I have been the lead programmer on many projects (some of which are no longer being developed).
I currently am actively developing
- PHLAWD - a program written in C++ that constructs datasets from NCBI data (GenBank). This uses the megaphylogeny method to construct extremely large datasets, but is convenient for small ones too.
- phyutility - a Java program to perform simple but essential tasks on sequences and trees from the command line. This was originally a product of the Dunn et al., 2008 and Smith and Dunn 2008 work.
- lagrange - this began as a Python program with Rick Ree. In order to speed the program up and extend it a bit, I developed it in C++ and added some features.
- phyx - this is a C++ program that was started as a set of unix like command tools that perform many phylogenetics operations and is not limited by tree size.
For more detailed information click on the individual links for the programs phyutility, phlawd, and lagrange.