Computational genomics

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)

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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

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PyxMPI

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

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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.

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Scripts for chrX.tar.gz

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Updated:  26 March 2017/Responsible Officer:  Director, JCSMR/Page Contact:  Web Manager