We develop statistical models and computational tools for comparative analysis of sequence data, especially large and rich data sets from measurably evolving pathogens. We relish scientific and engineering challenges involved in creating scalable and useable tools for our own research and for use by the broader community. We are omnivorous in applied research problems and currently work on problems in molecular epidemiology of HIV, dynamics of immune repertoires, pathogenesis and within-host evolution of HIV and SIV, and optimal use of next generation sequencing data.