Codeml.ctl

From MolEvol
     seqfile = seqfile.txt   * sequence data filename
    treefile = tree.txt      * tree structure file name
     outfile = results.txt   * main result file name
       noisy = 9      * 0,1,2,3,9: how much rubbish on the screen
     verbose = 1      * 1:detailed output
     runmode = 0      * 0:user defined tree
     seqtype = 1      * 1:codons
   CodonFreq = 2      * 0:equal, 1:F1X4, 2:F3X4, 3:F61
       model = 0      * 0:one omega ratio for all branches
                      * 1:separate omega for each branch
                      * 2:user specified dN/dS ratios for branches
     NSsites = 0      * 
       icode = 0      * 0:universal code
   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 = 0.2    * initial omega
                      * comments:
                      * H0 in Table 3: model = 0
                      * H1 in Table 3: model = 2
                      * H2 in Table 3: model = 2
                      * H3 in Table 3: model = 2