link-ancestors: Fast simulation of local ancestry with tree sequence software

Abstract

SummaryIt is challenging to simulate realistic tracts of genetic ancestry on a scale suitable for simulation based inference. We present an algorithm that enables this information to be extracted efficiently from tree sequences produced by simulations run with msprime and SLiM. Availability and ImplementationA C-based implementation of the link-ancestors algorithm is in tskit (https://tskit.dev/tskit/docs/stable/). We also provide a user-friendly wrapper for link-ancestors in tspop, a Python-based utility package. Contactgtsambos@uw.edu. Supplementary informationTechnical details of link-ancestors are in the Supplementary Information. Documentation for the tspop package is at http://tspop.readthedocs.io/.