Software
  • MAC-PRF (Model Averaged Clustering - Poisson Random Field): a software for estimating selection intensity for each single site in 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.
    • Access to the web application here
    • View the manual

  • 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.
  • MACML (Model Averaging Clustering by Maximum Likelihood): A program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
  • BAGEL (Bayesian Analysis of Gene Expression Levels): a program for the statistical analysis of spotted microarray data.
  • 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 genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.