Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2786_104x1051_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 48211080 . Log(lk) : * -> -16943.375027 . Log(lk) : -16943.375027 -> -16599.731790 15 swaps done . Log(lk) : -16599.731790 -> -16558.306464 8 swaps done . Log(lk) : -16558.306464 -> -16547.544830 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15698.913914 -> -15680.730324 1 swap done . Log(lk) : -15680.730324 -> -15679.103718 1 swap done . Log(lk) : -15679.103718 -> -15678.566630 0 swap done . Log(lk) : -15678.566630 -> -15678.267731 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15672.256994 -> -15671.502977 0 swap done . Log(lk) : -15671.502977 -> -15671.193927 0 swap done . Log(lk) : -15671.193927 -> -15670.998092 0 swap done . Log(lk) : -15670.998092 -> -15670.865066 0 swap done . Last optimization step... . Log(lk) : * -> -15670.714758 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.714758 -> -15670.428612 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.428612 -> -15670.345275 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.345275 -> -15670.294116 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.294116 -> -15670.263962 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.263962 -> -15670.244198 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.244198 -> -15670.236070 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.236070 -> -15670.232326 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.232326 -> -15670.230325 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.230325 -> -15670.229310 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.229310 -> -15670.228757 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228757 -> -15670.228461 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228461 -> -15670.228294 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228294 -> -15670.228201 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228201 -> -15670.228143 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228143 -> -15670.228105 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228105 -> -15670.228077 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228077 -> -15670.228055 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228055 -> -15670.228035 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228035 -> -15670.228017 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228017 -> -15670.228000 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.228000 -> -15670.227983 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227983 -> -15670.227966 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227966 -> -15670.227949 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227949 -> -15670.227933 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227933 -> -15670.227916 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227916 -> -15670.227899 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227899 -> -15670.227881 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227881 -> -15670.227864 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227864 -> -15670.227847 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227847 -> -15670.227829 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227829 -> -15670.227812 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227812 -> -15670.227794 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227794 -> -15670.227776 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227776 -> -15670.227758 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227758 -> -15670.227740 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227740 -> -15670.227722 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227722 -> -15670.227704 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227704 -> -15670.227685 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227685 -> -15670.227667 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227667 -> -15670.227648 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227648 -> -15670.227629 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227629 -> -15670.227610 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227610 -> -15670.227591 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227591 -> -15670.227572 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227572 -> -15670.227553 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227553 -> -15670.227533 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227533 -> -15670.227514 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227514 -> -15670.227494 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227494 -> -15670.227474 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227474 -> -15670.227454 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227454 -> -15670.227434 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227434 -> -15670.227414 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227414 -> -15670.227393 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227393 -> -15670.227373 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227373 -> -15670.227352 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227352 -> -15670.227331 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227331 -> -15670.227310 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227310 -> -15670.227289 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227289 -> -15670.227268 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227268 -> -15670.227247 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227247 -> -15670.227225 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227225 -> -15670.227204 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227204 -> -15670.227182 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227182 -> -15670.227160 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227160 -> -15670.227138 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227138 -> -15670.227115 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227115 -> -15670.227093 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227093 -> -15670.227070 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227070 -> -15670.227048 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227048 -> -15670.227025 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227025 -> -15670.227002 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.227002 -> -15670.226979 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226979 -> -15670.226955 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226955 -> -15670.226932 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226932 -> -15670.226908 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226908 -> -15670.226884 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226884 -> -15670.226860 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226860 -> -15670.226836 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226836 -> -15670.226812 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226812 -> -15670.226787 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226787 -> -15670.226763 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226763 -> -15670.226738 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226738 -> -15670.226713 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226713 -> -15670.226688 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226688 -> -15670.226662 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226662 -> -15670.226637 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226637 -> -15670.226611 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226611 -> -15670.226585 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226585 -> -15670.226559 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226559 -> -15670.226533 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226533 -> -15670.226507 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226507 -> -15670.226480 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226480 -> -15670.226454 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226454 -> -15670.226427 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226427 -> -15670.226400 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226400 -> -15670.226372 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226372 -> -15670.226345 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226345 -> -15670.226317 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -15670.226317 -> -15670.226289 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -15670.226289 . Time used 0h12m44s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 751.29user 0.00system 12:44.16elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps