seqfile = MouseLemurs.nuc
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 = 1 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2
model = 0
NSsites = 0
icode = 1 * 0:universal code; 1:mammalian mt; 2-10:see below
clock = 2 * 0:no clock, 1:global clock; 2:local clock
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 10 * initial or fixed kappa
fix_omega = 0 * 1: fix omega at omega (below), 0: estimate omega
omega = 0.1 * 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)
Malpha = 0 * different alphas for genes
ncatG = 3 * # 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)?
method = 1 * 0: simultaneous; 1: one branch at a time
fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed