Use 2011 to cite phangorn in a publication; 2017 for plotting
phylogenetic networks. As phangorn is evolving quickly, you may want to
cite also its version number (phangorn 2.12.1.1).

  Schliep K.P. 2011. phangorn: phylogenetic analysis in R.
  Bioinformatics, 27(4) 592-593

A BibTeX entry for LaTeX users is

  @Article{,
    title = {phangorn: phylogenetic analysis in R},
    author = {Klaus Schliep},
    journal = {Bioinformatics},
    year = {2011},
    volume = {27},
    number = {4},
    pages = {592--593},
    doi = {10.1093/bioinformatics/btq706},
  }

  Schliep, K., Potts, A. J., Morrison, D. A., Grimm, G. W. (2017),
  Intertwining phylogenetic trees and networks. Methods in Ecology and
  Evolution, 8: 1212--1220. doi: 10.1111/2041-210X.12760

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Klaus Schliep and Alastair J. Potts and David A. Morrison and Guido W. Grimm},
    title = {Intertwining phylogenetic trees and networks},
    journal = {Methods in Ecology and Evolution},
    volume = {8},
    number = {10},
    pages = {1212--1220},
    keywords = {exploratory data analysis, networks, phangorn, R, trees},
    year = {2017},
  }