Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2902_51x908_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: 19 N_GLOBL: 9 MAX_DIST: 9 . Log(lk) : * -> -8330.894027 . Log(lk) : -8330.894027 -> -8227.712053 6 swaps done . Log(lk) : -8227.712053 -> -8199.160454 7 swaps done . Log(lk) : -8199.160454 -> -8179.726512 7 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7634.362600 -> -7612.070313 6 swaps done . Log(lk) : -7612.070313 -> -7604.397816 3 swaps done . Log(lk) : -7604.397816 -> -7599.176660 4 swaps done . Log(lk) : -7599.176660 -> -7596.909653 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7594.276973 -> -7593.508215 1 swap done . Log(lk) : -7593.508215 -> -7588.695595 1 swap done . Log(lk) : -7588.695595 -> -7587.900155 1 swap done . Log(lk) : -7587.900155 -> -7587.690452 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7587.678357 -> -7587.623765 0 swap done . Log(lk) : -7587.623765 -> -7587.605125 0 swap done . Log(lk) : -7587.605125 -> -7587.598521 0 swap done . Log(lk) : -7587.598521 -> -7587.596145 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7587.595752 -> -7587.594823 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 83 -> 63 (1.232517) Log (lk): -7584.734882 . Log(lk) : -7584.734882 -> -7584.682030 1 swap done . Log(lk) : -7584.682030 -> -7584.666556 1 swap done . Log(lk) : -7584.666556 -> -7584.664954 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7584.642854 -> -7584.642255 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 12 -> 52 (2.172227) Log (lk): -7581.535430 . Log(lk) : -7581.535430 -> -7580.462243 1 swap done . Log(lk) : -7580.462243 -> -7580.164681 0 swap done . Log(lk) : -7580.164681 -> -7580.118829 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7580.083666 -> -7580.072362 0 swap done . Log(lk) : -7580.072362 -> -7580.069565 0 swap done . Log(lk) : -7580.069565 -> -7580.068841 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 5 -> 85 (4.183779) Log (lk): -7574.693763 . Log(lk) : -7574.693763 -> -7574.236253 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7574.187526 -> -7574.123193 0 swap done . Log(lk) : -7574.123193 -> -7574.106241 0 swap done . Log(lk) : -7574.106241 -> -7574.100928 0 swap done . Log(lk) : -7574.100928 -> -7574.099106 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7574.098887 -> -7574.098177 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 16 -> 22 (0.000069) Log (lk): -7574.098044 . Log(lk) : -7574.098044 -> -7574.097847 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -7574.097847 nr_d_L: 28900 nr_d_lk: 10952 nr_loc: 319 nr_glb: 10 . Time used 0h1m23s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 75.16user 0.00system 1:23.44elapsed 90%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps