Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2708_78x1107_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 . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 30913344 . Log(lk) : * -> -7117.883569 . Log(lk) : -7117.883569 -> -6927.303004 9 swaps done . Log(lk) : -6927.303004 -> -6866.981668 8 swaps done . Log(lk) : -6866.981668 -> -6836.069644 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6617.517260 -> -6575.518030 4 swaps done . Log(lk) : -6575.518030 -> -6568.527038 5 swaps done . Log(lk) : -6568.527038 -> -6564.139472 3 swaps done . Log(lk) : -6564.139472 -> -6578.748809 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6564.139472 -> -6548.835640 2 swaps done . Log(lk) : -6548.835640 -> -6543.295249 1 swap done . Log(lk) : -6543.295249 -> -6541.430437 0 swap done . Log(lk) : -6541.430437 -> -6540.721120 0 swap done . Log(lk) : -6540.721120 -> -6540.380465 1 swap done . Log(lk) : -6540.380465 -> -6540.138690 2 swaps done . Log(lk) : -6540.138690 -> -6539.790515 1 swap done . Log(lk) : -6539.790515 -> -6539.708318 1 swap done . Log(lk) : -6539.708318 -> -6539.458936 1 swap done . Log(lk) : -6539.458936 -> -6538.468505 1 swap done . Log(lk) : -6538.468505 -> -6538.294673 0 swap done . Log(lk) : -6538.294673 -> -6538.208499 1 swap done . Log(lk) : -6538.208499 -> -6537.924871 0 swap done . Log(lk) : -6537.924871 -> -6537.892290 0 swap done . Log(lk) : -6537.892290 -> -6537.933525 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6537.892290 -> -6535.623335 0 swap done . Log(lk) : -6535.623335 -> -6534.925276 0 swap done . Log(lk) : -6534.925276 -> -6534.776477 0 swap done . Log(lk) : -6534.776477 -> -6534.709528 0 swap done . Last optimization step... . Log(lk) : * -> -6534.552615 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6534.552615 -> -6534.162022 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6534.162022 -> -6533.923655 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.923655 -> -6533.823658 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.823658 -> -6533.766635 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.766635 -> -6533.723597 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.723597 -> -6533.688178 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.688178 -> -6533.656410 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.656410 -> -6533.626403 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.626403 -> -6533.598574 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.598574 -> -6533.571529 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.571529 -> -6533.552060 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.552060 -> -6533.550421 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550421 -> -6533.550123 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550123 -> -6533.550067 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550067 -> -6533.550040 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550040 -> -6533.550029 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550029 -> -6533.550024 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550024 -> -6533.550022 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550022 -> -6533.550020 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6533.550020 -> -6533.550019 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -6533.550019 . Time used 0h1m57s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 116.19user 0.00system 1:56.81elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps