Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2565_51x1951_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 24776136 . Log(lk) : * -> -16271.552753 . Log(lk) : -16271.552753 -> -16080.931278 6 swaps done . Log(lk) : -16080.931278 -> -16064.125136 3 swaps done . Log(lk) : -16064.125136 -> -16061.729310 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14713.179256 -> -14688.831186 2 swaps done . Log(lk) : -14688.831186 -> -14676.906555 1 swap done . Log(lk) : -14676.906555 -> -14671.009907 0 swap done . Log(lk) : -14671.009907 -> -14668.328078 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14663.748763 -> -14661.853278 0 swap done . Log(lk) : -14661.853278 -> -14660.861734 0 swap done . Log(lk) : -14660.861734 -> -14660.330836 0 swap done . Log(lk) : -14660.330836 -> -14660.046236 0 swap done . Last optimization step... . Log(lk) : * -> -14659.816013 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.816013 -> -14659.556321 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.556321 -> -14659.510130 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.510130 -> -14659.496709 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.496709 -> -14659.493249 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.493249 -> -14659.492353 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492353 -> -14659.492127 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492127 -> -14659.492065 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492065 -> -14659.492048 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492048 -> -14659.492043 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492043 -> -14659.492042 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14659.492042 -> -14659.492041 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -14659.492041 . Time used 0h0m48s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 47.30user 0.00system 0:47.82elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps