Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2946_110x1003_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: 43 N_GLOBL: 21 MAX_DIST: 21 . Log(lk) : * -> -19425.374607 . Log(lk) : -19425.374607 -> -19001.956528 10 swaps done . Log(lk) : -19001.956528 -> -18930.352522 9 swaps done . Log(lk) : -18930.352522 -> -18910.284444 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17177.001435 -> -17115.390217 8 swaps done . Log(lk) : -17115.390217 -> -17100.082764 4 swaps done . Log(lk) : -17100.082764 -> -17091.569484 3 swaps done . Log(lk) : -17091.569484 -> -17075.525578 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17064.296602 -> -17057.398077 2 swaps done . Log(lk) : -17057.398077 -> -17054.624124 0 swap done . Log(lk) : -17054.624124 -> -17052.704017 1 swap done . Log(lk) : -17052.704017 -> -17050.266016 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17049.954642 -> -17049.031969 0 swap done . Log(lk) : -17049.031969 -> -17048.511601 0 swap done . Log(lk) : -17048.511601 -> -17048.102852 1 swap done . Log(lk) : -17048.102852 -> -17047.596623 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17047.545168 -> -17047.312775 0 swap done . Log(lk) : -17047.312775 -> -17047.173414 0 swap done . Log(lk) : -17047.173414 -> -17047.085905 0 swap done . Log(lk) : -17047.085905 -> -17047.030280 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17047.017353 -> -17046.974627 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 128 -> 108 (8.282877) Log (lk): -17035.684148 . Log(lk) : -17035.684148 -> -17035.166260 2 swaps done . Log(lk) : -17035.166260 -> -17035.070723 0 swap done . Log(lk) : -17035.070723 -> -17035.045078 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17035.028807 -> -17035.013532 0 swap done . Log(lk) : -17035.013532 -> -17035.004930 0 swap done . Log(lk) : -17035.004930 -> -17034.999604 0 swap done . Log(lk) : -17034.999604 -> -17034.996221 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -17034.999145 . Last optimization step... . Log(lk) : * -> -17034.997328 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.997328 -> -17034.996526 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996526 -> -17034.996471 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996471 -> -17034.996462 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996462 -> -17034.996458 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996458 -> -17034.996454 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996454 -> -17034.996450 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996450 -> -17034.996447 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996447 -> -17034.996444 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996444 -> -17034.996441 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996441 -> -17034.996438 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996438 -> -17034.996436 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996436 -> -17034.996433 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996433 -> -17034.996431 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996431 -> -17034.996429 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996429 -> -17034.996427 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996427 -> -17034.996425 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996425 -> -17034.996423 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996423 -> -17034.996421 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996421 -> -17034.996419 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996419 -> -17034.996417 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996417 -> -17034.996416 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996416 -> -17034.996414 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996414 -> -17034.996413 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996413 -> -17034.996411 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996411 -> -17034.996410 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996410 -> -17034.996409 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996409 -> -17034.996408 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996408 -> -17034.996407 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -17034.996407 -> -17034.996406 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 91672 nr_d_lk: 20558 nr_loc: 131 nr_glb: 21 . Time used 0h4m24s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 244.62user 0.00system 4:24.29elapsed 92%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps