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