Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2661_66x1027_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 . 9 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 25 N_GLOBL: 12 MAX_DIST: 12 . Log(lk) : * -> -9600.616303 . Log(lk) : -9600.616303 -> -9499.233001 8 swaps done . Log(lk) : -9499.233001 -> -9489.002878 3 swaps done . Log(lk) : -9489.002878 -> -9487.073461 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9173.998077 -> -9147.468725 0 swap done . Log(lk) : -9147.468725 -> -9145.433913 0 swap done . Log(lk) : -9145.433913 -> -9144.776767 0 swap done . Log(lk) : -9144.776767 -> -9144.532447 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9139.081838 -> -9137.951284 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 60 -> 65 (0.050414) Log (lk): -9137.214575 . Log(lk) : -9137.214575 -> -9137.167087 1 swap done . Log(lk) : -9137.167087 -> -9137.153293 0 swap done . Log(lk) : -9137.153293 -> -9137.146706 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9136.823339 -> -9136.757304 0 swap done . Log(lk) : -9136.757304 -> -9136.749263 0 swap done . Log(lk) : -9136.749263 -> -9136.746314 0 swap done . Log(lk) : -9136.746314 -> -9136.744734 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 41 -> 38 (0.001412) Log (lk): -9136.743321 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9136.724152 -> -9136.719163 0 swap done . Log(lk) : -9136.719163 -> -9136.718435 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -9136.718435 nr_d_L: 45304 nr_d_lk: 10771 nr_loc: 200 nr_glb: 13 . Time used 0h1m18s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 75.78user 0.00system 1:18.68elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps