Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2921_54x966_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 21 N_GLOBL: 10 MAX_DIST: 10 . Log(lk) : * -> -7272.766108 . Log(lk) : -7272.766108 -> -7175.370167 6 swaps done . Log(lk) : -7175.370167 -> -7164.803555 3 swaps done . Log(lk) : -7164.803555 -> -7163.130267 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6472.257021 -> -6458.692520 4 swaps done . Log(lk) : -6458.692520 -> -6454.348601 3 swaps done . Log(lk) : -6454.348601 -> -6451.330362 1 swap done . Log(lk) : -6451.330362 -> -6450.761857 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6446.976813 -> -6446.563144 1 swap done . Log(lk) : -6446.563144 -> -6446.395252 0 swap done . Log(lk) : -6446.395252 -> -6446.360029 0 swap done . Log(lk) : -6446.360029 -> -6446.348452 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6446.334619 -> -6446.326829 0 swap done . Log(lk) : -6446.326829 -> -6446.323792 0 swap done . Log(lk) : -6446.323792 -> -6446.322528 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 10 -> 103 (1.273788) Log (lk): -6444.415101 . Log(lk) : -6444.415101 -> -6444.382707 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6444.343862 -> -6444.336462 0 swap done . Log(lk) : -6444.336462 -> -6444.334380 0 swap done . Log(lk) : -6444.334380 -> -6444.333678 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -6444.336094 nr_d_L: 16120 nr_d_lk: 5034 nr_loc: 103 nr_glb: 10 . Time used 0h0m34s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 33.31user 0.00system 0:33.65elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps