When my collaborators and I develop new statistical methodology, we make the code implementing
the methodology publicly available.
So nearly all methodological papers listed on the Research
page have a link to accompanying software.
Most of these software packages are not designed to be super user friendly,
but rather are there for reproducibility purposes.
phylodyn: R package for estimating effective population size changes from gene genealogies.
Available on CRAN and
Last modified: May, 2017