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

The algorithm for the inside_outside and maximization methods is described in our Science paper (citation below, preprint here). Another repository provides code to reproduce evaluations of the accuracy and computational requirements of these methods. The default variational_gamma method has not yet been described in print. For the moment, please cite this github repository if you need a citable reference.

The original tsdate algorithm, which you should cite in published work, is published in:

Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) A unified genealogy of modern and ancient genomes. Science 375: eabi8264; doi: https://doi.org/10.1126/science.abi8264

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

    (citation)=

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