seed = -1 seqfile = ./Redeye/BPP_Redeye_complex1_loci.prn Imapfile = ./Redeye/BPP_Redeye_complex1.Imap.txt outfile = ./Redeye/Redeye1_out.txt mcmcfile = ./Redeye/Redeye1_mcmc.txt speciesdelimitation = 0 * fixed species tree * speciesdelimitation = 1 0 2 * speciesdelimitation algorithm0 and finetune(e) * speciesdelimitation = 1 1 1.5 2 * speciesdelimitation algorithm1 finetune (a m) speciestree = 0 * species tree NNI/SPR * speciestree = 1 1 1.5 2 * species-tree by NNI speciesmodelprior = 1 * 0: uniform LH; 1:uniform rooted trees; 2: uniformSLH; 3: uniformSRooted species&tree = 3 Mcah Mcoo Mtal 6 6 4 ((Mcah, Mcoo), Mtal); diploid = 1 1 1 usedata = 1 * 0: no data (prior); 1:seq like nloci = 1497 * number of data sets in seqfile cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? thetaprior = 5 0.000786 E # invgamma(a, b) for theta tauprior = 21 0.0182 # invgamma(a, b) for root tau & Dirichlet(a) for other tau's finetune = 1: 3 0.003 0.002 0.00002 0.005 0.9 0.001 0.001 # finetune for GBtj, GBspr, theta, tau, mix Threads = 20 checkpoint = 250000 200000 print = 1 0 0 0 * MCMC samples, locusrate, heredityscalars Genetrees burnin = 50000 sampfreq = 50 nsample = 150000