My lab develops statistical tools and software for the analysis of DNA sequence data, and we collaborate with researchers in a variety of biological areas.
HyPhy
The HyPhy software system and programming language originated in my lab as a collaboration between myself and Sergei Kosakovsky Pond and has remained under constant development for almost 20 years.
Key papers from my career
Statistical Methods and Theory
- Relative Rate Test via maximum likelihood
- The MG94 model for codon evolution
- An evolutionary model for secondary structure/compensatory changes
- Estimating dS and dN- a theoretical look at definitions of these “parameters”
- Codon models with variation of synonymous substitution rates across sites (SRV)
- Bias correction for codon models
Software
Biological Applications