Citation

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