seqfile = MouseLemurs.aa
treefile = MouseLemurs.trees
outfile = mlc * main result file name
noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
verbose = 1 * 0: concise; 1: detailed, 2: too much
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
* 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
seqtype = 2 * 1:codons; 2:AAs; 3:codons-->AAs
aaRatefile = mtmam.dat
model = 3 * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
clock = 6 * 0:no clock, 1:global clock; 2:local clock
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0.37886 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * different alphas for genes
ncatG = 5 * # 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 = 1e-6
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
* fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 1 * 0: simultaneous; 1: one branch at a time