While the R software is becoming a standard for the analysis of genetic data, classical population genetics tools are being challenged by the increasing availability of genomic sequences. Dedicated tools are needed for harnessing the large amount of information generated by next-generation sequencing technologies. We introduce new tools implemented in the adegenet 1.3-1 package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using a bit-level coding scheme for SNP data and parallelized computation, adegenet enables the analysis of large genome-wide SNPs datasets using standard personal computers.