Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2623_139x1044_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 . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 55 N_GLOBL: 27 MAX_DIST: 27 . Log(lk) : * -> -50285.174144 . Log(lk) : -50285.174144 -> -49414.884616 16 swaps done . Log(lk) : -49414.884616 -> -49189.021858 12 swaps done . Log(lk) : -49189.021858 -> -49122.643000 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46615.695673 -> -46428.078493 6 swaps done . Log(lk) : -46428.078493 -> -46375.965213 8 swaps done . Log(lk) : -46375.965213 -> -46322.638157 7 swaps done . Log(lk) : -46322.638157 -> -46288.689658 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46244.573591 -> -46205.667599 3 swaps done . Log(lk) : -46205.667599 -> -46176.059195 4 swaps done . Log(lk) : -46176.059195 -> -46176.282284 4 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46176.059195 -> -46158.896098 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46158.896075 -> -46152.583705 2 swaps done . Log(lk) : -46152.583705 -> -46149.504524 0 swap done . Log(lk) : -46149.504524 -> -46149.841457 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46149.504524 -> -46145.749110 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46145.749099 -> -46143.949614 0 swap done . Log(lk) : -46143.949614 -> -46142.876258 0 swap done . Log(lk) : -46142.876258 -> -46142.211654 0 swap done . Log(lk) : -46142.211654 -> -46141.806304 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 33 -> 56 (6.906776) making move: 58 -> 34 (1.917812) making move: 67 -> 102 (10.326112) making move: 95 -> 92 (13.913383) making move: 96 -> 90 (4.177332) making move: 97 -> 67 (3.519960) making move: 143 -> 193 (20.410789) making move: 148 -> 201 (67.628070) making move: 150 -> 238 (8.951384) making move: 151 -> 205 (0.750370) making move: 161 -> 257 (44.057208) Log (lk): -45914.642614 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45913.395052 -> -45906.524131 3 swaps done . Log(lk) : -45906.524131 -> -45903.206874 1 swap done . Log(lk) : -45903.206874 -> -45899.936545 1 swap done . Log(lk) : -45899.936545 -> -45899.190795 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45899.088770 -> -45898.728888 1 swap done . Log(lk) : -45898.728888 -> -45896.025677 1 swap done . Log(lk) : -45896.025677 -> -45890.860633 2 swaps done . Log(lk) : -45890.860633 -> -45888.761510 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45888.734347 -> -45886.482527 1 swap done . Log(lk) : -45886.482527 -> -45886.048094 0 swap done . Log(lk) : -45886.048094 -> -45886.794277 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45886.048094 -> -45884.500330 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45884.500324 -> -45883.706379 1 swap done . Log(lk) : -45883.706379 -> -45883.248257 0 swap done . Log(lk) : -45883.248257 -> -45883.109920 0 swap done . Log(lk) : -45883.109920 -> -45883.068150 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45883.059591 -> -45883.060487 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 104 -> 158 (0.046425) Log (lk): -45882.522714 . Log(lk) : -45882.522714 -> -45881.983978 1 swap done . Log(lk) : -45881.983978 -> -45881.878531 1 swap done . Log(lk) : -45881.878531 -> -45881.832675 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45881.828902 -> -45881.805299 1 swap done . Log(lk) : -45881.805299 -> -45881.797689 0 swap done . Log(lk) : -45881.797689 -> -45881.803026 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45881.797689 -> -45881.775676 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45881.775580 -> -45881.773124 0 swap done . Log(lk) : -45881.773124 -> -45881.771877 0 swap done . Log(lk) : -45881.771877 -> -45881.771331 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 58 -> 46 (0.266802) Log (lk): -45880.823092 . Log(lk) : -45880.823092 -> -45880.600881 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45880.596735 -> -45880.512616 0 swap done . Log(lk) : -45880.512616 -> -45880.467729 0 swap done . Log(lk) : -45880.467729 -> -45880.443121 0 swap done . Log(lk) : -45880.443121 -> -45880.429381 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45880.428967 -> -45880.421160 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 67 -> 110 (1.144173) Log (lk): -45879.405612 . Log(lk) : -45879.405612 -> -45879.079963 0 swap done . Log(lk) : -45879.079963 -> -45879.006551 0 swap done . Log(lk) : -45879.006551 -> -45878.980698 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.977348 -> -45878.968284 0 swap done . Log(lk) : -45878.968284 -> -45878.965439 0 swap done . Log(lk) : -45878.965439 -> -45878.965865 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -45878.969231 . Last optimization step... . Log(lk) : * -> -45878.965527 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.965527 -> -45878.964717 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.964717 -> -45878.964678 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.964678 -> -45878.964666 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.964666 -> -45878.964665 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.964665 -> -45878.964664 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -45878.964664 -> -45878.964663 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 371912 nr_d_lk: 82456 nr_loc: 302 nr_glb: 48 . Time used 0h18m57s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1110.82user 0.00system 18:57.25elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps