seqfile = CephSeq.nuc
     treefile = CephTree.trees

      outfile = mlb       * main result file
        noisy = 3   * 0,1,2,3: how much rubbish on the screen
      verbose = 0   * 1: detailed output, 0: concise output

        model = 3   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
        Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff

        clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
        kappa = 2.3   * initial or fixed kappa

    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
        alpha = 0.5  * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
        ncatG = 5  * # of categories in the dG, AdG, or nparK models of rates

        getSE = 1   * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 0   * (0,1,2): rates (alpha>0) or ancestral states
       method = 0  * 0: simultaneous; 1: one branch at a time
   Small_Diff = 1e-6
*    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?