computer programs and methodologies for the simulation of dna sequence data with recombination

Computer simulations are useful in evolutionary biology for hypothesis testing, to verify analytical methods, to analyze interactions among evolutionary processes and to estimate evolutionary parameters. In particular, the simulation of DNA sequences with recombination may help in understanding the role of recombination in diverse evolutionary questions, such as the genome structure. Consequently, plenty of computer simulators have been developed to simulate DNA sequence data with recombination. However, the choice of an appropriate tool, among all currently available simulators, is critical if recombination simulations are to be biologically meaningful. This review provides a practical survival guide to commonly used computer programs and methodologies for the simulation of coding and non-coding DNA sequences with recombination. It may help in the correct design of computer simulation experiments of recombination. In addition, the study includes a review of simulation studies investigating the impact of ignoring recombination when performing various evolutionary analyses, such as phylogenetic tree and ancestral sequence reconstructions. Alternative analytical methodologies accounting for recombination are also reviewed.