Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 31 N_GLOBL: 15 MAX_DIST: 15 . Log(lk) : * -> -3687.632843 . Log(lk) : -3687.632843 -> -3603.557198 15 swaps done . Log(lk) : -3603.557198 -> -3564.586794 12 swaps done . Log(lk) : -3564.586794 -> -3550.620317 11 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3462.799642 -> -3451.948689 6 swaps done . Log(lk) : -3451.948689 -> -3450.449021 5 swaps done . Log(lk) : -3450.449021 -> -3447.513026 3 swaps done . Log(lk) : -3447.513026 -> -3445.370838 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3444.102447 -> -3442.819054 4 swaps done . Log(lk) : -3442.819054 -> -3442.740468 2 swaps done . Log(lk) : -3442.740468 -> -3442.726175 3 swaps done . Log(lk) : -3442.726175 -> -3442.721512 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.673604 -> -3442.700144 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.673604 -> -3442.658066 2 swaps done . Log(lk) : -3442.658066 -> -3442.673526 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.658066 -> -3442.641118 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.641111 -> -3442.639937 1 swap done . Log(lk) : -3442.639937 -> -3442.643583 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.639937 -> -3442.624517 1 swap done . Log(lk) : -3442.624517 -> -3442.617623 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.617615 -> -3442.644135 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3442.617615 -> -3442.617053 3 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 5 -> 121 (20.875944) making move: 55 -> 62 (0.553075) making move: 56 -> 105 (0.432206) making move: 62 -> 46 (2.655623) making move: 99 -> 125 (0.844706) making move: 102 -> 96 (1.669321) making move: 114 -> 111 (0.039916) making move: 121 -> 150 (1.287908) making move: 122 -> 128 (0.148856) making move: 125 -> 5 (1.615136) making move: 128 -> 127 (0.032312) making move: 138 -> 121 (4.609185) making move: 150 -> 2 (4.025557) Log (lk): -3385.308594 . Log(lk) : -3385.308594 -> -3381.526078 8 swaps done . Log(lk) : -3381.526078 -> -3376.771990 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3375.925376 -> -3371.846256 3 swaps done . Log(lk) : -3371.846256 -> -3370.471983 5 swaps done . Log(lk) : -3370.471983 -> -3366.476416 3 swaps done . Log(lk) : -3366.476416 -> -3364.827008 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.773193 -> -3364.774740 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.773193 -> -3364.502512 2 swaps done . Log(lk) : -3364.502512 -> -3364.492035 1 swap done . Log(lk) : -3364.492035 -> -3364.693544 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.492035 -> -3364.362162 0 swap done . Log(lk) : -3364.362162 -> -3364.445069 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.362162 -> -3364.330523 2 swaps done . Log(lk) : -3364.330523 -> -3364.335476 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.330523 -> -3364.320357 2 swaps done . Log(lk) : -3364.320357 -> -3364.317714 1 swap done . Log(lk) : -3364.317714 -> -3364.332160 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.317714 -> -3364.311525 0 swap done . Log(lk) : -3364.311525 -> -3364.344038 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.311525 -> -3364.309757 0 swap done . Log(lk) : -3364.309757 -> -3364.311220 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.309757 -> -3364.307969 0 swap done . Log(lk) : -3364.307969 -> -3364.306650 0 swap done . Log(lk) : -3364.306650 -> -3364.309384 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.306650 -> -3364.304894 0 swap done . Log(lk) : -3364.304894 -> -3364.304733 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 44 -> 14 (0.002369) Log (lk): -3364.300378 . Log(lk) : -3364.300378 -> -3364.295036 2 swaps done . Log(lk) : -3364.295036 -> -3364.296849 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3364.295036 -> -3364.289263 1 swap done . Log(lk) : -3364.289263 -> -3364.279760 0 swap done . Log(lk) : -3364.279760 -> -3364.274257 0 swap done . Log(lk) : -3364.274257 -> -3364.272688 0 swap done . Log(lk) : -3364.272688 -> -3364.272483 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 75 -> 77 (0.001847) Log (lk): -3364.256040 . Log(lk) : -3364.256040 -> -3364.255776 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -3364.255773 nr_d_L: 68948 nr_d_lk: 22198 nr_loc: 300 nr_glb: 17 . Time used 0h1m50s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 103.33user 0.00system 1:49.93elapsed 93%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps