* mcmctree.ctl for mammal analysis (dos Reis et al. 2012):
seed = -1
seqfile = dummy-20P.phys
treefile = Ense36.tree
outfile = out
ndata = 20
usedata = 2 * 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 = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
alpha = 1 * 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 = 5 .5 * gamma prior for kappa
alpha_gamma = 1 .5 * gamma prior for alpha
* rgene_gamma = 1 1 * gamma prior for overall rates for genes (prior from dos Reis et al. 2012 PRSL B 279:3491-3500)
rgene_gamma = 2 40 * gamma prior for overall rates for genes (prior from dos Reis et al. 2014 Syst Biol 63:555-565)
sigma2_gamma = 1 1 * gamma prior for sigma^2 (for clock=2 or 3)
finetune = 1: .001 0.033 0.0077 0.03 .23 * times, rates, mixing, paras, RateParas
print = 1
burnin = 100000
sampfreq = 150
nsample = 10000
*** Note: Make your window wider (100 columns) before running the program