Projects

treeducken

treeducken is my phylogenetic simulation package with the primary purpose of simulating host and symbiont phylogenies simultaneously using the machinery of birth-death models. This extends work on simulating cophylogenetic systems by allowing for scenarios where speciation in the host does not always imply speciation in the symbiont (Keller-Schmidt et al. 2011). This simulation also accounts for extinction in its simulation of host-symbiont systems. treeducken also can simulate under the three-tree model in a manner similar to that used in the SimPhy program (Mallo et al. 2016). See Publications for the paper on treeducken. I am the main contributor and maintainer for treeducken.

RevBayes

I am also a developer on the RevBayes probabilistic programming language. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks. I mostly have worked on biogeography models within the language itself. I am also a contributor to tutorials, documentation, and have been an instructor in several workshops for RevBayes.