To cite aphid in publications use:

  Wilkinson SP (2019) aphid: an R package for analysis with profile
  hidden Markov models. Bioinformatics.
  https://doi.org/10.1093/bioinformatics/btz159.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {aphid: an R package for analysis with profile hidden Markov models},
    author = {Shaun Wilkinson},
    url = {https://doi.org/10.1093/bioinformatics/btz159},
    journal = {Bioinformatics},
    year = {2019},
    doi = {10.1093/bioinformatics/btz159},
  }