seed = -1357
seqfile = ../H1.txt
* seqfile = ../H1.CP123.txt
treefile = ../H1.tre
outfile = out
seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
noisy = 3
usedata = 0 ../in.BV.HKYG5 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
ndata = 1 *
clock = 1 * 1: global clock; 2: independent rates; 3: correlated rates
TipDate = 1 100 * TipDate (1) & time unit
* fossilerror = 0 * no fossil errors
* RootAge = B(1.1, 2.1, .025, .025) * used if no fossil for root
RootAge = B(1, 5, .001, .001) * used if no fossil for root
* RootAge = B(4, 6, .001, .001) * used if no fossil for root
model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
aaRatefile = wag.dat
alpha = 0.5 * alpha for gamma rates at sites
ncatG = 5 * No. categories in discrete gamma
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
* BDparas = 10 5 .001 * lambda, mu, rho, psi for birth-death-sampling model
* BDparas = 2 1 0 1.8 * lambda, mu, rho, psi for birth-death-sampling model
* BDparas = 4 2 0 3.6 * lambda, mu, rho, psi for birth-death-sampling model
* BDparas = 1 0.5 0 0.9 * lambda, mu, rho, psi for birth-death-sampling model
* BDparas = 20 10 0 18 * lambda, mu, rho, psi for birth-death-sampling model
* BDparas = 0.2 0.1 0 0.18 * lambda, mu, rho, psi for birth-death-sampling model
BDparas = 2 1 0 1.8 * lambda, mu, rho, psi for birth-death-sampling model
kappa_gamma = 2 1 * gamma prior for kappa
alpha_gamma = 2 4 * gamma prior for alpha
rgene_gamma = 2 10 * gamma prior for rate for genes
sigma2_gamma = 1 20 * gamma prior for sigma^2 (for clock=2)
finetune = 1: 0.2 0.04 .05 .05 .05 .05 * auto (0 or 1) : times, rates, mixing, paras, RateParas, FossilErr
print = 1
burnin = 10000
sampfreq = 5
nsample = 20000