Software Bayesian Analysis of Gene Expression Levels (BAGEL): a program for the statistical analysis of spotted microarray data. Download the archive for Macintosh OS X Macintosh OS 9 Windows Mark Voorhies' compile for Linux Ryan Weddle's compile for Linux (buggy) Download the BAGEL Tutorial View some papers that have used the BAGEL software. Pathway Processor: A program that tests for overrepresentation of differentially expressed genes within known pathways of S. cerevisiae or B. subtilis. Available in Virtual-machine Java. 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: A program adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator. Download the archive for Linux/Unix/Windows MLCluster: A program that uses a tripartite divide-and-conquer strategy to hierarchically cluster sequences into heterogeneous regions based on maximum likelihood estimation. Download the archive for Linux/Unix/Windows Download the MLCluster Poster View MLCluster Web Server