diff --git a/docs/_toc.yml b/docs/_toc.yml index 120fa1d542..168e7e8dd8 100644 --- a/docs/_toc.yml +++ b/docs/_toc.yml @@ -27,3 +27,7 @@ parts: chapters: - file: development - file: changelogs +- caption: Miscellaneous + chapters: + - file: citation + diff --git a/docs/citation.md b/docs/citation.md new file mode 100644 index 0000000000..fa46737408 --- /dev/null +++ b/docs/citation.md @@ -0,0 +1,60 @@ +(sec_citation)= + +# 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](https://doi.org/10.1534/genetics.120.303253): + +> 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: + +```bibtex +@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} +} +``` \ No newline at end of file diff --git a/docs/introduction.md b/docs/introduction.md index 2399fa25b1..02ad3a34f9 100644 --- a/docs/introduction.md +++ b/docs/introduction.md @@ -39,6 +39,10 @@ For a gentle introduction, you might like to read "{ref}`tutorials:sec_what_is`" on our {ref}`tutorials site`. There you can also find further tutorial material to introduce you to the key concepts behind succinct tree sequences. +:::{important} +If you use `tskit` in your work, please remember to cite it appropriately: see the {ref}`citations` page for details. +::: + :::{note} This documentation is under active development and may be incomplete in some areas. If you would like to help improve it, please open an issue or