To cite CNEr in publications use:

  Ge Tan, Dimitris Polychronopoulos, Boris Lenhard (2019). CNEr: A
  toolkit for exploring extreme noncoding conservation PLoS Comput.
  Biol. 15, e1006940.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {CNEr: A toolkit for exploring extreme noncoding conservation},
    author = {Ge Tan and Dimitris Polychronopoulos and Boris Lenhard},
    journal = {PLoS computational biology},
    year = {2019},
    volume = {15},
    issue = {8},
    pages = {e1006940},
    url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006940},
  }