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 Bayesian methods of Yang (2002), Rannala & Yang (2003), Burgess & Yang (2008), and Yang & Rannala (2010) are implemented in the program BP&P (bpp2.1b.tgz). The mac OSX versions are here, for 32-bit (bpp2.1-mac-i386.tar.gz) and 64-bit (bpp2.1-mac-x86_64.tar.gz).

The likelihood methods of Yang (2002) and Yang (2010) are implemented in the program 3s (3s.v2.0a.tgz).

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.

Thornian Time Traveler (T³)

T³ (archive T3.v1.tar.gz) is Jeff Thorne's Bayesian MCMC program for estimating species divergence times under a model of rate change over time. Jeff Thorne now has a web site for the program. The two versions are the same as far as analysis is concerned, but I believe they require slightly different user file formats. I suggest that you download from Jeff's web site.

Thorne, J. L., Kishino, H. & Painter, I. S. 1998 Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647-1657.

Kishino, H., Thorne, J. L. & Bruno, W. J. 2001 Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352-361.

MrBayes 3.1.2 with Dirichlet priors on branch lengths

The archive name is mb3.1.2.Dirichlet.tgz. This is a modified version of MrBayes Version 3.1.2, modified to use the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. submitted). 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 mb3.1_modified.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, Zhu T, Yang Z. 2011. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol Biol Evol. in press
Zhang C, Rannala B, Yang Z. 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol. submitted

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.

Go back to Professor Yang's group web page

Last modified, 22 November 2011