- Likelihood-based methods for phylogenetic tree reconstruction, involving evolutionary rate estimation, evolutionary distance estimation and distance-based methods for tree reconstruction.
- The importance of the guide tree in progressive multiple sequence alignment, and the estimation of alignment sensitivity to errors in the guide tree.
Applied biological research:
- Co-evolution of homing endonucleases with their host genes, and its implications for the discovery and use of homing endonucleases in gene targeting (especially for gene therapy).
- Co-evolution of viral and host genes, especially in herpesviridae and lentiviridae. Specifically, the co-evolution of antisense regulatory RNA with their targets and the co-evolution of viral proteins with host inate immunity factors.
- Bacterial phylogeny reconstruction.