seqfile = H1.txt
treefile = H1.tre
outfile = mlb * main result file
noisy = 9 * 0,1,2,3: how much rubbish on the screen
verbose = 1 * 1: detailed output, 0: concise output
runmode = 0 * 0:user tree; 1:semi-automatic; 2:automatic
* 3:StepwiseAddition; (4,5):PerturbationNNI
seqtype = 0 * 0 (4x4 models); 5 (RNA editing models); 4 (binary models)
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 = 1 * 0:rates, 1:separate; 2:diff pi, 3:diff kappa, 4:all diff
TipDate = 1 100
clock = 1 * 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 kappas
fix_alpha = 0 * 0: estimate alpha; 1: fix alpha at value below
alpha = 0.25 * initial or fixed alpha, 0:infinity (constant rate)
ncatG = 5 * # of categories in the dG, AdG, or nparK models of rates
fix_rho = 1 * 0: estimate rho; 1: fix rho at value below
rho = 0 * initial or fixed rho, 0:no correlation
* Malpha = 0 * 1: different alpha's for genes, 0: one alpha
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, 5:user
getSE = 1 * 0: don't want SEs of estimates, 1: want SEs
RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states
method = 0 * Optimization method 0: simultaneous; 1: one branch a time
Small_Diff = 0.5e-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 = 0 * 0: ignore, -1: random, 1: initial, 2: fixed