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Code

Data, code, and analysis for publications

We regularly publish code and analysis accompanying our publications. Associated repositories are linked on the Papers page. Just follow the links labeled [code]. Most relevant code repositories can also be found on our lab GitHub page.

Software

  • popDMS
    Population genetics-inspired inference of mutation effects from DMS experiments.

  • mplot
    Simple Python scripts for high quality figures in matplotlib.

  • ACE
    Fast and flexible code for solving the inverse Ising/Potts inference problem.

  • simple-rebound-simulation
    Code to simulate HIV-1 rebound following the model of Hill et al., PNAS 2014.

Teaching materials

  • popgen-lectures
    This repository contains a set of Jupyter notebooks accompanying a brief series of introductory lectures in population genetics.

  • Python-workshop
    Material for a set of workshops introducing new coders to Python. Workshops include example activities and exercises that may also interest more experienced coders.

  • Physics-177
    Lecture notes, exercises, and homework assignments for the course Physics 177: Computational Physics taught at UC Riverside. Credit to Flip Tanedo for earlier versions of this course.