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seqfile = ECP_EDN_15.nuc * sequence data filename
treefile = tree.txt * tree structure file name
outfile = mlc * main result file name
noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
verbose = 0 * 0: concise; 1: detailed, 2: too much
runmode = 0 * 0: user tree
seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
* Model C: model = 3 NSsites = 2
* Model D: model = 3 NSsites = 3
model = 3 * 3 = clade models
NSsites = 3 * choose "2" or "3"
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 2 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = 0.1234 * initial or fixed omega, for codons or codon-based AAs
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
ncatG = 2 * # of categories in dG of NSsites models
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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