seqfile = treefile = outfile = noisy = 9 verbose = 0 runmode = 0 icode = 0 fix_omega = 0 ncatG = 4 fix_alpha = 0 ndata = 1 clock = 0 seqtype = 2 aaRatefile = dat/wag.dat fix_blength = 0 omega = 2 Mgene = 0 Small_Diff = .5e-6 getSE = 0 RateAncestor = 1 alpha = 0.5 fix_kappa = 0 model = 2 kappa = 2 CodonFreq = 2 aaDist = 0 cleandata = 1 Malpha = 1