bpp -cfile=bpp.ctl (This is the functionality of MCcoal in bpp3.4)
The archive bpp3.4a.tgz
includes the source code for all platforms, as well as executables for
(Make sure that you save the file using the correct file name. If Internet Explorer changes the file extension to .gz, you should change it back to .tgz before double-clicking).
Download bpp3.4.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. If you are new and want to get started with the program, you can go through the command-line tutorial at the top of this page (choose the right pdf file depending on whether you use windows, mac, or linux), and then go through the tutorial in the following paper:
Yang, Z. 2015. A tutorial of BPP for species tree estimation and species delimitation. Current Zoology 61:854-865. pdf
Flouris, T., et al. (2018). Species tree inference with BPP using genomic sequences and the multispecies coalescent. Mol. Biol. Evol. 35(10): 2585-2593. pdf
If you have questions about either bpp3.4 or bpp4, after having struggled through the tutorial, please post them at the google bpp discussion site.
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. I think this may not be working with the new versions of bpp, such as 3.4 and 4.
Bruce Rannala has written another BPPgui. The executables are for Windows and Mac OSX. You can use this to prepare the bpp control files, and also read in the species trees in the MCMC sample file, produced by either bpp3.4 or bpp4. Please download from Bruce's group web site.
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.Zhu T, Yang Z. 2012. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol. Biol. Evol. 29:3131-3142.
Dalquen D, Zhu T, Yang Z. 2017. Maximum likelihood implementation of an isolation-with-migration model for three species. Syst. Biol. 66:379-398.
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.