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mcmctree_orig.ctl
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mcmctree_orig.ctl
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seed = -1 * Used timestamp to define seed number
seqfile = mtCDNApri.phy * Path to input sequence file
treefile = mtCDNApri.trees * Path to input tree file
mcmcfile = mcmc.txt * Path to output file with MCMC samples
outfile = out.txt * Path to log output file
ndata = 1 * Number of partitions
seqtype = 2 * 0: nucleotides; 1:codons; 2:AAs
usedata = 2 * 0: no data (prior); 1:exact likelihood; 2:approximate likelihood; 3:out.BV (in.BV)
clock = 2 * 1: global clock; 2: independent rates; 3: correlated rates
model = 3 * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F
* 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)
alpha = 0.5 * alpha for gamma rates at sites
ncatG = 5 * No. categories in discrete gamma
aaRatefile = ../lg.dat * Path to the file with the LG matrix
cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
BDparas = 1 1 0.1 * birth, death, sampling
rgene_gamma = 2 20 * gammaDir prior for rate for genes
sigma2_gamma = 1 10 * gammaDir prior for sigma^2 (for clock=2 or 3)
print = 1 * 0: no mcmc sample; 1: everything except branch rates 2: everything
burnin = 10000 * Number of iterations that will be discarded as part of burn-in
sampfreq = 500 * Sampling frequency
nsample = 20000 * Number of samples to be collected
*** Note: Make your window wider (100 columns) before running the program.