Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2856_61x970_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 23 N_GLOBL: 11 MAX_DIST: 11 . Log(lk) : * -> -27359.736425 . Log(lk) : -27359.736425 -> -26992.992986 5 swaps done . Log(lk) : -26992.992986 -> -26927.462960 4 swaps done . Log(lk) : -26927.462960 -> -26919.496797 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25211.622612 -> -25178.281170 2 swaps done . Log(lk) : -25178.281170 -> -25172.855376 1 swap done . Log(lk) : -25172.855376 -> -25170.370880 1 swap done . Log(lk) : -25170.370880 -> -25169.020078 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25142.007771 -> -25137.456419 0 swap done . Log(lk) : -25137.456419 -> -25135.463939 0 swap done . Log(lk) : -25135.463939 -> -25134.364421 0 swap done . Log(lk) : -25134.364421 -> -25133.713155 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25131.876482 -> -25130.580319 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 27 (1.025750) Log (lk): -25128.896071 . Log(lk) : -25128.896071 -> -25128.607776 1 swap done . Log(lk) : -25128.607776 -> -25128.526313 0 swap done . Log(lk) : -25128.526313 -> -25128.482713 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25127.499308 -> -25127.192766 0 swap done . Log(lk) : -25127.192766 -> -25127.014783 0 swap done . Log(lk) : -25127.014783 -> -25126.898487 0 swap done . Log(lk) : -25126.898487 -> -25126.820802 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 27 (0.043785) Log (lk): -25126.730426 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.474080 -> -25126.347896 1 swap done . Log(lk) : -25126.347896 -> -25126.298721 0 swap done . Log(lk) : -25126.298721 -> -25126.269066 0 swap done . Log(lk) : -25126.269066 -> -25126.249064 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.217757 -> -25126.185421 0 swap done . Log(lk) : -25126.185421 -> -25126.164130 0 swap done . Log(lk) : -25126.164130 -> -25126.149443 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -25126.150724 . Last optimization step... . Log(lk) : * -> -25126.140982 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.140982 -> -25126.103090 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.103090 -> -25126.075634 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.075634 -> -25126.063020 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.063020 -> -25126.060418 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.060418 -> -25126.059183 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.059183 -> -25126.058161 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.058161 -> -25126.056608 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.056608 -> -25126.054257 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.054257 -> -25126.053304 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.053304 -> -25126.052989 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.052989 -> -25126.052012 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.052012 -> -25126.050363 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050363 -> -25126.050226 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050226 -> -25126.050213 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050213 -> -25126.050202 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050202 -> -25126.050193 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050193 -> -25126.050184 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050184 -> -25126.050177 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050177 -> -25126.050170 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050170 -> -25126.050164 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050164 -> -25126.050158 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050158 -> -25126.050152 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050152 -> -25126.050146 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050146 -> -25126.050141 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050141 -> -25126.050135 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050135 -> -25126.050130 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050130 -> -25126.050126 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050126 -> -25126.050121 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050121 -> -25126.050116 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050116 -> -25126.050112 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050112 -> -25126.050107 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050107 -> -25126.050103 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050103 -> -25126.050099 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050099 -> -25126.050095 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050095 -> -25126.050092 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050092 -> -25126.050088 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050088 -> -25126.050085 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050085 -> -25126.050082 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050082 -> -25126.050079 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050079 -> -25126.050076 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050076 -> -25126.050073 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050073 -> -25126.050070 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050070 -> -25126.050067 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050067 -> -25126.050064 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050064 -> -25126.050062 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050062 -> -25126.050059 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050059 -> -25126.050057 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050057 -> -25126.050055 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050055 -> -25126.050053 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050053 -> -25126.050051 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050051 -> -25126.050049 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050049 -> -25126.050047 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050047 -> -25126.050045 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050045 -> -25126.050043 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050043 -> -25126.050042 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050042 -> -25126.050040 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050040 -> -25126.050038 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050038 -> -25126.050037 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050037 -> -25126.050035 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050035 -> -25126.050034 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050034 -> -25126.050033 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050033 -> -25126.050031 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050031 -> -25126.050030 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050030 -> -25126.050029 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050029 -> -25126.050028 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050028 -> -25126.050026 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050026 -> -25126.050025 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050025 -> -25126.050024 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -25126.050024 -> -25126.050023 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 37104 nr_d_lk: 9225 nr_loc: 300 nr_glb: 13 . Time used 0h4m28s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 208.94user 0.00system 4:28.54elapsed 77%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps