Computer software

Phylogenetic analysis by maximum likelihood (PAML)

Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
Yang, Z. 2007 PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591.

Coalescent analysis on a species tree (BP&P and 3s)

The program BP&P (bpp3.tgz) implements a series of Bayesian inference methods under the multispecies coalescent model. The analyses may include estimation of population size (theta's) and species divergence times (tau's), species tree inference and species delimitation. Windows executables and C source code (for unix/linux/macosx) are all in the same archive (bpp3.tgz). Please read the documentation before you use this program. 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.

  Source code  bppX1.2-src.tgz
  Windows  bppX1.2+bpp3-win32.tgz
  Mac OSX  bppX1.2+bpp3-osx-x86_64.dmg
  Linux(coming soon)

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.).

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.

MrBayes 3.2.1 with Dirichlet priors on branch lengths

The archive name is mb3.2.1.Dir.tgz. This is a modified version of MrBayes Version 3.2.1, modified to use the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). There is a brief description of the changes in the file mb3.2.Dirichlet.Notes.pdf inside the archive. If you use the modified program, please cite MrBayes as well as the papers that describe the modifications.

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.

oncoSpectrum v1.2: ML program for estimating mutation rates using cancer mutation databases.

Yang Z, Ro S, Rannala B. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165:695-705.

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