[TYPE] NUCLEOTIDE 1 // nucleotide simulation using algorithm from method 1
[SETTINGS]
    [ancestralprint] NEW
    [output] FASTA
[MODEL] m1 // no insertions, no gamma
  [submodel] HKY 2.5 // HKY with kappa=2.5
  [statefreq] 0.1 0.2 0.3 0.4 // frequencies for T C A G
[NGSPHYPARTITION] t1 m1 1000
