Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2702_54x886_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 Starting tree : BIONJ Optimise tree topology : yes Optimise branch lengths and rate parameters : yes . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 13156080 . Log(lk) : * -> -5963.310120 . Log(lk) : -5963.310120 -> -5901.773054 3 swaps done . Log(lk) : -5901.773054 -> -5895.379137 3 swaps done . Log(lk) : -5895.379137 -> -5894.199310 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5411.047909 -> -5399.310277 1 swap done . Log(lk) : -5399.310277 -> -5395.664497 1 swap done . Log(lk) : -5395.664497 -> -5392.856892 0 swap done . Log(lk) : -5392.856892 -> -5392.110618 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5388.655879 -> -5387.882031 1 swap done . Log(lk) : -5387.882031 -> -5387.373345 0 swap done . Log(lk) : -5387.373345 -> -5387.178930 0 swap done . Log(lk) : -5387.178930 -> -5387.090374 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.990009 -> -5386.918964 0 swap done . Log(lk) : -5386.918964 -> -5386.796155 1 swap done . Log(lk) : -5386.796155 -> -5386.502725 0 swap done . Log(lk) : -5386.502725 -> -5386.433892 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.422230 -> -5386.394696 0 swap done . Log(lk) : -5386.394696 -> -5386.382370 0 swap done . Log(lk) : -5386.382370 -> -5386.376421 0 swap done . Log(lk) : -5386.376421 -> -5386.373465 0 swap done . Last optimization step... . Log(lk) : * -> -5386.371271 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.371271 -> -5386.366225 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.366225 -> -5386.365418 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.365418 -> -5386.365149 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.365149 -> -5386.365085 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.365085 -> -5386.365068 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.365068 -> -5386.365064 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5386.365064 -> -5386.365064 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -5386.365064 . Time used 0h0m34s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 33.89user 0.00system 0:34.26elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps