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, population_size=100, mutation_rate=1e-8)
The rest of this documentation is organised into the following sections:
Source code#
The source code for tsdate 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 is described in our Science paper (citation below, 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.
Please cite the following paper if you use tsdate in published work:
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