Please cite the paper below for the motifStack package.

  Ou J. motifStack for the analysis of transcription factor binding
  site evolution. Nature Methods 15, 8-9 (2018)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {motifStack for the analysis of transcription factor binding site evolution},
    author = {Jianhong Ou and Scot A Wolfe and Michael H Brodsky and Lihua Julie Zhu},
    journal = {Nature Methods},
    volume = {15},
    year = {2018},
    pages = {8-9},
    url = {http://dx.doi.org/10.1038/nmeth.4555},
    doi = {10.1038/nmeth.4555},
  }