I'm a big fan of Python over other languages like C and Java. Python has many virtues that make it easy to quickly write useful code, from throwaway scripts to large web or gui applications. R is also very useful, but it is like having a screwdriver, whereas Python is the whole toolbox.
- Phylografter: Collaborative phylogenetic tree assembly. This is a web application that lets you combine source trees (e.g. from published literature) into large "megatrees." View the demo or install it on your own computer.
- lagrange: Likelihood analysis of geographic range evolution. Developed in collaboration with Stephen Smith. An implementation of biogeographic inference methods described in Ree et al. (2005) and Ree and Smith, 2008.
- Stochastic mapping and key innovation tests (please email me for advice in running this).
- gapcode.py, a python script for coding indels in sequence alignments as binary characters for phylogeny reconstruction (version 2.1, 13 Jan 2008; thanks to Pieter Pelser for helpful suggestions)
- Web utilites for phylogenetics:
Saturday, 27 December 2008