Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 14235200 . Log(lk) : * -> -3678.974423 . Log(lk) : -3678.974423 -> -3582.372190 15 swaps done . Log(lk) : -3582.372190 -> -3539.132555 12 swaps done . Log(lk) : -3539.132555 -> -3528.500941 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3441.354537 -> -3432.970556 8 swaps done . Log(lk) : -3432.970556 -> -3430.916923 6 swaps done . Log(lk) : -3430.916923 -> -3427.605767 4 swaps done . Log(lk) : -3427.605767 -> -3426.363021 5 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3425.231758 -> -3423.945109 2 swaps done . Log(lk) : -3423.945109 -> -3422.120455 4 swaps done . Log(lk) : -3422.120455 -> -3421.688779 3 swaps done . Log(lk) : -3421.688779 -> -3421.595237 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.565994 -> -3421.552014 1 swap done . Log(lk) : -3421.552014 -> -3421.550109 1 swap done . Log(lk) : -3421.550109 -> -3421.549416 0 swap done . Last optimization step... . Log(lk) : * -> -3421.548730 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.548730 -> -3421.546950 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.546950 -> -3421.545896 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.545896 -> -3421.545045 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.545045 -> -3421.544307 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.544307 -> -3421.543728 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.543728 -> -3421.543147 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.543147 -> -3421.542600 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.542600 -> -3421.542108 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.542108 -> -3421.541614 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.541614 -> -3421.541118 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.541118 -> -3421.540619 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.540619 -> -3421.540118 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.540118 -> -3421.539615 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.539615 -> -3421.539109 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.539109 -> -3421.538601 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.538601 -> -3421.538090 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.538090 -> -3421.537577 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.537577 -> -3421.537061 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.537061 -> -3421.536543 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.536543 -> -3421.536022 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.536022 -> -3421.535498 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.535498 -> -3421.534972 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.534972 -> -3421.534443 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.534443 -> -3421.533912 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.533912 -> -3421.533378 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.533378 -> -3421.532841 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.532841 -> -3421.532301 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.532301 -> -3421.531759 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.531759 -> -3421.531214 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.531214 -> -3421.530666 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.530666 -> -3421.530115 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.530115 -> -3421.529562 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.529562 -> -3421.529005 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.529005 -> -3421.526764 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526764 -> -3421.526725 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526725 -> -3421.526685 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526685 -> -3421.526644 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526644 -> -3421.526602 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526602 -> -3421.526560 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526560 -> -3421.526516 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526516 -> -3421.526472 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526472 -> -3421.526426 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526426 -> -3421.526380 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526380 -> -3421.526332 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526332 -> -3421.526284 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526284 -> -3421.526234 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526234 -> -3421.526183 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526183 -> -3421.526132 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526132 -> -3421.526079 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526079 -> -3421.526024 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.526024 -> -3421.525969 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525969 -> -3421.525913 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525913 -> -3421.525855 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525855 -> -3421.525796 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525796 -> -3421.525735 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525735 -> -3421.525674 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525674 -> -3421.525610 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525610 -> -3421.525546 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525546 -> -3421.525480 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525480 -> -3421.525413 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525413 -> -3421.525344 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525344 -> -3421.525274 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525274 -> -3421.525202 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525202 -> -3421.525128 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525128 -> -3421.525053 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.525053 -> -3421.524976 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524976 -> -3421.524898 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524898 -> -3421.524818 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524818 -> -3421.524736 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524736 -> -3421.524652 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524652 -> -3421.524566 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524566 -> -3421.524479 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524479 -> -3421.524389 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524389 -> -3421.524298 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524298 -> -3421.524205 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524205 -> -3421.524109 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524109 -> -3421.524011 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.524011 -> -3421.523912 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523912 -> -3421.523810 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523810 -> -3421.523706 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523706 -> -3421.523599 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523599 -> -3421.523490 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523490 -> -3421.523379 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523379 -> -3421.523265 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523265 -> -3421.523149 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523149 -> -3421.523030 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.523030 -> -3421.522909 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522909 -> -3421.522785 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522785 -> -3421.522658 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522658 -> -3421.522528 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522528 -> -3421.522396 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522396 -> -3421.522261 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522261 -> -3421.522122 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.522122 -> -3421.521981 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.521981 -> -3421.521836 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.521836 -> -3421.521688 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.521688 -> -3421.521537 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.521537 -> -3421.521383 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3421.521383 -> -3421.521225 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -3421.521225 . Time used 0h2m56s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 174.25user 0.00system 2:56.43elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps