seed = -1357 seqfile = ../H1.txt * seqfile = ../H1.CP123.txt treefile = ../H1.tre outfile = out seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs noisy = 3 usedata = 0 ../in.BV.HKYG5 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV ndata = 1 * clock = 1 * 1: global clock; 2: independent rates; 3: correlated rates TipDate = 1 100 * TipDate (1) & time unit * fossilerror = 0 * no fossil errors * RootAge = B(1.1, 2.1, .025, .025) * used if no fossil for root RootAge = B(1, 5, .001, .001) * used if no fossil for root * RootAge = B(4, 6, .001, .001) * used if no fossil for root model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85 aaRatefile = wag.dat 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 = 10 5 .001 * lambda, mu, rho, psi for birth-death-sampling model * BDparas = 2 1 0 1.8 * lambda, mu, rho, psi for birth-death-sampling model * BDparas = 4 2 0 3.6 * lambda, mu, rho, psi for birth-death-sampling model * BDparas = 1 0.5 0 0.9 * lambda, mu, rho, psi for birth-death-sampling model * BDparas = 20 10 0 18 * lambda, mu, rho, psi for birth-death-sampling model * BDparas = 0.2 0.1 0 0.18 * lambda, mu, rho, psi for birth-death-sampling model BDparas = 2 1 0 1.8 * lambda, mu, rho, psi for birth-death-sampling model kappa_gamma = 2 1 * gamma prior for kappa alpha_gamma = 2 4 * gamma prior for alpha rgene_gamma = 2 10 * gamma prior for rate for genes sigma2_gamma = 1 20 * gamma prior for sigma^2 (for clock=2) finetune = 1: 0.2 0.04 .05 .05 .05 .05 * auto (0 or 1) : times, rates, mixing, paras, RateParas, FossilErr print = 1 burnin = 10000 sampfreq = 5 nsample = 20000