seqfile = seqfile.txt   * sequence data filename
      outfile = results.txt   * main result file name

        noisy = 9      * 0,1,2,3,9: how much rubbish on the screen
      verbose = 1      * 1:detailed output
      runmode = -2     * -2:pairwise

      seqtype = 1      * 1:codons
    CodonFreq = 0      * 0:equal, 1:F1X4, 2:F3X4, 3:F61          [change this]
        model = 0      *
      NSsites = 0      * 
        icode = 0      * 0:universal code

    fix_kappa = 1      * 1:kappa fixed, 0:kappa to be estimated  [change this]
        kappa = 1      * initial or fixed kappa

    fix_omega = 0      * 1:omega fixed, 0:omega to be estimated 
        omega = 0.5    * initial omega value


                       * EXCERCISE 2     
                       * Codon bias = none; Ts/Tv bias = none
                       * Codon bias = none; Ts/Tv bias = Yes (ML)

                       * Codon bias = yes (F3x4); Ts/Tv bias = none
                       * Codon bias = yes (F3x4); Ts/Tv bias = Yes (ML)

                       * Codon bias = yes (F61); Ts/Tv bias = none
                       * Codon bias = yes (F61); Ts/Tv bias = Yes (ML)