Software & Datasets

Software

  • CSI-MAC (Cancer Selection Intensity using Model Averaged Clustering): A program that can be used to identify genes, gene regions, and sites that contribute to tumorigenesis when mutated, as well as to estimate the relative contribution of those genes, gene regions, and mutations to the somatic evolution of cancer.
  • MASS-PRF (Model Averaged Site Selection with Poisson Random Field theory): A program that quantifies heterogeneity of selection intensity across sites within coding sequences by using polymorphism and divergence data. 
  • PhyDesign: a platform-independent web application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions.
  • LOX (Level Of eXpression): A program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.
  • Download the archive (Version 1.8, February, 2012)
  • MACML (Model Averaging Clustering by Maximum Likelihood): A program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
  • Download the archive (Version 1.1.2, December 2011) for
  • View the MACML paper
  • BAGEL (Bayesian Analysis of Gene Expression Levels): a program for the statistical analysis of spotted microarray data.
  • Download Version 4.1, July 2009
  • Download Version 4.0, March 2009
  • View BAGEL Tutorial
  • View some papers that have used the BAGEL software.
  • KaKs_Calculator: A program that adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates.
  • SeqPop: A program for computing population genetic statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

Datasets