seed = -1 seqfile = Atlapetes_4genes.txt Imapfile = Atlapetes.Imap outfile = Atlapetes_Run.txt mcmcfile = Atlapetes.mcmc.txt * speciesdelimitation = 0 * fixed species tree speciesdelimitation = 1 0 2 * rjMCMC speciesdelimitation algorithm0(e) * speciesdelimitation = 1 1 2 0.5 * speciesdelimitation algorithm1(a m) speciestree = 1 * species-tree by NNI speciesmodelprior = 3 * 0: uniform LH; 1:uniform rooted trees; 2: uniformSLH; 3: uniformSRooted species&tree = 9 R E A Q N T G Y U 12 16 26 6 12 12 10 6 12 ((((R, E), A), ((G, Y), U)), (Q, (N, T))); phase = 0 0 0 0 0 0 0 0 0 usedata = 1 * 0: no data (prior); 1:seq like nloci = 4 * number of data sets in seqfile model = GTR * JC69; GTR cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)? * thetaprior = 3 0.02 # inverse gamma(a, b) for theta thetaprior = 3 0.02 e # inverse gamma(a, b) for theta and estimate tauprior = 3 0.03 # inverse gamma(a, b) for root tau & Dirichlet(a) for other tau's phiprior = 1 1 # beta(a, b) for phi in the MSci model heredity = 2 Atlapetes_heredity.txt * locusrate = 0 # no variation among loci locusrate = 1 0 0 5 dir # estimate locus rates clock = 1 # all branches have same rate finetune = 1: 99.0000 0.00020 0.00300 0.00020 0.15000 0.25000 0 # finetune for GBtj, GBspr, theta, tau, mix, locusrate, seqerr print = 1 0 0 0 * MCMC samples, locusrate, heredityscalars, Genetrees burnin = 100000 sampfreq = 10 nsample = 100000