Jonathan M. Carlson
Statistical modeling of HIV adaptation. The idea is that we build independent
models of evolution for each amino acid in an HIV protein. One of those models is parameterized by the phylogenetic
structure, the rate of evolution in the absence of escape, and a model of adaptation in the leaves of the
phylogeny. Crucially, we assume that adaptation exists only in the leaves (ie, the observed patients). This
is clearly wrong, but quite useful in that it keeps the number of parameters linear, and empirically it's a
decent approximation. The primary methodological papers are
here. Code available here and web server for single
sites is here.
A visualization tool for sequence covariation and adaptation. This is the tool used to generate the circle plots.
Unfortunately, I haven't had a chance to finish make the code web friendly, but feel free to
email me if you would like a desktop version (requires windows and .NET).
False discovery rates for contingency tables
Visualization tool for viewing traits on a large phylogeny, developed by Bongshin Lee at MSR.
Paper is here.
.NET Bio is a bioinformatics library for .NET. Upcoming versions of PhyloD will be available as part of the suite of tools packaged with .NET Bio.