seqfile = bigmhc.phy
treefile = bigmhc.trees
outfile = mlc
noisy = 3
verbose = 0
runmode = 0
seqtype = 1
CodonFreq = 2
aaRatefile = jones.dat
model = 0
NSsites = 0 1 2 7 8
icode = 0
Mgene = 0 * for codons:
* 0:rates, 1:separate; 2:diff pi, 3:diff k&w, 4:all diff
fix_kappa = 0
kappa = 1.6
fix_omega = 0
omega = .9
fix_alpha = 1
alpha = 0
ncatG = 10
clock = 0
getSE = 0
RateAncestor = 0
Small_Diff = .1e-6
* cleandata = 1
method = 1
fix_blength = 2 * 0: ignore, -1: random, 1: initial, 2: fixed