Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2565_51x1951_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 19 N_GLOBL: 9 MAX_DIST: 9 . Log(lk) : * -> -16255.690579 . Log(lk) : -16255.690579 -> -16079.567878 6 swaps done . Log(lk) : -16079.567878 -> -16064.988001 3 swaps done . Log(lk) : -16064.988001 -> -16063.048764 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14715.512551 -> -14691.237636 1 swap done . Log(lk) : -14691.237636 -> -14679.370939 1 swap done . Log(lk) : -14679.370939 -> -14673.530102 0 swap done . Log(lk) : -14673.530102 -> -14670.885969 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14666.228610 -> -14664.330481 0 swap done . Log(lk) : -14664.330481 -> -14663.355760 0 swap done . Log(lk) : -14663.355760 -> -14662.839397 0 swap done . Log(lk) : -14662.839397 -> -14662.559604 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 12 -> 17 (0.588759) Log (lk): -14660.413058 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.260257 -> -14660.164425 2 swaps done . Log(lk) : -14660.164425 -> -14660.130966 0 swap done . Log(lk) : -14660.130966 -> -14660.113643 0 swap done . Log(lk) : -14660.113643 -> -14660.104250 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.100989 -> -14660.094539 0 swap done . Log(lk) : -14660.094539 -> -14660.091018 0 swap done . Log(lk) : -14660.091018 -> -14660.089085 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -14660.089225 . Last optimization step... . Log(lk) : * -> -14660.089155 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.089155 -> -14660.088897 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.088897 -> -14660.088704 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.088704 -> -14660.088694 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.088694 -> -14660.088692 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.088692 -> -14660.088691 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14660.088691 -> -14660.088690 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 13776 nr_d_lk: 4328 nr_loc: 107 nr_glb: 9 . Time used 0h1m3s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 62.68user 0.00system 1:03.24elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps