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).

Schliep K (2011). “phangorn: phylogenetic analysis in R.” Bioinformatics, 27(4), 592–593. doi:10.1093/bioinformatics/btq706.

Schliep K, Potts A, Morrison D, Grimm G (2017). “Intertwining phylogenetic trees and networks.” Methods in Ecology and Evolution, 8(10), 1212–1220.

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }