Sequence filename : /auto/dufayard/res/bigdatasets_2.4.5_nucl/nucleic_M2573_346x897_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 . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 146668808 . Log(lk) : * -> -10450.928608 . Log(lk) : -10450.928608 -> -10195.992487 62 swaps done . Log(lk) : -10195.992487 -> -10115.267636 48 swaps done . Log(lk) : -10115.267636 -> -10067.039164 36 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9781.640708 -> -9746.330078 38 swaps done . Log(lk) : -9746.330078 -> -9737.996855 24 swaps done . Log(lk) : -9737.996855 -> -9727.807892 23 swaps done . Log(lk) : -9727.807892 -> -9726.107687 17 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9721.263769 -> -9718.645854 14 swaps done . Log(lk) : -9718.645854 -> -9717.986111 15 swaps done . Log(lk) : -9717.986111 -> -9716.852335 15 swaps done . Log(lk) : -9716.852335 -> -9717.343258 13 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9716.852335 -> -9710.648825 13 swaps done . Log(lk) : -9710.648825 -> -9712.940715 10 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9710.648825 -> -9708.927171 10 swaps done . Log(lk) : -9708.927171 -> -9708.379604 9 swaps done . Log(lk) : -9708.379604 -> -9708.925107 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9708.379604 -> -9707.872186 7 swaps done . Log(lk) : -9707.872186 -> -9707.678290 7 swaps done . Log(lk) : -9707.678290 -> -9708.486645 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.678290 -> -9707.424601 8 swaps done . Log(lk) : -9707.424601 -> -9707.627207 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.424601 -> -9707.374410 7 swaps done . Log(lk) : -9707.374410 -> -9707.773517 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.374410 -> -9707.296685 5 swaps done . Log(lk) : -9707.296685 -> -9707.600467 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.296685 -> -9707.245046 5 swaps done . Log(lk) : -9707.245046 -> -9707.582591 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.245046 -> -9707.197412 5 swaps done . Log(lk) : -9707.197412 -> -9707.482181 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.197412 -> -9707.158723 5 swaps done . Log(lk) : -9707.158723 -> -9707.506317 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.158723 -> -9707.110010 5 swaps done . Log(lk) : -9707.110010 -> -9707.421841 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.110010 -> -9707.061580 6 swaps done . Log(lk) : -9707.061580 -> -9707.502856 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.061580 -> -9707.016627 6 swaps done . Log(lk) : -9707.016627 -> -9707.080483 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9707.016627 -> -9706.989842 5 swaps done . Log(lk) : -9706.989842 -> -9707.438319 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.989842 -> -9706.954640 5 swaps done . Log(lk) : -9706.954640 -> -9707.275467 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.954640 -> -9706.954439 5 swaps done . Last optimization step... . Log(lk) : * -> -9706.834880 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.834880 -> -9706.821524 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.821524 -> -9706.816501 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.816501 -> -9706.812970 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.812970 -> -9706.809379 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.809379 -> -9706.805590 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.805590 -> -9706.801587 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.801587 -> -9706.799228 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.799228 -> -9706.798370 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.798370 -> -9706.797565 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.797565 -> -9706.796749 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.796749 -> -9706.795921 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.795921 -> -9706.795081 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.795081 -> -9706.794229 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.794229 -> -9706.793404 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.793404 -> -9706.792603 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.792603 -> -9706.791790 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.791790 -> -9706.790965 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.790965 -> -9706.790127 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.790127 -> -9706.789276 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.789276 -> -9706.788412 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.788412 -> -9706.787534 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.787534 -> -9706.786645 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.786645 -> -9706.785743 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.785743 -> -9706.784827 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.784827 -> -9706.783895 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.783895 -> -9706.782954 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.782954 -> -9706.782335 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.782335 -> -9706.781929 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.781929 -> -9706.781525 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.781525 -> -9706.781130 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.781130 -> -9706.780726 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.780726 -> -9706.780314 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.780314 -> -9706.779890 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.779890 -> -9706.779456 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.779456 -> -9706.779019 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.779019 -> -9706.778574 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.778574 -> -9706.778118 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.778118 -> -9706.777648 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.777648 -> -9706.777165 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.777165 -> -9706.776668 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.776668 -> -9706.776157 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.776157 -> -9706.775637 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.775637 -> -9706.775105 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.775105 -> -9706.774557 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.774557 -> -9706.773992 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.773992 -> -9706.773409 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.773409 -> -9706.772808 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.772808 -> -9706.772188 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.772188 -> -9706.771547 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.771547 -> -9706.770885 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.770885 -> -9706.770214 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.770214 -> -9706.769604 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.769604 -> -9706.769161 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.769161 -> -9706.768705 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.768705 -> -9706.768240 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.768240 -> -9706.767753 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.767753 -> -9706.767245 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.767245 -> -9706.766713 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.766713 -> -9706.766157 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.766157 -> -9706.765575 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.765575 -> -9706.764966 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.764966 -> -9706.764327 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.764327 -> -9706.763657 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.763657 -> -9706.762955 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.762955 -> -9706.762217 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.762217 -> -9706.760215 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.760215 -> -9706.759836 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.759836 -> -9706.759578 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.759578 -> -9706.759317 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.759317 -> -9706.759053 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.759053 -> -9706.758785 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.758785 -> -9706.758512 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.758512 -> -9706.758234 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.758234 -> -9706.757958 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.757958 -> -9706.757679 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.757679 -> -9706.757393 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.757393 -> -9706.757102 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.757102 -> -9706.756804 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.756804 -> -9706.756506 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.756506 -> -9706.756208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.756208 -> -9706.755905 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.755905 -> -9706.755594 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.755594 -> -9706.755277 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.755277 -> -9706.755029 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.755029 -> -9706.754848 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.754848 -> -9706.754666 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.754666 -> -9706.754481 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.754481 -> -9706.754292 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.754292 -> -9706.754100 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.754100 -> -9706.753904 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.753904 -> -9706.753704 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.753704 -> -9706.753501 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.753501 -> -9706.753294 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.753294 -> -9706.753082 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.753082 -> -9706.752867 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.752867 -> -9706.752648 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.752648 -> -9706.752424 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.752424 -> -9706.752231 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9706.752231 -> -9706.752040 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -9706.752040 . Time used 0h28m8s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1678.77user 0.00system 28:07.93elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps