Efficient ancestry and mutation simulation with msprime 1.0
Year: 2026
Type: article
Abstract: Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime's many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
Source: UNC Libraries
DOI: 10.17615/wh2m-xz62
Authors: Galloway, Jared G, Eldon, Bjarki, Gladstein, Ariella L, Goldstein, Daniel, Kern, Andrew D, Wong, Yan, Pope, Nathaniel S, Quinto-Cortés, Consuelo D, Gorjanc, Gregor, Kretzschumar, Warren W, Baumdicker, Franz, Saunack, Kumar, Thornton, Kevin, Lohse, Konrad, Jeffery, Ben, Gravel, Simon, Nelson, Dominic, Ragsdale, Aaron P, Koskela, Jere, Ralph, Peter L, Wohns, Anthony W, Sellinger, Thibaut, Tsambos, Georgia, Matschiner, Michael, Ellerman, E Castedo, Guo, Bing, Zhu, Sha, Rodrigues, Murillo F, Gower, Graham, Bisschop, Gertjan, Kelleher, Jerome, van Kemenade, Hugo
Institution: University of North Carolina at Chapel Hill
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Funders: Velux Fonden, Robertson Foundation, Deutsche Forschungsgemeinschaft, Canada Research Chairs, Canadian Institutes of Health Research, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, National Human Genome Research Institute, National Institute of General Medical Sciences
OpenAlex ID: W7213580741