tsdate

Infer node ages from a tree sequence topology


License
MIT
Install
pip install tsdate==0.1.5

Documentation

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 Science paper (preprint here). 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 (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.