Software


Python Packages

All packages are available for install with pip (or pip3).

  • Pyvolve, a python platform to simulate sequences along a phylogeny using continuous-time Markov models.

  • phyphy, a Python library for faciliating and parsing HyPhy standard analyses

R Packages and Shiny Apps

  • alignfigR, an R package to create multiple sequence alignment figures. Available for install from CRAN.

  • shinyplot, a Shiny app for fundamental data visualization with ggplot2, largely used for pedagogical purposes. Source code is available here.

Collaborative Efforts

I am a contributor to the ongoing development of the bioinformatics software package HyPhy (“Hypothesis testing with Phylogenies), which contains a wide variety of methods (and features a customizable batch language!) for studying evolutionary dynamics in genetic/genomic data.