.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -12871.6129] [GTR parameters ] . ( 5 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 6 sec) [ -12665.5249] [ 2217] [depth= 1] . ( 6 sec) [ -12664.1456] [ 2216] [depth= 1] . ( 6 sec) [ -12663.3354] [ 2216] [depth= 1] . ( 7 sec) [ -12663.1474] [ 2216] [depth= 1] . ( 8 sec) [ -12656.2470] [ 2212] [depth= 1] . ( 8 sec) [ -12655.0119] [ 2216] [depth= 1] . ( 8 sec) [ -12651.8381] [ 2215] [depth= 1] . ( 8 sec) [ -12651.3335] [ 2215] [depth= 1] . ( 8 sec) [ -12651.1414] [ 2215] [depth= 1] . ( 9 sec) [ -12649.1448] [ 2219] [depth= 1] . ( 9 sec) [ -12637.6299] [ 2215] [depth= 1] . ( 9 sec) [ -12634.7804] [ 2215] [depth= 1] . ( 10 sec) [ -12629.7055] [ 2217] [depth= 1] . ( 10 sec) [ -12629.6293] [ 2217] [depth= 1] . ( 10 sec) [ -12626.8639] [ 2215] [depth= 1] . ( 11 sec) [ -12624.9417] [ 2215] [depth= 1] . ( 11 sec) [ -12623.6442] [ 2217] [depth= 1] . ( 11 sec) [ -12621.0609] [ 2215] [depth= 1] . ( 11 sec) [ -12618.2976] [ 2213] [depth= 1] . ( 12 sec) [ -12604.6241] [ 2215] [depth= 2] . ( 12 sec) [ -12603.1243] [ 2216] [depth= 1] . ( 12 sec) [ -12588.8571] [ 2212] [depth= 1] . ( 12 sec) [ -12587.9680] [ 2213] [depth= 1] . ( 12 sec) [ -12585.9881] [ 2216] [depth= 1] . ( 12 sec) [ -12583.0770] [ 2216] [depth= 1] . ( 13 sec) [ -12579.9664] [ 2219] [depth= 3] . ( 13 sec) [ -12572.9388] [ 2219] [depth= 1] . ( 13 sec) [ -12571.5051] [ 2219] [depth= 1] . ( 13 sec) [ -12564.3596] [ 2216] [depth= 1] . ( 13 sec) [ -12559.2770] [ 2219] [depth= 1] . ( 14 sec) [ -12554.3566] [ 2216] [depth= 3] . ( 14 sec) [ -12550.0206] [ 2208] [depth= 1] . ( 15 sec) [ -12439.7786] [Branch lengths ] . ( 18 sec) [ -12437.6775] [GTR parameters ] . ( 18 sec) [ -12375.7376] [Alpha ][ 0.288734] . ( 20 sec) [ -12374.1673] [ 2209] [depth= 1] . ( 20 sec) [ -12372.2907] [ 2206] [depth= 2] . ( 20 sec) [ -12371.7688] [ 2201] [depth= 1] . ( 21 sec) [ -12371.6598] [ 2201] [depth= 1] . ( 21 sec) [ -12371.0384] [ 2204] [depth= 1] . ( 23 sec) [ -12370.9949] [ 2204] [depth= 1] . ( 25 sec) [ -12369.2606] [ 2202] [depth= 1] . ( 26 sec) [ -12368.7826] [ 2202] [depth= 1] . ( 27 sec) [ -12367.4370] [ 2198] [depth= 1] . ( 28 sec) [ -12352.6831] [Branch lengths ] . ( 32 sec) [ -12351.7162] [GTR parameters ] . ( 32 sec) [ -12351.6846] [Alpha ][ 0.292114] . ( 33 sec) [ -12351.5080] [ 2196] [depth= 1] . ( 41 sec) [ -12349.4418] [Branch lengths ] . ( 43 sec) [ -12349.4242] [GTR parameters ] . ( 44 sec) [ -12349.4219] [Alpha ][ 0.292984] . ( 54 sec) [ -12349.0570] [Branch lengths ] . ( 114 sec) [ -12347.4250] [ 2202] [depth= 1] . ( 125 sec) [ -12347.0090] [Branch lengths ] . ( 127 sec) [ -12347.0061] [GTR parameters ] . ( 127 sec) [ -12347.0061] [Alpha ][ 0.292984] . ( 213 sec) [ -12346.9817] [Branch lengths ] . ( 213 sec) [ -12346.9817] [Topology ] . ( 216 sec) [ -12346.9727] [Topology ] . ( 218 sec) [ -12346.9245] [Topology ] . ( 221 sec) [ -12346.7454] [Topology ] . ( 223 sec) [ -12346.7149] [Topology ] . ( 226 sec) [ -12346.7086] [Topology ] . ( 229 sec) [ -12346.7067] [Topology ] . ( 230 sec) [ -12346.7065] [GTR parameters ] . ( 231 sec) [ -12346.7063] [Alpha ][ 0.293277] . ( 231 sec) [ -12346.7063] [Topology ] . ( 233 sec) [ -12346.7056] [Topology ] . ( 234 sec) [ -12346.7056] [GTR parameters ] . ( 235 sec) [ -12346.7056] [Alpha ][ 0.293277] . Checking for NNIs, optimizing five branches... . ( 254 sec) [ -12346.2914] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.291378. . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Time used 0h4m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 232.91user 0.00system 4:35.75elapsed 84%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps