My main interest is in making use of aligned protein sequences to extract sequence/structure/function relationships. Because aligned sequences are not mutually independent, this project requires a great deal of phylogenetic analysis. I wrote a program called RIND (for Reconstructed INDependence) to estimate position-specific residue frequencies from a protein alignment (Bruno 1996). I have begun to look at sequence covariation in this context. More generally my interests include sequence analysis, phylogenetic reconstruction, genomics, and pattern formation.
weighborhomepage. Weighbor is a fast, accurate, and essentially un-biased alternative method for constructing evolutionary trees from a sequence-derived distance matrix.
The RIND homepage.
distancehomepage. Distance is a program written by Lars Arvestad that implements a least-squares method for estimating general reversible DNA substitution matrices and evolutionary distances.