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Bioinformatics Advance Access published online on August 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl454
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 5, 2006
Revised August 16, 2006
Accepted August 18, 2006

Applications note

TESD: a transposable element dynamics simulation environment

Grégory Deceliere 1, Yann Letrillard 1, Sandrine Charles 1, and Christian Biémont 1 *

1 Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS, Université Claude Bernard Lyon 1, 69622, Villeubanne Cedex, France

* To whom correspondence should be addressed.
Christian Biémont, E-mail: biemont{at}biomserv.univ-lyon1.fr


  Abstract

Various mathematical models have been used to explore the dynamics of transposable elements within their host genomes. However, numerous factors can influence their dynamics, and we also know little about the dynamics of TEs when they first begin to invade populations. In addition, the influence of population structuring has only recently been investigated. TESD, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on 1) various TE parameters, such as the transposition and excision rates, the recombination rate, and the coefficient of selection against TE insertions, and 2) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics.

Availability: TESD is distributed under GPL from the Pôle Bioinformatique Lyonnais (PBIL) Web server at: http://pbil.univ-lyon1.fr/software/TESD.

Associate Editor: Charlie Hodgman
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