seqfile = D:\A\MySoft\paml4.6\examples\lysozyme\lysozymeSmall.nuc treefile = D:\A\MySoft\paml4.6\examples\lysozyme\lysozymeSmall.trees outfile = mlc noisy = 9 verbose = 1 runmode = 0 seqtype = 1 CodonFreq = 0 ndata = 1 clock = 0 aaDist = 0 model = 2 NSsites = 0 icode = 0 Mgene = 0 fix_kappa = 0 kappa = 2 fix_omega = 0 omega = 0.4 fix_alpha = 1 alpha = 0 Malpha = 0 ncatG = 8 getSE = 0 RateAncestor = 0 Small_Diff = .5e-6 cleandata = 0 method = 1