Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2845_68x1715_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 28311976 . Log(lk) : * -> -12326.119151 . Log(lk) : -12326.119151 -> -12197.005005 9 swaps done . Log(lk) : -12197.005005 -> -12173.707292 7 swaps done . Log(lk) : -12173.707292 -> -12166.250174 5 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11416.631540 -> -11388.752406 6 swaps done . Log(lk) : -11388.752406 -> -11374.277749 3 swaps done . Log(lk) : -11374.277749 -> -11368.826605 1 swap done . Log(lk) : -11368.826605 -> -11366.606337 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11364.720884 -> -11363.154801 1 swap done . Log(lk) : -11363.154801 -> -11361.923678 1 swap done . Log(lk) : -11361.923678 -> -11361.450266 0 swap done . Log(lk) : -11361.450266 -> -11361.166652 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11361.129532 -> -11360.873145 0 swap done . Log(lk) : -11360.873145 -> -11360.766130 0 swap done . Log(lk) : -11360.766130 -> -11360.708398 0 swap done . Log(lk) : -11360.708398 -> -11360.675926 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.673954 -> -11360.654644 0 swap done . Log(lk) : -11360.654644 -> -11360.643612 0 swap done . Last optimization step... . Log(lk) : * -> -11360.633648 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.633648 -> -11360.629754 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.629754 -> -11360.628670 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628670 -> -11360.628389 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628389 -> -11360.628315 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628315 -> -11360.628295 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628295 -> -11360.628290 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628290 -> -11360.628288 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -11360.628288 -> -11360.628288 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -11360.628288 . Time used 0h1m15s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 72.92user 0.00system 1:14.93elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps