- AReA: area reconstruction
- ConAr: continuous character reconstruction
- keymap: key innovations and stochastic mapping
- lagrange: area reconstruction (with Richard Ree)
- pebls (incl. jade): pebls evolutionary biology libraries
- phyutility: a phylogenetic utility program
- tREeBOOT: supertree bootstrapping
other contributions
- jebl: Java Evolutionary Biology Library (headed by Alexei Drummond and Andrew Rambaut)
- tolkin: headed by Nico Cellinese and Reed Beaman
