Phylogenetic Methods for Dating Whole Genome Duplication Events

Description

Whole genome duplications are known to play a major role in plant evolution. Even plants considered to have small genomes, such as Arabidopsis, show the remnants of ancient duplications. Given the importance and prevalence of these duplications, understanding their history and structure will help in utilizing genome information for the improvement of crop species.

This page describes software to date whole genome duplications within an evolutionary context. This technique has been used successfully in Arabidopsis and Yeast.

This implementation is written in the Python programming language using a number of freely available bioinformatics tools:

Download

The python source code is freely available for download. The latest release is from 27 September 2003:

The project is kindly hosted on bioinformatics.org CVS servers. More information on access in available from my bioinformatics.org website. The code is always under development and suggestions and comments are very welcome.

Documentation

Documentation on the setup and use of the scripts with be available.

Some sample python-based configuration files can be used as templates for your personal research organism:

Sample database download files for creating organism-specific databases for dating purposes:

Sample PBS file for running on a OpenPBS managed cluster using LAM/MPI:

Please direct questions or problems to Brad at: chapmanb@uga.edu