seqfile = CephSeq.nuc
treefile = CephTree.trees
outfile = mlb * main result file
noisy = 3 * 0,1,2,3: how much rubbish on the screen
verbose = 0 * 1: detailed output, 0: concise output
model = 3 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
* 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
Mgene = 0 * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
fix_kappa = 0 * 0: estimate kappa; 1: fix kappa at value below
kappa = 2.3 * initial or fixed kappa
fix_alpha = 0 * 0: estimate alpha; 1: fix alpha at value below
alpha = 0.5 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * 1: different alpha's for genes, 0: one alpha
ncatG = 5 * # of categories in the dG, AdG, or nparK models of rates
getSE = 1 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states
method = 0 * 0: simultaneous; 1: one branch at a time
Small_Diff = 1e-6
* cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?