seqfile = phyBDE.txt
treefile = phyBDE.trees
outfile = mlc * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
verbose = 0 * 1: detailed output, 0: concise output
runmode = 0
seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:Fcodon
aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
model = 2
NSsites = 2
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 5 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = 0.1
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = .0 * initial or fixed alpha, 0:infinity (constant rate)
ncatG = 3 * # of categories in dG of NSsites models
clock = 0 * 0:no clock, 1:global clock; 2:local clock; 3:TipDate
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
* cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
* ndata = 3
method = 0 * 0: simultaneous; 1: one branch at a time