seqfile = seqfile.txt * sequence data filename
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 = -2 * -2:pairwise
seqtype = 1 * 1:codons
CodonFreq = 3 * 0:equal, 1:F1X4, 2:F3X4, 3:F61
model = 0 *
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 = 1 * 1:omega fixed, 0:omega to be estimated
omega = 0.001 * 1st fixed omega value
*alternate fixed omega values
*omega = 0.005 * 2nd fixed value
*omega = 0.01 * 3rd fixed value
*omega = 0.05 * 4th fixed value
*omega = 0.10 * 5th fixed value
*omega = 0.20 * 6th fixed value
*omega = 0.40 * 7th fixed value
*omega = 0.80 * 8th fixed value
*omega = 1.60 * 9th fixed value
*omega = 2.00 * 10th fixed value