To cite the DiffLogo package in publications:

  M. Nettling, H. Treutler, J. Grau, J. Keilwagen, S. Posch, and I.
  Grosse. DiffLogo: a comparative visualization of sequence motifs. BMC
  bioinformatics, 2015 Nov 17;16:387. doi: 10.1186/s12859-015-0767-x.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {M. Nettling and H. Treutler and J. Grau and J. Keilwagen and S. Posch and I. Grosse},
    title = {DiffLogo: a comparative visualization of sequence motifs.},
    journal = {BMC bioinformatics},
    year = {2015},
    volume = {16},
    issn = {1471--2105},
    keywords = {logo, motif, sequence, tool},
    pmid = {26577052},
    url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0767-x},
  }