This paper provides an overview and a tutorial of theBPP program, which is a Bayesian MCMC program for analyz-ing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and popula-tion size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species de-limitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are in-troduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assign-ment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of theBPP analysis [Current Zoology 61 (5): 854–865, 2015].
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