tsdate 0.2.6

Infer node ages from a tree sequence topology.

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 (stable • latest) for information on installing and using the software.

Installation

python -m pip install tsdate

If using the variational_gamma algorithm (the default from version 0.2 onwards), please cite the preprint:

Nathaniel S. Pope, Sam Tallman, Ben Jeffery, Duncan Robertson, Yan Wong, Savita Karthikeyan, Peter L. Ralph, and Jerome Kelleher (2026) Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs. bioRxiv: 2026.01.07.698223; doi: https://doi.org/10.64898/2026.01.07.698223

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

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