To cite ape in a publication please use:

  Paradis E, Schliep K (2019). “ape 5.0: an environment for modern
  phylogenetics and evolutionary analyses in R.” _Bioinformatics_,
  *35*, 526-528. doi:10.1093/bioinformatics/bty633
  <https://doi.org/10.1093/bioinformatics/bty633>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
    author = {Emmanuel Paradis and Klaus Schliep},
    journal = {Bioinformatics},
    year = {2019},
    volume = {35},
    pages = {526-528},
    doi = {10.1093/bioinformatics/bty633},
  }

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