Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2856_61x970_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 = 26775952 . Log(lk) : * -> -27519.746385 . Log(lk) : -27519.746385 -> -27000.567321 4 swaps done . Log(lk) : -27000.567321 -> -26930.626681 5 swaps done . Log(lk) : -26930.626681 -> -26927.243659 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25232.366099 -> -25180.997020 3 swaps done . Log(lk) : -25180.997020 -> -25174.653217 0 swap done . Log(lk) : -25174.653217 -> -25172.536253 1 swap done . Log(lk) : -25172.536253 -> -25171.248873 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25143.328764 -> -25138.730617 0 swap done . Log(lk) : -25138.730617 -> -25136.721661 0 swap done . Log(lk) : -25136.721661 -> -25135.612791 0 swap done . Log(lk) : -25135.612791 -> -25134.956040 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25133.091058 -> -25131.784186 0 swap done . Last optimization step... . Log(lk) : * -> -25130.652715 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25130.652715 -> -25129.356479 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25129.356479 -> -25128.527489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25128.527489 -> -25128.011618 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25128.011618 -> -25127.701401 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.701401 -> -25127.517166 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.517166 -> -25127.405437 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.405437 -> -25127.337411 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.337411 -> -25127.295900 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.295900 -> -25127.270154 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.270154 -> -25127.254037 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.254037 -> -25127.243988 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.243988 -> -25127.237610 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.237610 -> -25127.233581 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.233581 -> -25127.231037 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.231037 -> -25127.229480 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.229480 -> -25127.228262 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.228262 -> -25127.227640 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.227640 -> -25127.227170 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.227170 -> -25127.226912 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226912 -> -25127.226754 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226754 -> -25127.226655 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226655 -> -25127.226590 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226590 -> -25127.226545 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226545 -> -25127.226521 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226521 -> -25127.226508 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226508 -> -25127.226497 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226497 -> -25127.226492 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226492 -> -25127.226489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226489 -> -25127.226486 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226486 -> -25127.226484 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.226484 -> -25127.226484 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -25127.226483 . Time used 0h1m29s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 89.08user 0.00system 1:29.72elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps