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

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 codin...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Miguel Arenas, David Posada
• Keywords: BMCBI 2007, Coalescent, Dna Sequences, Simulation