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}, }