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