To cite pegas in a publication use:

Paradis E. 2010. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419-420.

As pegas is evolving quickly, you may want to cite also its version number (found with 'library(help = pegas)').

Corresponding BibTeX entry:

  @Article{,
    title = {pegas: an {R} package for population genetics with an
      integrated--modular approach},
    author = {E. Paradis},
    journal = {Bioinformatics},
    year = {2010},
    volume = {26},
    pages = {419-420},
  }