In my current position at Temple University, I am an active developer contributing to the software package HyPhy (“Hypothesis testing with Phylogenies), which contains a wide variety of approaches and features a customizable batch language for studying evolutionary dynamics in genetic/genomic data.

Software packages I have developed separately include the following:

  • Pyvolve, a python platform to simulate sequences along a phylogeny using continuous-time Markov models.
    • Available for install with pip
  • alignfigR, an R package to create multiple sequence alignment figures.
    • Available for install from CRAN
  • phyphy, a Python library for faciliating and parsing HyPhy standard analyses
    • Available for install with pip