seed = -1
seqfile = mtCDNApri123.txt
treefile = mtCDNApri.trees
outfile = out
ndata = 3
seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
usedata = 1 * 0: no data; 1:seq like; 2:normal approximation; 3:out.BV (in.BV)
clock = 2 * 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 0.1 * 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 rate for genes
sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3)
finetune = 1: .1 .1 .1 .1 .1 .1 * auto (0 or 1): times, rates, mixing, paras, RateParas, FossilErr
* finetune = 1: 0.05 0.2 0.15 0.1 .5 * 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.