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hyanwong authored Jun 11, 2024
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Expand Up @@ -10,8 +10,9 @@ The method is frequently combined with the [tsinfer](https://tsinfer.readthedocs

Please refer to the [documentation](https://tskit.dev/tsdate/docs/latest/) for information on installing and using the software.

The discrete-time estimation methods are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2)). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in [another repository](https://github.com/awohns/unified_genealogy_paper).
The algorithms for the original `inside_outside` and `maximization` [methods](https://tskit.dev/tsdate/docs/latest/methods.html) are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2), evaluations in [another repository](https://github.com/awohns/unified_genealogy_paper)). The new `variational_gamma` method, which is now the default, has not yet been described in print. For the moment, please cite this github repository if you need a citable reference.

The citation to use for the original tsdate algorithms is:

> 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
Please cite this paper if you use ``tsdate`` in published work.

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