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Infer node ages from a tree sequence topology

Project description

tsdate

CircleCI codecov Documentation Status

tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").

The method is designed to operate on the output of tsinfer, which efficiently infers tree sequence topologies from large genetic datasets.

Please refer to the documentation for information on installing and using the software.

The algorithm is described in this BioRxiv preprint. 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.

Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2021) A unified genealogy of modern and ancient genomes. bioRxiv 2021.02.16.431497; doi: https://doi.org/10.1101/2021.02.16.431497

Please cite this preprint if you use tsdate in published work.

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