To cite aphid in publications use:

Wilkinson SP (2018) The 'aphid' package for analysis with profile hidden Markov models. R package version 1.1.0. https://cran.r-project.org/package=aphid

Corresponding BibTeX entry:

  @Manual{,
    title = {The {aphid} package for analysis with profile hidden
      Markov models},
    author = {Shaun Wilkinson},
    url = {https://cran.r-project.org/package=aphid},
    year = {2017},
    doi = {10.5281/zenodo.1227696},
  }