Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2566_73x918_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: 28 N_GLOBL: 14 MAX_DIST: 14 . Log(lk) : * -> -13469.856830 . Log(lk) : -13469.856830 -> -13237.166465 7 swaps done . Log(lk) : -13237.166465 -> -13206.067520 5 swaps done . Log(lk) : -13206.067520 -> -13197.734607 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12052.880848 -> -12033.003142 5 swaps done . Log(lk) : -12033.003142 -> -12016.534461 1 swap done . Log(lk) : -12016.534461 -> -12011.585120 1 swap done . Log(lk) : -12011.585120 -> -12010.387528 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12005.339693 -> -12004.641082 0 swap done . Log(lk) : -12004.641082 -> -12004.355990 0 swap done . Log(lk) : -12004.355990 -> -12004.226632 0 swap done . Log(lk) : -12004.226632 -> -12004.166155 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12004.128104 -> -12004.086567 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 140 -> 2 (1.285888) Log (lk): -12002.307779 . Log(lk) : -12002.307779 -> -12002.037846 0 swap done . Log(lk) : -12002.037846 -> -12002.015361 0 swap done . Log(lk) : -12002.015361 -> -12002.010066 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12001.964617 -> -12001.961056 0 swap done . Log(lk) : -12001.961056 -> -12001.959827 0 swap done . Log(lk) : -12001.959827 -> -12001.959304 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 1 -> 3 (0.144445) Log (lk): -12001.764992 . Log(lk) : -12001.764992 -> -12001.712160 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12001.709377 -> -12001.703452 0 swap done . Log(lk) : -12001.703452 -> -12001.701819 0 swap done . Log(lk) : -12001.701819 -> -12001.701263 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -12001.713326 nr_d_L: 58352 nr_d_lk: 13334 nr_loc: 256 nr_glb: 26 . Time used 0h2m1s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 120.43user 0.00system 2:01.42elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps