seed = -1
seqfile = examples/DatingSoftBound/mtCDNApri123.txt
treefile = examples/DatingSoftBound/mtCDNApri.trees
outfile = out
ndata = 3
seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
usedata = 1 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates
RootAge = <1.0 * safe constraint on root age, used if no fossil for root.
model = 0 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
alpha = 0 * 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 = 1 1 0 * birth, death, sampling
kappa_gamma = 6 2 * gamma prior for kappa
alpha_gamma = 1 1 * gamma prior for alpha
rgene_gamma = 2 2 * gamma prior for overall rates for genes
sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3)
finetune = 1: .05 0.1 0.12 0.1 .3 * auto (0 or 1) : times, rates, mixing, paras, RateParas, FossilErr
print = 1
burnin = 2000
sampfreq = 2
nsample = 20000
*** Note: Make your window wider (100 columns) before running the program.