Download bpp3.3.tgz (source code for all platforms, including executables for Windows. Don't let Internet Explorer change the file name.)
Download bpp3.2.macosx.tgz (source code and executables for mac osx 7 and later)
Please read the documentation in the package (bppDOC.pdf) before using the program. The following paper includes a tutorial that works for bpp 3.1 through 3.3.
Yang, Z. 2015. A tutorial of BPP for species tree estimation and species delimitation. Current Zoology 61:854-865. pdf
If you have questions, after having struggled through the tutorial, please post them at the google bpp discussion site, at this link.
BP&P replaces the old program MCMCcoal, which implements the Bayesian method of Rannala & Yang (2003) and Burgess & Yang (2008). 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.
The program 3s implements likelihood ratio tests to test for gene flow between two closely related species. Click on the link above for more information.
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.