seqfile = lysozymeLarge.nuc
     treefile = lysozymeLarge.trees

      outfile = mlc 
        noisy = 3
      verbose = 0
      runmode = 0

      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
        clock = 0   * 0:no clock, 1:global clock; 2:local clock; 3:TipDate
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = /../wag.dat
        model = 2
                   * models for codons:
                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches

      NSsites = 2  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                   * 13:3normal>0

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
        kappa = 3  * initial or fixed kappa
    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
        omega = 1  * initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
        alpha = 0  * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0  * different alphas for genes
        ncatG = 10  * # of categories in dG of NSsites models

        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 0  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

   Small_Diff = .5e-6
*    cleandata = 1
*       method = 1   * 0: simultaneous; 1: one branch at a time