Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2588_68x1196_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 = 31845520 . Log(lk) : * -> -13586.486384 . Log(lk) : -13586.486384 -> -13245.557799 10 swaps done . Log(lk) : -13245.557799 -> -13198.438408 6 swaps done . Log(lk) : -13198.438408 -> -13188.198938 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12134.375012 -> -12079.325374 5 swaps done . Log(lk) : -12079.325374 -> -12072.259658 5 swaps done . Log(lk) : -12072.259658 -> -12067.497315 4 swaps done . Log(lk) : -12067.497315 -> -12066.093921 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12043.434528 -> -12039.213895 1 swap done . Log(lk) : -12039.213895 -> -12038.073531 0 swap done . Log(lk) : -12038.073531 -> -12037.607831 0 swap done . Log(lk) : -12037.607831 -> -12037.512741 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12036.031747 -> -12035.440968 0 swap done . Log(lk) : -12035.440968 -> -12035.252893 0 swap done . Log(lk) : -12035.252893 -> -12035.502283 0 swap done . Last optimization step... . Log(lk) : * -> -12033.784589 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.784589 -> -12033.451580 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.451580 -> -12033.355847 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.355847 -> -12033.306755 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.306755 -> -12033.283336 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.283336 -> -12033.267946 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.267946 -> -12033.258564 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.258564 -> -12033.255622 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.255622 -> -12033.254774 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.254774 -> -12033.254033 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.254033 -> -12033.252538 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.252538 -> -12033.249130 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.249130 -> -12033.248513 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.248513 -> -12033.247875 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.247875 -> -12033.247223 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.247223 -> -12033.246550 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.246550 -> -12033.245870 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.245870 -> -12033.245178 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.245178 -> -12033.244464 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.244464 -> -12033.243725 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.243725 -> -12033.242964 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.242964 -> -12033.242175 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.242175 -> -12033.241363 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.241363 -> -12033.239811 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.239811 -> -12033.235621 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.235621 -> -12033.234893 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234893 -> -12033.234742 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234742 -> -12033.234590 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234590 -> -12033.234440 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234440 -> -12033.234287 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234287 -> -12033.234135 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.234135 -> -12033.233981 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233981 -> -12033.233829 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233829 -> -12033.233674 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233674 -> -12033.233520 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233520 -> -12033.233364 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233364 -> -12033.233210 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233210 -> -12033.233122 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233122 -> -12033.233104 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233104 -> -12033.233089 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233089 -> -12033.233073 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.233073 -> -12033.232822 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.232822 -> -12033.232813 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -12033.232813 -> -12033.232812 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -12033.232812 . Time used 0h3m5s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 180.10user 0.00system 3:04.95elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps