To cite ape in a publication use:

Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

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

Corresponding BibTeX entry:

  @Article{,
    title = {A{PE}: analyses of phylogenetics and evolution in {R}
      language},
    author = {E. Paradis and J. Claude and K. Strimmer},
    journal = {Bioinformatics},
    year = {2004},
    volume = {20},
    pages = {289-290},
  }