seqfile = Bsub_holin_aln_del_codeml.phy   * sequence data filename
     treefile = Bsub_holin_del_codeml_tree.nwk      * tree structure file name
      outfile = Bsub_holin_codeml_output_012del.txt   * main result file name

        noisy = 9      * 0,1,2,3,9: how much rubbish on the screen
      verbose = 1      * 1:detailed output
    cleandata = 0
      runmode = 0     * 0:ML distances in pairwise comparisons
 RateAncestor = 0     * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

      seqtype = 1      * 1:codons
    CodonFreq = 2      * 0:equal, 1:F1X4, 2:F3X4, 3:F61

        model = 0 1 2    * 0:one omega ratio for all branches
       aaDist = 0
      NSsites = 0  1  2

        icode = 0      * 0:universal code
        Mgene = 0      * 0:rates, 1:separate; 2:diff pi, 3:diff kappa

    fix_kappa = 0      * 1:kappa fixed, 0:kappa to be estimated
        kappa = 2      * initial or fixed kappa

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

   *fix_alpha = 1      * 0: estimate gamma shape parameter; 1: fix it at alpha
       *alpha = 1.     * initial or fixed alpha, 0:infinity (constant rate)
      *Malpha = 0      *different alphas for genes
        ncatG = 2      * # of categories in dG of NSsites models

        clock = 0      * 0:no clock, 1:global clock; 2:local clock; 3:TipDate
        getSE = 1      * 0: don't want them, 1: want S.E.s of estimates
       method = 0      * 0: simulataneous; 1: one branch at a time
   Small_Diff = .5e-6


                       *set ncatG for models M3, M7, and M8!!!
       *ncatG = 3      * # of site categories for M3 in Table 4
       *ncatG = 10     * # of site categories for M7 and M8 in Table 4