Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2764_57x803_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 22864224 . Log(lk) : * -> -10695.202636 . Log(lk) : -10695.202636 -> -10511.412879 6 swaps done . Log(lk) : -10511.412879 -> -10486.398541 3 swaps done . Log(lk) : -10486.398541 -> -10481.596934 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10168.530438 -> -10161.921245 4 swaps done . Log(lk) : -10161.921245 -> -10160.360517 3 swaps done . Log(lk) : -10160.360517 -> -10159.664780 2 swaps done . Log(lk) : -10159.664780 -> -10159.261124 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10158.728553 -> -10158.603106 2 swaps done . Log(lk) : -10158.603106 -> -10158.388899 2 swaps done . Log(lk) : -10158.388899 -> -10158.396995 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10158.388899 -> -10158.133068 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10158.133065 -> -10158.064942 0 swap done . Log(lk) : -10158.064942 -> -10158.034026 0 swap done . Log(lk) : -10158.034026 -> -10158.017124 0 swap done . Log(lk) : -10158.017124 -> -10158.007502 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10158.004511 -> -10157.997573 0 swap done . Log(lk) : -10157.997573 -> -10157.993539 0 swap done . Last optimization step... . Log(lk) : * -> -10157.989810 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.989810 -> -10157.987766 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.987766 -> -10157.987121 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.987121 -> -10157.986885 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.986885 -> -10157.986822 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.986822 -> -10157.986802 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.986802 -> -10157.986796 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.986796 -> -10157.986794 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10157.986794 -> -10157.986793 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -10157.986793 . Time used 0h0m52s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 51.88user 0.00system 0:52.40elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps