To cite the adegenet package:

  Jombart, T. (2008) adegenet: a R package for the multivariate
  analysis of genetic markers. Bioinformatics 24: 1403-1405. doi:
  10.1093/bioinformatics/btn129

A BibTeX entry for LaTeX users is

  @Article{,
    title = {adegenet: a R package for the multivariate analysis of genetic markers},
    journal = {Bioinformatics},
    year = {2008},
    author = {T. Jombart},
    volume = {24},
    pages = {1403-1405},
    doi = {10.1093/bioinformatics/btn129},
  }

  Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the
  analysis of genome-wide SNP data. Bioinformatics. doi:
  10.1093/bioinformatics/btr521

A BibTeX entry for LaTeX users is

  @Article{,
    title = {adegenet 1.3-1: new tools for the analysis of genome-wide SNP data},
    journal = {Bioinformatics},
    year = {2011},
    author = {T. Jombart and I. Ahmed},
    doi = {10.1093/bioinformatics/btr521},
  }