To cite ape in a publication use:

Paradis E. & Schliep K. 2018. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.

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

Corresponding BibTeX entry:

  @Article{,
    title = {ape 5.0: an environment for modern phylogenetics and
      evolutionary analyses in {R}},
    author = {E. Paradis and K. Schliep},
    journal = {Bioinformatics},
    year = {2018},
    volume = {35},
    pages = {526-528},
  }