) [ -25663.2486] [ 6322] [depth= 1] . ( 7 sec) [ -25645.8279] [ 6321] [depth= 1] . ( 8 sec) [ -25644.8841] [ 6325] [depth= 1] . ( 8 sec) [ -25613.7274] [ 6321] [depth= 1] . ( 8 sec) [ -25610.6254] [ 6315] [depth= 1] . ( 9 sec) [ -25610.2353] [ 6321] [depth= 1] . ( 9 sec) [ -25603.1721] [ 6325] [depth= 2] . ( 9 sec) [ -25601.1863] [ 6319] [depth= 1] . ( 9 sec) [ -25599.5298] [ 6318] [depth= 2] . ( 9 sec) [ -25589.3879] [ 6317] [depth= 1] . ( 10 sec) [ -25587.2064] [ 6323] [depth= 1] . ( 10 sec) [ -25581.9004] [ 6330] [depth= 1] . ( 10 sec) [ -25571.0055] [ 6330] [depth= 1] . ( 11 sec) [ -25568.1439] [ 6337] [depth= 1] . ( 11 sec) [ -25565.1961] [ 6342] [depth= 2] . ( 11 sec) [ -25558.3858] [ 6339] [depth= 1] . ( 11 sec) [ -25547.6821] [ 6342] [depth= 1] . ( 11 sec) [ -25533.3166] [ 6337] [depth= 1] . ( 11 sec) [ -25528.1986] [ 6338] [depth= 2] . ( 12 sec) [ -25519.9391] [ 6345] [depth= 5] . ( 12 sec) [ -25519.3026] [ 6347] [depth= 1] . ( 12 sec) [ -25492.9153] [ 6356] [depth= 1] . ( 12 sec) [ -25480.8205] [ 6347] [depth= 1] . ( 12 sec) [ -25463.5785] [ 6357] [depth= 1] . ( 12 sec) [ -25453.7727] [ 6346] [depth= 3] . ( 12 sec) [ -25444.9652] [ 6355] [depth= 3] . ( 12 sec) [ -25444.2532] [ 6349] [depth= 3] . ( 13 sec) [ -25436.1849] [ 6353] [depth= 1] . ( 13 sec) [ -25428.1178] [ 6348] [depth= 1] . ( 13 sec) [ -25421.3539] [ 6339] [depth= 4] . ( 13 sec) [ -25420.6965] [ 6342] [depth= 1] . ( 13 sec) [ -25419.0576] [ 6343] [depth= 1] . ( 14 sec) [ -25412.3345] [ 6346] [depth= 1] . ( 14 sec) [ -25403.9203] [ 6342] [depth= 1] . ( 14 sec) [ -25403.2716] [ 6346] [depth= 1] . ( 14 sec) [ -25401.0608] [ 6351] [depth= 3] . ( 14 sec) [ -25399.8385] [ 6351] [depth= 1] . ( 15 sec) [ -25398.4449] [ 6345] [depth= 4] . ( 15 sec) [ -25259.6230] [Branch lengths ] . ( 18 sec) [ -25228.8373] [GTR parameters ] . ( 18 sec) [ -25215.1313] [Alpha ][ 0.418957] . ( 21 sec) [ -25213.1995] [ 6341] [depth= 1] . ( 22 sec) [ -25193.9020] [ 6334] [depth= 1] . ( 23 sec) [ -25188.9409] [ 6334] [depth= 1] . ( 23 sec) [ -25186.0249] [ 6333] [depth= 2] . ( 23 sec) [ -25184.5957] [ 6331] [depth= 1] . ( 24 sec) [ -25184.0624] [ 6333] [depth= 1] . ( 24 sec) [ -25177.1292] [ 6332] [depth= 1] . ( 26 sec) [ -25175.9585] [ 6331] [depth= 1] . ( 27 sec) [ -25172.5163] [ 6327] [depth= 1] . ( 28 sec) [ -25172.2133] [ 6329] [depth= 1] . ( 28 sec) [ -25171.0182] [ 6329] [depth= 1] . ( 29 sec) [ -25137.1760] [Branch lengths ] . ( 32 sec) [ -25133.5479] [GTR parameters ] . ( 32 sec) [ -25133.5472] [Alpha ][ 0.419473] . ( 37 sec) [ -25132.8941] [ 6325] [depth= 1] . ( 43 sec) [ -25126.4129] [Branch lengths ] . ( 45 sec) [ -25125.9114] [GTR parameters ] . ( 46 sec) [ -25125.9114] [Alpha ][ 0.419473] . ( 56 sec) [ -25123.7702] [Branch lengths ] . ( 116 sec) [ -25123.1291] [Branch lengths ] . ( 116 sec) [ -25123.1291] [Topology ] . ( 118 sec) [ -25123.0298] [Topology ] . ( 120 sec) [ -25122.9895] [Topology ] . ( 121 sec) [ -25122.9672] [Topology ] . ( 123 sec) [ -25122.9539] [Topology ] . ( 125 sec) [ -25122.9459] [Topology ] . ( 127 sec) [ -25122.9410] [Topology ] . ( 129 sec) [ -25122.2835] [GTR parameters ] . ( 129 sec) [ -25122.2829] [Alpha ][ 0.418928] . ( 129 sec) [ -25122.2829] [Topology ] . ( 131 sec) [ -25122.1370] [Topology ] . ( 133 sec) [ -25122.0636] [Topology ] . ( 134 sec) [ -25122.0194] [Topology ] . ( 136 sec) [ -25121.9923] [Topology ] . ( 138 sec) [ -25121.9755] [Topology ] . ( 140 sec) [ -25121.9650] [Topology ] . ( 142 sec) [ -25121.8839] [GTR parameters ] . ( 142 sec) [ -25121.8834] [Alpha ][ 0.418431] . ( 142 sec) [ -25121.8834] [Topology ] . ( 144 sec) [ -25121.8475] [Topology ] . ( 145 sec) [ -25121.8273] [Topology ] . ( 147 sec) [ -25121.8147] [Topology ] . ( 149 sec) [ -25121.8068] [Topology ] . ( 151 sec) [ -25121.8019] [Topology ] . ( 152 sec) [ -25121.7988] [Topology ] . ( 154 sec) [ -25121.7745] [GTR parameters ] . ( 154 sec) [ -25121.7744] [Alpha ][ 0.418013] . ( 154 sec) [ -25121.7744] [Topology ] . ( 156 sec) [ -25121.7635] [Topology ] . ( 158 sec) [ -25121.7572] [Topology ] . ( 160 sec) [ -25121.7533] [Topology ] . ( 161 sec) [ -25121.7509] [Topology ] . ( 163 sec) [ -25121.7493] [Topology ] . ( 165 sec) [ -25121.7484] [Topology ] . ( 167 sec) [ -25121.7411] [GTR parameters ] . ( 167 sec) [ -25121.7411] [Alpha ][ 0.418013] . ( 167 sec) [ -25121.7411] [Topology ] . ( 169 sec) [ -25121.7376] [Topology ] . ( 170 sec) [ -25121.7356] [Topology ] . ( 172 sec) [ -25121.7343] [Topology ] . ( 174 sec) [ -25121.7335] [Topology ] . ( 175 sec) [ -25121.7324] [GTR parameters ] . ( 175 sec) [ -25121.7324] [Alpha ][ 0.418013] . ( 175 sec) [ -25121.7324] [Topology ] . ( 177 sec) [ -25121.7313] [Topology ] . ( 179 sec) [ -25121.7306] [Topology ] . ( 180 sec) [ -25121.7302] [GTR parameters ] . ( 180 sec) [ -25121.7302] [Alpha ][ 0.418013] . ( 180 sec) [ -25121.7302] [Topology ] . ( 182 sec) [ -25121.7293] [Topology ] . ( 183 sec) [ -25121.7292] [GTR parameters ] . ( 183 sec) [ -25121.7292] [Alpha ][ 0.418013] . ( 183 sec) [ -25121.7292] [Topology ] . ( 185 sec) [ -25121.7287] [Topology ] . ( 185 sec) [ -25121.7287] [GTR parameters ] . ( 186 sec) [ -25121.7287] [Alpha ][ 0.418013] . Checking for NNIs, optimizing five branches... . ( 202 sec) [ -25121.6886] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25121.688640. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 0h3m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 213.11user 0.00system 3:38.28elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps