seed = -1 seqfile = BPP_sequences.txt Imapfile = BPP_lmap.txt outfile = DMW_bpp_out_Algo1_dPrior.txt mcmcfile = mcmc.txt * speciesdelimitation = 0 * fixed species tree * speciesdelimitation = 1 0 2.5 * speciesdelimitation algorithm0 and finetune(e) speciesdelimitation = 1 1 2 1 * speciesdelimitation algorithm1 finetune (a m) speciesmodelprior = 1 * 0: uniform labeled histories; 1:uniform rooted trees; 2:user probs species&tree = 9 gilli AngWDRC CamNig BotZam VicLendu KimMal BWLang Niew wCapeLgs 1 4 5 3 10 12 9 10 16 (gilli,((AngWDRC,(VicLendu,(BotZam,CamNig))),((KimMal,BWLang),(Niew, wCapeLgs)))); usedata = 1 * 0: no data (prior); 1:seq like nloci = 10 * number of data sets in seqfile cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? thetaprior = 2 1000 # gamma(a, b) for theta tauprior = 2 1000 # gamma(a, b) for root tau & Dirichlet(a) for other tau's * finetune = 0: 5 0.0005 0.002 0.0005 0.5 0.2 1.0 # auto (0 or 1): finetune for GBtj, GBspr, theta, tau, mix, locusrate, seqerr finetune = 1: .01 .01 .01 .01 .01 .01 .01 .01 # auto (0 or 1): finetune for GBtj, GBspr, theta, tau, mix, locusrate, seqerr print = 1 burnin = 20000 sampfreq = 2 nsample = 100000