tsdate

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 frequently combined with the tsinfer algorithm, which efficiently infers tree sequence topologies from large genetic datasets.

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

The algorithms for the original inside_outside and maximization methods are described in this Science paper (citation below, preprint here, evaluations in another repository). The new variational_gamma method, the default from version 0.2 onwards, 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