I attempt to write and maintain some bioinformatics software.

My language of choice is C++, because it runs fast, but I am currently doing much development in Java because that part is quick, with a view to translating to C++ the compute-intensive bits.

My favourite program, and the cause of most of my headaches, is TreeMap, which is a Macintosh (Classic) application desiged to uncover the relationships among ecologically linked organisms. Check out TreeMap 3.

In another life I created Spectrum, which can be used to show phylogenetic information in a data set, without requiring you to estimate an evolutionary tree. I think this has been largely superceded by other software such as SplitsTree.

CoSpec is another application that models cophylogenetic evolution very simply: I used it to demonstrate the large range of possible coevolutionary patterns that can arise.

Joshua Ho has written GNLab, which is a program for large-scale analysis of Gene Regulatory Networks. It is now compiled for and moderately tested on Windows and Mac OS X platforms.

Markov invariants are useful objects for phylogenetic inference (see http://arxiv.org/abs/0711.3503).

Filo is a Java program designed to read in simple #NEXUS-like files and generate artificial molecular sequence data according to some very general constraints. It was supported by ARC grant DP0770991.