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. Download the archive (Version 1.0, October 2012) for Linux/Mac/Windows 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. Download the archive (Version 1.8, February, 2012) Linux/Mac/Windows View the LOX Tutorial Download Implementation of LOX in R with Graphics Capabilities  New! 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 Linux/Mac/Windows 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 Macintosh OS X Linux Windows Download Version 4.0, March 2009 Macintosh OS X Linux Windows Mark Voorhies' command-line compile View the 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. Download the archive (Version 1.2) for Linux/Mac/Windows View the KaKs_Calculator paper Contact information 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. Download the archive for Macintosh OS X Macintosh OS 9