Jonathan M. Carlson


PhyloD
  • 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 and here. Code available here and web server for single sites is here.
PhyloD Viewer
  • 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).
Phylo Detective
  • Visualization tool for viewing traits on a large phylogeny, developed by Bongshin Lee at MSR. Paper is here.
False discovery rates for contingency tables .NET Bio
  • .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.