Welcome to tsdate#
This is the documentation for tsdate, a method for efficiently inferring the age of ancestors in a genetic genealogy or “ARG”.
Basic usage is as simple as running the following python command
import tsdate
output_ts = tsdate.date(input_ts, mutation_rate=1e-8)
The rest of this documentation is organised into the following sections:
Source code#
Tsdate is open source software released under the liberal MIT licence. The code is freely available on GitHub. Bug reports and suggestions for improvements can be made by opening an issue on that repository: we suggest also checking the discussions list. Pull requests are welcome: we largely follow the tskit development workflow.
Citing#
The algorithm for the inside_outside and maximization methods is described
in our Science paper (citation below,
preprint here).
Another repository provides
code to reproduce evaluations of the accuracy and computational requirements of these methods.
The default variational_gamma method has not yet been described in print. For the moment,
please cite this github repository if you need a citable reference.
The original tsdate algorithm, which you should cite in published work, is published in:
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