seqfile = ../aa_alignment.phylip
outfile = codeml_aa_pairwise.out
treefile = ../species.tree
verbose = 0
CodonFreq = 2
cleandata = 1
fix_blength = 1
NSsites = 0
fix_omega = 0
clock = 0
runmode = -2
fix_kappa = 0
fix_alpha = 1
alpha = 0
method = 0
Malpha = 0
RateAncestor = 0
icode = 0
seqtype = 2
omega = 1
getSE = 0
noisy = 0
Mgene = 0
kappa = 4.54006
model = 0
