Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 37108280 . Log(lk) : * -> -38302.116155 . Log(lk) : -38302.116155 -> -37566.181672 7 swaps done . Log(lk) : -37566.181672 -> -37439.405132 8 swaps done . Log(lk) : -37439.405132 -> -37421.771121 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35304.997043 -> -35261.256049 2 swaps done . Log(lk) : -35261.256049 -> -35252.688635 1 swap done . Log(lk) : -35252.688635 -> -35247.802635 2 swaps done . Log(lk) : -35247.802635 -> -35242.525596 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35203.591237 -> -35193.146571 1 swap done . Log(lk) : -35193.146571 -> -35186.738769 0 swap done . Log(lk) : -35186.738769 -> -35182.056166 0 swap done . Log(lk) : -35182.056166 -> -35178.241884 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35173.907473 -> -35167.623125 0 swap done . Log(lk) : -35167.623125 -> -35161.927506 1 swap done . Log(lk) : -35161.927506 -> -35155.628343 1 swap done . Log(lk) : -35155.628343 -> -35151.267796 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35149.520975 -> -35145.433114 0 swap done . Log(lk) : -35145.433114 -> -35142.583517 0 swap done . Log(lk) : -35142.583517 -> -35140.529394 0 swap done . Log(lk) : -35140.529394 -> -35139.020726 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35137.796840 -> -35135.904555 0 swap done . Last optimization step... . Log(lk) : * -> -35133.737830 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35133.737830 -> -35131.101697 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35131.101697 -> -35129.274394 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35129.274394 -> -35128.030172 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35128.030172 -> -35127.256503 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35127.256503 -> -35126.786246 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.786246 -> -35126.512336 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.512336 -> -35126.353828 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.353828 -> -35126.264705 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.264705 -> -35126.214396 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.214396 -> -35126.186639 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.186639 -> -35126.171359 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.171359 -> -35126.163031 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.163031 -> -35126.158497 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.158497 -> -35126.155846 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.155846 -> -35126.154533 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.154533 -> -35126.153858 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153858 -> -35126.153453 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153453 -> -35126.153266 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153266 -> -35126.153149 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153149 -> -35126.153093 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153093 -> -35126.153064 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153064 -> -35126.153046 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153046 -> -35126.153038 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153038 -> -35126.153033 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153033 -> -35126.153030 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153030 -> -35126.153029 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35126.153029 -> -35126.153028 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -35126.153028 . Time used 0h2m17s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 137.23user 0.00system 2:18.00elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps