seed = -1 seqfile = Cetacea_partition_mcmctree_3.aln treefile = MCMCTREE.tre mcmcfile = mcmc.txt outfile = out.txt ndata = 3 seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs usedata = 2 * 0: no data (prior); 1:exact likelihood; * 2:approximate likelihood; 3:out.BV (in.BV) clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates RootAge = B(0.524,1.646,1e-300,0.01) model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85 alpha = 0.5 * 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 = 1 1 * gamma prior for kappa alpha_gamma = 1 1 * gamma prior for alpha rgene_gamma = 2 40 * gammaDir prior for rate for genes sigma2_gamma = 1 1 *s 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 sampfreq = 100 nsample = 100000 *** Note: Make your window wider (100 columns) before running the program.