COGENT
This project aims to be a largely self-contained one-stop shop for comparative genomics research. Included capabilities include data-base querying, built-in multiple sequence alignment (including a true codon sequence aligner), evolutionary modelling, sequence simulation, controlling third-party applications and producing publication quality graphics.

Most available comparative genomics (or molecular evolution) software interfaces are some form of scripting, typically as a control file or a menu-driven interactive interface. COGENT adopts the former approach, but differs from most other applications by using a programming language, the language in which the application has been largely written. While this may seem daunting to non-programmers, the user doesn't have to know how to 'program' in order to use the toolkit and the language used (Python) is easy to read.

The software, published under the name PyCogent, is now hosted at sourceforge. See the 'PyCogent Sourceforge page' for instructions on downloading.

VESTIGE
A maximum likelihood based phylogenetic footprinting application based on COGENT. Vestige can be used to assess the temporal consistency of a spatial molecular evolutionary process. Conventional footprinting, which uses evolutionary distance to identify regions of conservation, is one application.

PyEvolve - see COGENT

PyxMPI
A pyrex/python wrapper to a subset of MPI. A dependency for COGENT's parallel module.

LCH

Scripts to estimate the length of complete heterozygosity from haplotype data. These were used for analyses reported in MacArthur et al (In press) Nature Genetics.