seed = -1 seqfile = examples/DatingSoftBound/mtCDNApri123.txt treefile = examples/DatingSoftBound/mtCDNApri.trees outfile = out ndata = 3 seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs usedata = 1 * 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 = 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 * 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 overall rates for genes sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3) finetune = 1: 0.1 0.1 0.1 0.01 .5 * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr print = 1 burnin = 2000 sampfreq = 2 nsample = 20000 *** Note: Make your window wider (100 columns) before running the program.