Citing tskit

If you use tskit in your work, we recommend citing the 2024 ARG Genetics paper and the 2016 msprime PLOS Computational Biology paper:

Yan Wong, Anastasia Ignatieva, Jere Koskela, Gregor Gorjanc, Anthony W Wohns, Jerome Kelleher, A general and efficient representation of ancestral recombination graphs, Genetics, Volume 228, Issue 1, September 2024, iyae100, https://doi.org/10.1093/genetics/iyae100

Jerome Kelleher, Alison M Etheridge and Gilean McVean (2016), Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes, PLOS Comput Biol 12(5): e1004842. doi: 10.1371/journal.pcbi.1004842

If you use summary statistics, please cite the 2020 Genetics paper:

Peter Ralph, Kevin Thornton, Jerome Kelleher, Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes, Genetics, Volume 215, Issue 3, 1 July 2020, Pages 779–797, https://doi.org/10.1534/genetics.120.303253

Bibtex records:

@article{Wong2024ARGs,
  author    = {Wong, Yan and Ignatieva, Anastasia and Koskela, Jere and Gorjanc, Gregor and 
               Wohns, Anthony W and Kelleher, Jerome},
  title     = {A general and efficient representation of ancestral recombination graphs},
  journal   = {Genetics},
  volume    = {228},
  number    = {1},
  pages     = {iyae100},
  year      = {2024},
  doi       = {10.1093/genetics/iyae100}
}

@article{Kelleher2016msprime,
  author    = {Kelleher, Jerome and Etheridge, Alison M and McVean, Gilean},
  title     = {Efficient coalescent simulation and genealogical analysis for large sample sizes},
  journal   = {PLoS Computational Biology},
  volume    = {12},
  number    = {5},
  pages     = {e1004842},
  year      = {2016},
  publisher = {Public Library of Science}
}

@article{Ralph2020Stats,
  author    = {Ralph, Peter and Thornton, Kevin and Kelleher, Jerome},
  title     = {Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes},
  journal   = {Genetics},
  volume    = {215},
  number    = {3},
  pages     = {779--797},
  year      = {2020},
  doi       = {10.1534/genetics.120.303253}
}