Yang, Z. 2015. A tutorial of BPP for species tree estimation and species delimitation. Curr. Zool. pdf
BP&P replaces the old program MCMCcoal, which implements the Bayesian method of Rannala & Yang (2003) and Burgess & Yang (2008). A mac OSX version is here (bpp2.2-mac-x86_64.tar.gz) for 64-bit intel chips (sorry this is an old version).
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). A new version (3s.v3.0.tgz) allows the use of loci with arbitrary configurations (such as 123, 112, 113, 12, etc.).
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.
Yang, Z. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genom. Biol. Evol. 2:200-211.
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.