Sequence filename : 		 /auto/dufayard/res/parc_wim/nucleic_M2786_104x1051_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

. 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')...

. Compressing sequences...

. Computing pairwise distances...

. Building BIONJ tree...

N_RGRFT: 41  N_GLOBL: 20  MAX_DIST: 20


. Log(lk) :               * ->   -16900.792836 
. Log(lk) :   -16900.792836 ->   -16614.878500  15 swaps done 
. Log(lk) :   -16614.878500 ->   -16551.927466   9 swaps done 
. Log(lk) :   -16551.927466 ->   -16537.371266   5 swaps done 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15697.795484 ->   -15675.154222   3 swaps done 
. Log(lk) :   -15675.154222 ->   -15670.320387   2 swaps done 
. Log(lk) :   -15670.320387 ->   -15668.582322   0 swap  done
. Log(lk) :   -15668.582322 ->   -15668.139958   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15661.621943 ->   -15660.791451   0 swap  done
. Log(lk) :   -15660.791451 ->   -15660.460302   0 swap  done
. Log(lk) :   -15660.460302 ->   -15660.250728   0 swap  done
. Log(lk) :   -15660.250728 ->   -15660.107382   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
  making move: 65 -> 76 (0.181059)
Log (lk): -15659.812478


. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.617689 ->   -15659.574180   1 swap  done
. Log(lk) :   -15659.574180 ->   -15659.550369   0 swap  done
. Log(lk) :   -15659.550369 ->   -15659.533373   0 swap  done
. Log(lk) :   -15659.533373 ->   -15659.520720   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.519581 ->   -15659.509268   0 swap  done
. Log(lk) :   -15659.509268 ->   -15659.501472   0 swap  done
. Log(lk) :   -15659.501472 ->   -15659.495546   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
  making move: 94 -> 120 (0.157738)
Log (lk): -15659.310538

. Log(lk) :   -15659.310538 ->   -15659.268102   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.260055 ->   -15659.249617   0 swap  done
. Log(lk) :   -15659.249617 ->   -15659.245848   0 swap  done
. Log(lk) :   -15659.245848 ->   -15659.243302   0 swap  done
. Log(lk) :   -15659.243302 ->   -15659.241424   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.241357 ->   -15659.239814   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
  making move: 85 -> 9 (0.051787)
Log (lk): -15659.188656

. Log(lk) :   -15659.188656 ->   -15659.176069   0 swap  done
. Log(lk) :   -15659.176069 ->   -15659.174654   0 swap  done
. Log(lk) :   -15659.174654 ->   -15659.174106   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
  making move: 76 -> 65 (0.000252)
Log (lk): -15659.172630


. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.170356 ->   -15659.177604   1 swap  done

. Moving backward (topology + branch lengths) 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15659.170356 ->   -15659.166799   1 swap  done
. Log(lk) :   -15659.166799 ->   -15659.162950   1 swap  done
. Log(lk) :   -15659.162950 ->   -15659.162496   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
Log (lk): -15659.165510
nr_d_L:  204896
nr_d_lk: 46379
nr_loc:  500
nr_glb:  63



. Time used 0h8m38s

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

442.67user 0.00system 8:38.85elapsed 85%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps