Reading Genetic Data Files Into R with adegenet and pegas

adegenet [1] and pegas [3] are two packages that complement each other for population genetic analyses in R. Since various computer programs have been used by population genetists, most of them with their own data file formats, it is crucial that R can read them to ease users to switch to R. The present document explains how to read several file formats commonly used in population genetics. The following formats are considered: Text (ASCII) in tabular form, VCF files, Fstat data format, Genetix data format, Genepop data format, Structure data format, Excel. Except the last one, these files are stored in text (usually standard ASCII) format the differences being in the layout of the data. 1 Data Structures in adegenet and pegas First, let’s have a brief look on the way allelic data are stored by our two pack-ages. adegenet has the class "genind " where individuals are rows and alleles are columns in a matrix named tab. This is an S4 class, so the elements are accessed with the operator (e.g.