diff --git a/README.md b/README.md index a77258c3b4..17cac3ed23 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ and [C](https://tskit.dev/tskit/docs/stable/c-api.html) API. A Rust API is provi Most users of `tskit` will use the python API as it provides a convenient, high-level API to access, analyse and create tree sequences. Full documentation is -[here](https://tskit.dev/tskit/docs/stable/python-api.html). +[here](https://tskit.dev/tskit/docs/stable/python-api.html). #### C API [![C99](https://img.shields.io/badge/Language-C99-steelblue.svg)](https://en.wikipedia.org/wiki/C99) @@ -71,3 +71,14 @@ python -m pip install tskit # or conda install -c conda-forge tskit ``` + +## Funding and acknowledgements + +The tskit software has benefited from input and contributions from +too many people to list here +(but see the author list for [the tskit paper](https://arxiv.org/abs/2602.09649)). +We also gratefully acknowledge funding from the Robertson Foundation, the NIH +(research grants HG011395 and HG012473), and the NSF +(research grant [OAC-2104115](https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2104115)), +that has supported core tskit development. + diff --git a/docs/citation.md b/docs/citation.md index fa46737408..42607b2974 100644 --- a/docs/citation.md +++ b/docs/citation.md @@ -2,7 +2,25 @@ # 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](): +If you use `tskit` in your work, we recommend citing the "tskit paper": +> Ben Jeffery, Yan Wong, Kevin Thornton, Georgia Tsambos, Gertjan Bisschop, Yun +> Deng, E. Castedo Ellerman, Thomas B. Forest, Halley Fritze, Daniel Goldstein, +> Gregor Gorjanc, Graham Gower, Simon Gravel, Jeremy Guez, Benjamin C. Haller, +> Andrew D. Kern, Lloyd Kirk, Ivan Krukov, Hanbin Lee, Brieuc Lehmann, +> Hossameldin Loay, Matthew M. Osmond, Duncan S. Palmer, Nathaniel S. Pope, Aaron +> P. Ragsdale, Duncan Robertson, Murillo F. Rodrigues, Hugo van Kemenade, Clemens +> L. Weiß, Anthony Wilder Wohns, Shing H. Zhan, Brian C. Zhang, Marianne Aspbury, +> Nikolas A. Baya, Saurabh Belsare, Arjun Biddanda, Francisco Campuzano Jiménez, +> Ariella Gladstein, Bing Guo, Savita Karthikeyan, Warren W. Kretzschmar, Inés +> Rebollo, Kumar Saunack, Ruhollah Shemirani, Alexis Simon, Chris Smith, Jeet +> Sukumaran, Jonathan Terhorst, Per Unneberg, Ao Zhang, Peter Ralph, Jerome +> Kelleher, *Population-scale Ancestral Recombination Graphs with tskit 1.0*, +> arXiv:2602.09649v2, +> doi: [10.48550/arXiv.2602.09649](https://doi.org/10.48550/arXiv.2602.09649) + +For citations that discuss ARGs and how these are represented in a tree sequence, +we recommend 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, @@ -24,6 +42,29 @@ If you use summary statistics, please cite the Bibtex records: ```bibtex +@misc{jeffery2026tskit, + title={Population-scale Ancestral Recombination Graphs with tskit 1.0}, + author={Ben Jeffery and Yan Wong and Kevin Thornton and Georgia Tsambos + and Gertjan Bisschop and Yun Deng and E. Castedo Ellerman and Thomas B. Forest + and Halley Fritze and Daniel Goldstein and Gregor Gorjanc and Graham Gower and + Simon Gravel and Jeremy Guez and Benjamin C. Haller and Andrew D. Kern and + Lloyd Kirk and Ivan Krukov and Hanbin Lee and Brieuc Lehmann and Hossameldin + Loay and Matthew M. Osmond and Duncan S. Palmer and Nathaniel S. Pope and Aaron + P. Ragsdale and Duncan Robertson and Murillo F. Rodrigues and Hugo van Kemenade + and Clemens L. Weiß and Anthony Wilder Wohns and Shing H. Zhan and Brian C. + Zhang and Marianne Aspbury and Nikolas A. Baya and Saurabh Belsare and Arjun + Biddanda and Francisco Campuzano Jiménez and Ariella Gladstein and Bing Guo and + Savita Karthikeyan and Warren W. Kretzschmar and Inés Rebollo and Kumar Saunack + and Ruhollah Shemirani and Alexis Simon and Chris Smith and Jeet Sukumaran and + Jonathan Terhorst and Per Unneberg and Ao Zhang and Peter Ralph and Jerome + Kelleher}, + year={2026}, + eprint={2602.09649}, + archivePrefix={arXiv}, + primaryClass={q-bio.PE}, + url={https://arxiv.org/abs/2602.09649}, +} + @article{Wong2024ARGs, author = {Wong, Yan and Ignatieva, Anastasia and Koskela, Jere and Gorjanc, Gregor and Wohns, Anthony W and Kelleher, Jerome}, @@ -57,4 +98,15 @@ Bibtex records: year = {2020}, doi = {10.1534/genetics.120.303253} } -``` \ No newline at end of file +``` + +# Funding and acknowledgements + + +The tskit software has benefited from input and contributions from +too many people to list here (but see the author list above). +We also gratefully acknowledge funding from the Robertson Foundation, the NIH +(research grants HG011395 and HG012473), and the NSF +(research grant [OAC-2104115](https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2104115)), +that has supported core tskit development. +