pegas: an R package for population genetics with an integrated-modular approach.

Abstract

pegas (Population and Evolutionary Genetics Analysis System) is a new package for the analysis of population genetic data. It is written in R and is integrated with two other existing R packages (ape and adegenet). pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and efficient graphical capabilities of R are used for plotting haplotype networks as well as for other functionalities. pegas emphasizes the need to further develop an integrated-modular approach for software dedicated to the analysis of population genetic data. pegas is distributed through the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/pegas/index.html. Further information may be found at: http://ape.mpl.ird.fr/pegas/.