The program BP&P (bpp2.2.tgz) implements the Bayesian methods of Yang (2002), Rannala & Yang (2003), Burgess & Yang (2008), and Yang & Rannala (2010), for estimating population sizes (theta's), species divergence times (tau's), and for delimiting species using multi-locus sequence data from several closely related species. A mac OSX version is here (bpp2.2-mac-x86_64.tar.gz) for 64-bit intel chips.
Bo Xu has written a graphics user interface for BPP, called bppX. The compiled executables are here for Windows, Mac OSX, and linux. You install (unpack and compile) the current version of bpp first. Then unpack the GUI bppX. Then go to Function-Configuration to specify the folder name for the bpp files. Questions and discussions about bp&p should go to this link.
The program 3s (3s.v2.1.tgz) implements the likelihood ratio tests of Yang (2002, 2010) and Zhu & Yang (2012).
BP&P replaces the old program MCMCcoal, which implements the Bayesian method of Rannala & Yang (2003) and Burgess & Yang (2008). 3s replaces the program Ne3sML (which was included in the MCMCcoal package), which implements the likelihood method of Yang (2002).
Yang, Z. 2002 Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics 162, 1811-1823.
Rannala, B. & Yang, Z. 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656.
Burgess, R. and Z. Yang 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25, 1979-1994.
Yang, Z. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genom. Biol. Evol. 2:200-211.
Yang, Z., and B. Rannala. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. U.S.A. 107:9264-9269.
Zhu, T., and Z. Yang. 2012. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol. Bio.l Evol. 29, 3131-3142.
Yang, Z 2007 Fair-balance paradox, star-tree paradox and Bayesian phylogenetics. Mol. Biol. Evol. 24, 1639-1655.
Yang, Z & Rannala, B. 2005 Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54, 455-470.
Rannala, B., T. Zhu, and Z. Yang. 2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.
Zhang, C., B. Rannala, and Z. Yang. 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst. Biol. 61:779-784.
Yang Z, Ro S, Rannala B. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165:695-705.