To cite package ‘apex’ in publications use:

  Schliep K, Jombart T, Kamvar Z, Archer E, Harris R (2024). _apex:
  Phylogenetic Methods for Multiple Gene Data_. R package version
  1.0.6, <https://github.com/thibautjombart/apex>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {apex: Phylogenetic Methods for Multiple Gene Data},
    author = {Klaus Schliep and Thibaut Jombart and Zhian Namir Kamvar and Eric Archer and Rebecca Harris},
    year = {2024},
    note = {R package version 1.0.6},
    url = {https://github.com/thibautjombart/apex},
  }