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

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.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.Coalescent theory [1] provides a very powerful framework for the simulation of samples of DNA sequences. Coalescent simulations can be very useful to understand the statistical properties of these samples under different evolutionary scenarios [2], to evaluate and compare different analytical methods [3], to estimate population parameters [4] and for hypothesis testing [5]. Not surprisingly, several simulation programs have recently been developed under this framework [6-12]. In order to obtain meaningful biological inferences from simulated data it is important that the generating models are as realistic as possible. However, increasing model complexity usually results in longer computing times, and most programs usually focus on a restricted set of biological scenarios. Currently, we lack a tool for the simulation of samples of coding sequences that have evolved in structured populations with recombination and fluctuating size, typical for example of fast evolving pathogens and MHC genes [13,14]. Here, we introduce a new simulation program, called Recodon, to fill this gap.The simulation of data in Recodon