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Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography

Miguel Arenas* and David Posada

Author Affiliations

Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310 Vigo, Spain

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BMC Bioinformatics 2007, 8:458  doi:10.1186/1471-2105-8-458

Published: 20 November 2007

Abstract

Background

Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth.

Results

We introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models.

Conclusion

Recodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/ webcite.