To cite PhenotypeSimulator in publications use:

  Hannah V Meyer, Ewan Birney (2018). PhenotypeSimulator: A
  comprehensive framework for simulating multi-trait, multi-locus
  genotype to phenotype relationships. Bioinformatics, 34(17),
  2951-2956. URL https://doi.org/10.1093/bioinformatics/bty197.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships},
    author = {Hannah V Meyer and Ewan Birney},
    journal = {Bioinformatics},
    year = {2018},
    volume = {34},
    number = {17},
    pages = {2951--2956},
  }