How to cite tskit-dev software

tskit

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}
}

Citation details for tskit can be found at: https://tskit.dev/tskit/docs/stable/citation.html

msprime

Citing msprime

If you use msprime in your work, please cite the 2022 Genetics paper marking the 1.0 release:

Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E Castedo Ellerman, Jared G Galloway, Ariella L Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S Pope, Consuelo D Quinto-Cortés, Murillo F Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W Wohns, Yan Wong, Simon Gravel, Andrew D Kern, Jere Koskela, Peter L Ralph and Jerome Kelleher (2022), Efficient ancestry and mutation simulation with msprime 1.0, Genetics, Volume 220, Issue 3. http://doi.org/10.1093/genetics/iyab229

You may also wish to cite the original 2016 PLOS Computational Biology paper:

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 the Discrete Time Wright Fisher model, please cite the 2020 PLOS Genetics paper:

Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Claudia Moreau, Gil McVean and Simon Gravel (2020), Accounting for long-range correlations in genome-wide simulations of large cohorts, PLOS Genetics 16(5): e1008619. https://doi.org/10.1371/journal.pgen.1008619

Bibtex records:

@article{baumdicker2022efficient,
  title={Efficient ancestry and mutation simulation with msprime 1.0},
  author = {Baumdicker, Franz and Bisschop, Gertjan and Goldstein, Daniel
    and Gower, Graham and Ragsdale, Aaron P and Tsambos, Georgia and Zhu, Sha
    and Eldon, Bjarki and Ellerman, E Castedo and Galloway, Jared G
    and Gladstein, Ariella L and Gorjanc, Gregor and Guo, Bing
    and Jeffery, Ben and Kretzschumar, Warren W and Lohse, Konrad
    and Matschiner, Michael and Nelson, Dominic and Pope, Nathaniel S
    and Quinto-Cortés, Consuelo D and Rodrigues, Murillo F
    and Saunack, Kumar and Sellinger, Thibaut and Thornton, Kevin
    and van Kemenade, Hugo and Wohns, Anthony W and Wong, Yan
    and Gravel, Simon and Kern, Andrew D and Koskela, Jere
    and Ralph, Peter L and Kelleher, Jerome},
  journal={Genetics},
  volume={220},
  number={3},
  pages={iyab229},
  year={2022},
  publisher={Oxford University Press}
}

@article{kelleher2016efficient,
  title={Efficient coalescent simulation and genealogical analysis for large sample sizes},
  author={Kelleher, Jerome and Etheridge, Alison M and McVean, Gilean},
  journal={PLoS computational biology},
  volume={12},
  number={5},
  pages={e1004842},
  year={2016},
  publisher={Public Library of Science}
}

@article{nelson2020accounting,
  title={Accounting for long-range correlations in genome-wide simulations of large cohorts},
  author={Nelson, Dominic and Kelleher, Jerome and Ragsdale, Aaron P and
    Moreau, Claudia and McVean, Gil and Gravel, Simon},
  journal={PLoS genetics},
  volume={16},
  number={5},
  pages={e1008619},
  year={2020},
  publisher={Public Library of Science}
}

Citation details for msprime can be found at: https://tskit.dev/msprime/docs/stable/CITATION.html

tsinfer

Citing tsinfer

If you use tsinfer in your work, please cite the 2019 Nature Genetics paper:

Jerome Kelleher, Yan Wong, Anthony W. Wohns, Chaimaa Fadil, Patrick K. Albers & Gil McVean (2019) Inferring whole-genome histories in large population datasets, Nature Genetics, Volume 51, 1330–1338. https://doi.org/10.1038/s41588-019-0483-y

Bibtex record:

@article{Kelleher2019,
  doi = {10.1038/s41588-019-0483-y},
  url = {https://doi.org/10.1038/s41588-019-0483-y},
  year = {2019},
  month = sep,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {51},
  number = {9},
  pages = {1330--1338},
  author = {Jerome Kelleher and Yan Wong and Anthony W. Wohns and Chaimaa Fadil and Patrick K. Albers and Gil McVean},
  title = {Inferring whole-genome histories in large population datasets},
  journal = {Nature Genetics}
}

Citation details for tsinfer can be found at: https://tskit.dev/tsinfer/docs/stable/CITATION.html

tsdate

Citation details for tsdate can be found at: https://tskit.dev/tsdate/docs/stable/#citing

pyslim

Citation details for pyslim can be found at: https://zenodo.org/records/8205346

tsbrowse

Citation details for tsbrowse can be found at: https://doi.org/10.1101/2025.04.23.649987

tstrait

Citing tstrait

If you use tstrait in your research project, please cite the following paper:

Daiki Tagami, Gertjan Bisschop, and Jerome Kelleher (2024), tstrait: a quantitative trait simulator for ancestral recombination graphs,Bioinformatics, Volume 40, Issue 6. https://doi.org/10.1093/bioinformatics/btae334

Bibtex records:

@article{10.1093/bioinformatics/btae334,
    author = {Tagami, Daiki and Bisschop, Gertjan and Kelleher, Jerome},
    title = "{tstrait: a quantitative trait simulator for ancestral recombination graphs}",
    journal = {Bioinformatics},
    volume = {40},
    number = {6},
    pages = {btae334},
    year = {2024},
    month = {05},
    doi = {10.1093/bioinformatics/btae334},
}

Citation details for tstrait can be found at: https://tskit.dev/tstrait/docs/stable/citation.html