link-ancestors: fast simulation of local ancestry with tree sequence software
Georgia Tsambos, Jerome Kelleher, Peter L. Ralph, Stephen Leslie, Damjan Vukcevic
Abstract
Summary: It 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 implementation: A 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.
Topics & Concepts
Sequence (biology)Tree (set theory)Computer scienceSoftwareComputational biologyBiologyEvolutionary biologyOperating systemGeneticsMathematicsCombinatoricsGenomics and Phylogenetic StudiesGenetic diversity and population structureBiomedical Text Mining and Ontologies