Data in Published Papers

Back to Ziheng's home

• Inoue J, Donoghue PCH, Yang Z. 2010. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol 59:74-89. Data file Inoue2010SB.tar.gz

• Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25:1979-1994.
  Data file (ApeNeBY2008.tar.gz) (note: I have changed the data file format so that the files don't work with MCMCcoal 1.2. They will work with the new version of the program, called bpp. Please look at the software page to download a copy. The data file names should be self-explanatory with reference to table 1 in the paper.

• Yang, Z. & Nielsen, R. 2008 Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol. Biol. Evol. 25, 568-579. Data file (YangNielsen2008MBE.MutSel.tar.gz)

• Furlong, R. F. & Yang, Z. 2008 Diversifying and purifying selection in the peptide binding region of DRB in mammals. J. Mol. Evol. 66: 384-394. Data file (FurlongYang2008JMEdata.tar.gz)

• Rannala B, Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Syst Biol 56:453-466. cat alignment file Johnson2006.AXY38s.txt and tree file Johnson2006.38s.trees

• Bielawski, J.P. and Z. Yang, 2005 Maximum likelihood methods for detecting adaptive protein evolution, in Statistical Methods in Molecular Evolution, R. Nielsen, Editor. Springer-Verlag: New York. p. 103-124.
  Data files in this book chapter are example1and2_GstD1.zip, example3_Ldh.zip, example4_HIV2nef.zip. Also a PAML Demo, prepared by Joe Bielawski.

• Yang, W., J. Bielawski and Z. Yang 2003. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57:212-221.
  The HIV data analyzed in this paper are here HIVdata.YBY2003.tar.gz.

• Yang, Z. and W.J. Swanson. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19: 49-57.
  Yang, Z., W.S.W. Wong, and R. Nielsen. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22: 1107-1118.
  The MHC data files: bigmhc.codeml.ctl, bigmhc.phy and bigmhc.trees.

• Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
  Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22:2472-2479.
  BRCA1: BRCA1.codeml.ctl, BRCA1.8s.txt, BRCA1.trees
  phyACF: phyACF.codeml.ctl, phyACF.txt, phyACF.trees
  phyBDE: phyBDE.codeml.ctl, phyBDE.txt, phyBDE.trees

• Yang, Nielsen, Goldman, and Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
  The data are results are here YNGP2000.tar.gz.

• Yang Z. 2000. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J Mol Evol 51:423-432. fluHAcdc349.nuc and fluHAcdc349.trees

• Yang and Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Mol. Biol. Evol. 14:717-724.
  The 9-species 888-bp primate dataset: mtprim9.txt.
  A Mathematica notebook for calculating the kernel density of coalescent times under the birth-death process model with species sampling is BirthDeathSample.nb. This can be used to draw figure 2 in the paper. See also Rannala, Huelsenbeck, Yang, and Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-709.

• Yang, Z., and D. Roberts. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:451-458.
  The four-species sequence alignment is here.

• Yang Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
  The psi-eta globin pseudogene dataset: psieta.nuc
  The 9-species 888-bp primate dataset: mtprim9.txt.