Computer Software
Computer Software for Evolutionary Biology from the Revell Lab
1. Lab PI Revell is responsible for developing & maintaining phytools, a popular R package for phylogenetic comparative methods & a wide range of other phylogenetic analyses. Also check out the phytools GitHub page, the old development page for phytools, and the phytools development blog.
2. Revell lab postdoc Klaus Schliep is responsible for phangorn: an R package for phylogeny estimation & various types of phylogenetic analysis. Also see Klaus's GitHub page for more information about his work on this & other projects.
3. Several years ago Revell & collaborator Scott Chamberlain developed Rphylip, An R interface for the PHYLIP phylogeny software.
4. physketch is a small package for freehand drawing phylogenetic trees in R.
5. ishihara is a fun R package (still in development) for conducting an Ishihara colorblindness test.
6. tps.process.R contains couple of functions for processing .tps files produced by the morphometrics program tpsDIG.
7. Finally, Lab PI Revell has developed PopGen, an R package for population genetic & evolutionary simulations & numerical analyses. This package used to be distributed as popgen (all lower case). I recommend installing from GitHub, but a previous build (version 0.2) can be downloaded here.
Webpages of General Usefulness
1. Felsenstein's phylogeny programs page.
2. R Project for Statistical Computing page. Also see the CRAN phylogenetics task view.
3. The "ape" homepage. "ape" (by Paradis et al. 2004) is the most important R library for phylogenetic analyses.
4. More links coming soon. . . .