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

Tsambos G., Kelleher J., Ralph P., Leslie S., Vukcevic D.

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.

More information Original publication

DOI

10.1093/bioadv/vbad163

Type

Journal article

Publication Date

2023-01-01T00:00:00+00:00

Volume

3

Addresses

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