Jonathan M. Carlson

  • Statistical modeling of HIV adaptation. Here's the big idea: HIV mutates so fast, that there's a tremendous amount of genetic variation both within and between patients. This means that HIV "samples the search" space very efficiently. The bad news is, this means HIV adapts to dugs and our immune system very quickly. The good news is, we can use this as a research tool: identify what is adapting, and what is driving adaptation, and you've learned something about virology and immunology. See my home page and paper descriptions for some cool examples of how this plays out. The primary methodological papers are here and here. Code available here and web server for single sites is here. Note that this code is VERY OLD. I will at some point get around to updating this, but code drops are a lot of work, so it keeps getting pushed off. If you would use this, email me and it will add pressure to bump this up the priority queue!
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.