Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2928_81x1651_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 = 26441064 . Log(lk) : * -> -7604.971760 . Log(lk) : -7604.971760 -> -7549.287065 13 swaps done . Log(lk) : -7549.287065 -> -7544.296953 7 swaps done . Log(lk) : -7544.296953 -> -7543.588084 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6734.230017 -> -6726.571308 3 swaps done . Log(lk) : -6726.571308 -> -6724.143811 3 swaps done . Log(lk) : -6724.143811 -> -6722.417539 3 swaps done . Log(lk) : -6722.417539 -> -6721.885002 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6712.162375 -> -6711.922990 3 swaps done . Log(lk) : -6711.922990 -> -6711.832584 0 swap done . Log(lk) : -6711.832584 -> -6711.795702 0 swap done . Log(lk) : -6711.795702 -> -6711.780216 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6690.426839 -> -6690.117211 1 swap done . Log(lk) : -6690.117211 -> -6690.037092 0 swap done . Log(lk) : -6690.037092 -> -6690.006993 1 swap done . Log(lk) : -6690.006993 -> -6689.994883 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.979370 -> -6689.971243 1 swap done . Log(lk) : -6689.971243 -> -6689.967950 0 swap done . Log(lk) : -6689.967950 -> -6689.966549 0 swap done . Log(lk) : -6689.966549 -> -6689.965913 0 swap done . Last optimization step... . Log(lk) : * -> -6689.965433 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.965433 -> -6689.964679 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.964679 -> -6689.964386 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.964386 -> -6689.964138 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.964138 -> -6689.963940 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.963940 -> -6689.963758 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.963758 -> -6689.963571 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.963571 -> -6689.963380 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.963380 -> -6689.963183 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.963183 -> -6689.962981 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.962981 -> -6689.962774 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.962774 -> -6689.962562 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.962562 -> -6689.962344 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.962344 -> -6689.962120 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.962120 -> -6689.961890 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.961890 -> -6689.961655 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.961655 -> -6689.961413 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.961413 -> -6689.961165 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.961165 -> -6689.960910 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.960910 -> -6689.960649 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.960649 -> -6689.960381 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.960381 -> -6689.960105 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.960105 -> -6689.959823 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.959823 -> -6689.959533 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.959533 -> -6689.959236 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.959236 -> -6689.958931 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.958931 -> -6689.958618 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.958618 -> -6689.958297 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.958297 -> -6689.957967 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.957967 -> -6689.957628 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.957628 -> -6689.957281 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.957281 -> -6689.956925 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.956925 -> -6689.956559 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.956559 -> -6689.956184 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.956184 -> -6689.955799 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.955799 -> -6689.955404 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.955404 -> -6689.954998 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.954998 -> -6689.954582 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.954582 -> -6689.954155 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.954155 -> -6689.953717 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.953717 -> -6689.953267 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.953267 -> -6689.952806 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.952806 -> -6689.952332 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.952332 -> -6689.951846 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.951846 -> -6689.951348 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.951348 -> -6689.950836 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.950836 -> -6689.950311 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.950311 -> -6689.949773 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.949773 -> -6689.949444 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.949444 -> -6689.949286 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.949286 -> -6689.949131 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.949131 -> -6689.949090 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6689.949090 -> -6689.949090 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -6689.949090 . Time used 0h2m38s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 153.51user 0.00system 2:37.61elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps