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