Citation

The default variational_gamma method is described in a preprint, and should be cited by published work using tsdate versions 0.2 or higher:

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 algorithm for the inside_outside and maximization methods (the defaults prior to version 0.2) 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.

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