Professor of Biology · Institute for Genomics and Evolutionary Medicine (iGEM)
Associate Dean for Research and Innovation · College of Science and Technology, Temple University
I am an applied mathematician and computational biologist developing statistical models, evolutionary inference algorithms, and high-throughput software for comparative genomics and pathogen surveillance. My group's active open-source development lives here and in the @veg (Viral Evolution Group) organization.
- HyPhy & HyPhy v3 (hyphy.org) — Hypothesis testing using phylogenies: codon substitution models, selection inference (FEL, MEME, BUSTED, aBSREL, FUBAR, RELAX, PRIME), and joint alignment-phylogeny inference.
- Datamonkey (datamonkey.org) — Browser and cloud platform for comparative sequence analysis and evolutionary model fitting.
- HIV-TRACE (hivtrace.org) — High-throughput molecular epidemiology and transmission network reconstruction for HIV and rapidly evolving pathogens.
- HyphAeon & RhizAeon — Phylogenetic foundation models, evolutionary circuit embeddings, and recombination/mosaic architecture screening (rhiztype).
- phylotree.js — Interactive JavaScript/TypeScript library for phylogenetic tree visualization and manipulation.
CV & Publications (slkp.info) · Google Scholar · Lab (lab.hyphy.org) · @veg on GitHub