Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2933_99x1634_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 = 36968880 . Log(lk) : * -> -8221.088939 . Log(lk) : -8221.088939 -> -8075.006772 16 swaps done . Log(lk) : -8075.006772 -> -8030.353030 14 swaps done . Log(lk) : -8030.353030 -> -8012.859722 12 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7727.924404 -> -7683.300070 13 swaps done . Log(lk) : -7683.300070 -> -7670.247853 10 swaps done . Log(lk) : -7670.247853 -> -7663.841828 11 swaps done . Log(lk) : -7663.841828 -> -7660.934543 8 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7657.338812 -> -7653.402900 8 swaps done . Log(lk) : -7653.402900 -> -7652.284525 6 swaps done . Log(lk) : -7652.284525 -> -7647.015004 6 swaps done . Log(lk) : -7647.015004 -> -7646.170238 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7645.980229 -> -7641.398163 6 swaps done . Log(lk) : -7641.398163 -> -7642.014377 4 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7641.398163 -> -7640.688916 4 swaps done . Log(lk) : -7640.688916 -> -7641.230910 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.688916 -> -7640.482921 3 swaps done . Log(lk) : -7640.482921 -> -7640.557872 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.482921 -> -7640.360254 3 swaps done . Log(lk) : -7640.360254 -> -7640.697782 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.360254 -> -7640.339256 3 swaps done . Log(lk) : -7640.339256 -> -7640.412545 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.339256 -> -7640.281221 3 swaps done . Log(lk) : -7640.281221 -> -7640.425180 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.281221 -> -7640.267224 5 swaps done . Log(lk) : -7640.267224 -> -7640.305860 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.267224 -> -7640.241715 3 swaps done . Log(lk) : -7640.241715 -> -7640.314451 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.241715 -> -7640.199660 3 swaps done . Log(lk) : -7640.199660 -> -7640.191698 3 swaps done . Log(lk) : -7640.191698 -> -7640.226512 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.191698 -> -7640.178117 0 swap done . Log(lk) : -7640.178117 -> -7640.179007 1 swap done . Last optimization step... . Log(lk) : * -> -7640.142559 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.142559 -> -7640.118451 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.118451 -> -7640.097366 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.097366 -> -7640.078796 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.078796 -> -7640.061983 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.061983 -> -7640.046291 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.046291 -> -7640.031244 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.031244 -> -7640.016518 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.016518 -> -7640.001883 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.001883 -> -7639.987182 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.987182 -> -7639.972902 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.972902 -> -7639.967447 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.967447 -> -7639.966298 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.966298 -> -7639.965489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.965489 -> -7639.964871 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.964871 -> -7639.964451 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.964451 -> -7639.964106 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.964106 -> -7639.963804 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.963804 -> -7639.963529 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.963529 -> -7639.963270 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.963270 -> -7639.963019 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.963019 -> -7639.962790 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.962790 -> -7639.962570 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.962570 -> -7639.962350 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.962350 -> -7639.962129 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.962129 -> -7639.961906 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.961906 -> -7639.961680 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.961680 -> -7639.961452 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.961452 -> -7639.961220 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.961220 -> -7639.960986 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.960986 -> -7639.960748 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.960748 -> -7639.960506 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.960506 -> -7639.960261 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.960261 -> -7639.960012 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.960012 -> -7639.959759 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.959759 -> -7639.959503 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.959503 -> -7639.959242 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.959242 -> -7639.958978 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.958978 -> -7639.958709 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.958709 -> -7639.958436 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.958436 -> -7639.958159 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.958159 -> -7639.957878 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.957878 -> -7639.957592 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.957592 -> -7639.957302 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.957302 -> -7639.957007 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.957007 -> -7639.956708 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.956708 -> -7639.956404 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.956404 -> -7639.956095 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.956095 -> -7639.955781 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.955781 -> -7639.955463 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.955463 -> -7639.955139 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.955139 -> -7639.954810 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.954810 -> -7639.954476 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.954476 -> -7639.954137 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.954137 -> -7639.953793 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.953793 -> -7639.953442 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.953442 -> -7639.953087 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.953087 -> -7639.952725 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.952725 -> -7639.952358 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.952358 -> -7639.951985 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.951985 -> -7639.951606 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.951606 -> -7639.951221 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.951221 -> -7639.950830 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.950830 -> -7639.950432 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.950432 -> -7639.950028 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.950028 -> -7639.949617 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.949617 -> -7639.949216 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.949216 -> -7639.948814 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.948814 -> -7639.948406 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.948406 -> -7639.947996 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947996 -> -7639.947775 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947775 -> -7639.947577 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947577 -> -7639.947333 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947333 -> -7639.947163 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947163 -> -7639.947082 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947082 -> -7639.947000 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.947000 -> -7639.946918 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946918 -> -7639.946836 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946836 -> -7639.946753 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946753 -> -7639.946670 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946670 -> -7639.946587 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946587 -> -7639.946504 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946504 -> -7639.946420 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946420 -> -7639.946336 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946336 -> -7639.946277 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946277 -> -7639.946236 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946236 -> -7639.946195 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946195 -> -7639.946154 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946154 -> -7639.946112 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946112 -> -7639.946070 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946070 -> -7639.946027 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.946027 -> -7639.945984 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945984 -> -7639.945940 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945940 -> -7639.945896 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945896 -> -7639.945851 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945851 -> -7639.945806 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945806 -> -7639.945760 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945760 -> -7639.945714 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945714 -> -7639.945668 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.945668 -> -7639.945624 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -7639.945624 . Time used 0h7m1s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 419.90user 0.00system 7:01.23elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps