seqfile = file.phy
treefile = msy.tre
outfile = mlb * main result file
noisy = 0 * 0,1,2,3: how much rubbish on the screen
verbose = 0 * 1: detailed output, 0: concise output
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
* 3: StepwiseAddition; (4,5):PerturbationNNI
model = 4 * 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
* ndata = 5
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 * initial or fixed kappa
fix_alpha = 1 * 0: estimate alpha; 1: fix alpha at value below
alpha = 0 * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * 1: different alpha's for genes, 0: one alpha
ncatG = 0 * # of categories in the dG, AdG, or nparK models of rates
nparK = 0 * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK
nhomo = 0 * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
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
Small_Diff = 7e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
* icode = 0 * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * 0: simultaneous; 1: one branch at a time