Sequence filename : 		 /auto/dufayard/res/parc_wim/nucleic_M2932_68x1712_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

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

. Compressing sequences...

. Computing pairwise distances...

. Building BIONJ tree...

N_RGRFT: 26  N_GLOBL: 13  MAX_DIST: 13


. Log(lk) :               * ->   -15833.292222 
. Log(lk) :   -15833.292222 ->   -15609.479538  11 swaps done 
. Log(lk) :   -15609.479538 ->   -15542.914336   7 swaps done 
. Log(lk) :   -15542.914336 ->   -15528.684910   7 swaps done 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -15032.919465 ->   -14986.972741   6 swaps done 
. Log(lk) :   -14986.972741 ->   -14973.731010   6 swaps done 
. Log(lk) :   -14973.731010 ->   -14960.351157   4 swaps done 
. Log(lk) :   -14960.351157 ->   -14959.298592   3 swaps done 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -14949.455914 ->   -14942.946549   3 swaps done 
. Log(lk) :   -14942.946549 ->   -14940.919889   3 swaps done 
. Log(lk) :   -14940.919889 ->   -14939.260504   3 swaps done 
. Log(lk) :   -14939.260504 ->   -14939.800959   2 swaps done 

. Moving backward (topology + branch lengths) 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -14939.260504 ->   -14934.307812   2 swaps done 
. Log(lk) :   -14934.307812 ->   -14933.234900   0 swap  done
. Log(lk) :   -14933.234900 ->   -14932.867843   1 swap  done
. Log(lk) :   -14932.867843 ->   -14932.420310   1 swap  done
. Log(lk) :   -14932.420310 ->   -14932.050995   0 swap  done
. Log(lk) :   -14932.050995 ->   -14931.853462   1 swap  done
. Log(lk) :   -14931.853462 ->   -14931.769528   0 swap  done
. Log(lk) :   -14931.769528 ->   -14931.694676   0 swap  done
. Log(lk) :   -14931.694676 ->   -14931.585507   0 swap  done
. Log(lk) :   -14931.585507 ->   -14931.595640   0 swap  done

. Moving backward (topology + branch lengths) 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -14931.585507 ->   -14931.249201   0 swap  done
. Log(lk) :   -14931.249201 ->   -14931.167999   0 swap  done
. Log(lk) :   -14931.167999 ->   -14931.142867   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  making move: 5 -> 19 (0.266485)
  making move: 6 -> 21 (0.116013)
  making move: 7 -> 18 (0.158794)
  making move: 8 -> 17 (0.017063)
  making move: 8 -> 30 (0.122434)
  making move: 9 -> 17 (0.011145)
  making move: 9 -> 18 (0.026286)
  making move: 11 -> 30 (0.025741)
  making move: 14 -> 12 (0.010571)
  making move: 14 -> 17 (0.058683)
  making move: 16 -> 14 (0.095133)
  making move: 17 -> 11 (0.010923)
  making move: 18 -> 25 (2.581396)
  making move: 19 -> 22 (0.310069)
  making move: 20 -> 11 (0.081605)
  making move: 21 -> 16 (0.079661)
  making move: 21 -> 22 (0.408825)
  making move: 29 -> 5 (0.150643)
  making move: 60 -> 66 (0.034115)
  making move: 70 -> 60 (0.553729)
Log (lk): -14923.446333

. Log(lk) :   -14923.446333 ->   -14922.923081   3 swaps done 
. Log(lk) :   -14922.923081 ->   -14922.750278   3 swaps done 
. Log(lk) :   -14922.750278 ->   -14922.747080   1 swap  done
. Log(lk) :   -14922.747080 ->   -14922.745848   0 swap  done
. Log(lk) :   -14922.745848 ->   -14922.745208   0 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
  making move: 16 -> 7 (0.000311)
Log (lk): -14922.744393

. Log(lk) :   -14922.744393 ->   -14922.888610   1 swap  done

. Moving backward (topology + branch lengths) 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :   -14922.744393 ->   -14922.727916   1 swap  done
. Log(lk) :   -14922.727916 ->   -14922.726307   1 swap  done
. Log(lk) :   -14922.726307 ->   -14922.725759   1 swap  done
Trying SPR moves
  -calculating tree distances and estimating likelihoods
  -performing local edge length optimizations
  -performing global edge length optimization
Log (lk): -14922.725732
nr_d_L:  41760
nr_d_lk: 11619
nr_loc:  200
nr_glb:  14



. Time used 0h4m40s

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248.41user 0.00system 4:40.63elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps