Software BAGEL (Bayesian Analysis of Gene Expression Levels, Version 4.1): a program for the statistical analysis of spotted microarray data. Download the archive for (Version 4.1, July 2009) Macintosh OS X Linux Windows Mark Voorhies' command-line compile View the BAGEL Tutorial View some papers that have used the BAGEL software. 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 KaKs_Calculator (Version 1.2): A program adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates. In addition, several existing algorithms for calculating Ka and Ks are also incorporated into KaKs_Calculator. Download the archive for Linux/Mac/Windows View the KaKs_Calculator paper MACML (Model Averaging Clustering by Maximum Likelihood, Version 1.1): A program clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge. Download the archive (Version 1.1, Jun. 2009) for Linux/Mac/Windows View the MACML paper LOX (Version 1.0): under construction Download the archive (Version 1.1, Jun. 2009) for Linux/Mac/Windows View the LOX Tutorial