ngene2_mgene012.ctl

      seqfile = lysinYangSwanson2002.nuc
     treefile = lysin.trees

      outfile = codeml_ngene2_mgene012.out          * main result file name
        noisy = 3   * 0,1,2,3,9: how much rubbish on the screen
      verbose = 0   * 1: detailed output, 0: concise output
      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
                    * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

      seqtype = 1   * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2   * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
        model = 0   * codonml:  0:one, 1:b, 2:2 or more dN/dS ratios for branches

      NSsites = 0   * 0:one w;1:neutral;2:positive; 3:discrete;4:freqs;
                    * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                    * 10:beta&1+gamma; 11:beta&1>normal; 12:0&2normal; 13:3normal
        icode = 0   * 0:standard genetic code; 1:mammalian mt; 2-10:see below
        Mgene = 0   * codonml: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff

    fix_kappa = 0   * 1: kappa fixed, 0: kappa to be estimated
        kappa = 1.6   * initial or fixed kappa
    fix_omega = 0   * 1: omega or omega_1 fixed, 0: estimate 
        omega = .8  * initial or fixed omega, for codons or codon-based AAs

        ncatG = 3   * # of categories in dG of NSsites models

        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates

   Small_Diff = 3e-7
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
       method = 0  * 0: simultaneous; 1: one branch at a time