seqfile = BRCA1.8s.txt    lysozyme.nuc
     treefile = BRCA1.trees   lysozyme.trees
      outfile = mlc 

        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
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = 
        model = 0
      NSsites = 1
        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 3.1415926 * 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

        clock = 0   * 0:no clock, 1:global clock; 2:local clock; 3:TipDate
        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 = 0   * 0: simultaneous; 1: one branch at a time