seed = -1
seqfile = All.phylip
treefile = outtree-rooted.tree
mcmcfile = mcmc.txt
outfile = out2.0.txt
ndata = 1
usedata = 3 *0:no data;1:seq; 2:approximation; 3:out.BV(in.BV)
clock = 2 *1:global clock; 2:independent; and 3:correlated rates
RootAge = '<1.0' *safe constraint on root age,used if no fossil for root.
model = 7 *0:JC69,1:K80,2:F81,3:F84,4:HKY85
alpha = 0.5 *alpha for gamma rate satsites
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 20 1 *gamma Dir prior for rate for genes
sigma2_gamma = 1 10 1 *gamma Dir prior for sigma^2(forclock=2or3)
finetune = 1: .1 .1 .1 .1 .1 .1 *auto(0or1):times,rates,mixing...
print = 1 *0:nomcmcsample;1:everythingexceptbranch2:ev...
burnin = 50000
sampfreq = 50
nsample = 50000