Report on estimating prokaryotic recombination landscapes from genomic data

Recombination plays a crucial role in the evolution of prokaryotic life. As genomic sequencing data become more widely available, many methods to estimate the rate of recombination have been developed to meet the increasingly high computation demand. Methods for estimating recombination rely on a number of signals resulting from recombination, including differentiation in linkage, phylogeny, and substitution rate. Here, I discuss different signals used to detect recombination, how they are incorporated into current recombination estimation software, and the potential limitations of that software or algorithm. I also discuss which of these methods can be applied to different types of sequencing data. Finally, I provide a detailed description of four commonly used programs for estimating recombination from genomic data in prokaryotes.