Sequence filename : 		 /auto/dufayard/res/parc_wim/nucleic_M2655_50x872_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) :               * ->    -7328.895334 
. Log(lk) :    -7328.895334 ->    -7239.006726   5 swaps done 
. Log(lk) :    -7239.006726 ->    -7227.526232   2 swaps done 
. Log(lk) :    -7227.526232 ->    -7223.865903   1 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6547.916919 ->    -6535.541658   1 swap  done
. Log(lk) :    -6535.541658 ->    -6531.364479   1 swap  done
. Log(lk) :    -6531.364479 ->    -6528.769212   0 swap  done
. Log(lk) :    -6528.769212 ->    -6528.150163   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6521.703727 ->    -6521.102284   0 swap  done
. Log(lk) :    -6521.102284 ->    -6520.871592   0 swap  done
. Log(lk) :    -6520.871592 ->    -6520.772203   0 swap  done
. Log(lk) :    -6520.772203 ->    -6520.727031   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  making move: 64 -> 90 (0.316887)
Log (lk): -6519.649919


. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6519.552777 ->    -6517.947349   1 swap  done
. Log(lk) :    -6517.947349 ->    -6517.705742   0 swap  done
. Log(lk) :    -6517.705742 ->    -6517.675064   0 swap  done
. Log(lk) :    -6517.675064 ->    -6517.666237   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6517.652585 ->    -6517.649007   0 swap  done
. Log(lk) :    -6517.649007 ->    -6517.647665   0 swap  done
. Log(lk) :    -6517.647665 ->    -6517.647107   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
Log (lk): -6517.649026


. Last optimization step...

. Log(lk) :               * ->    -6517.648713 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6517.648713 ->    -6517.648585 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6517.648585 ->    -6517.648582 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -6517.648582 ->    -6517.648582 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...
nr_d_L:  14016
nr_d_lk: 4194
nr_loc:  101
nr_glb:  9



. Time used 0h0m34s

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

30.49user 0.00system 0:33.53elapsed 90%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps