TY - JOUR T1 - Efficient ancestry and mutation simulation with msprime 1.0 JF - bioRxiv DO - 10.1101/2021.08.31.457499 SP - 2021.08.31.457499 AU - Franz Baumdicker AU - Gertjan Bisschop AU - Daniel Goldstein AU - Graham Gower AU - Aaron P. Ragsdale AU - Georgia Tsambos AU - Sha Zhu AU - Bjarki Eldon AU - Castedo E. Ellerman AU - Jared G. Galloway AU - Ariella L. Gladstein AU - Gregor Gorjanc AU - Bing Guo AU - Ben Jeffery AU - Warren W. Kretzschmar AU - Konrad Lohse AU - Michael Matschiner AU - Dominic Nelson AU - Nathaniel S. Pope AU - Consuelo D. Quinto-Cortés AU - Murillo F. Rodrigues AU - Kumar Saunack AU - Thibaut Sellinger AU - Kevin Thornton AU - Hugo van Kemenade AU - Anthony W. Wohns AU - H. Yan Wong AU - Simon Gravel AU - Andrew D. Kern AU - Jere Koskela AU - Peter L. Ralph AU - Jerome Kelleher Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/09/01/2021.08.31.457499.abstract N2 - 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 necessity, a large number of specialised 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 tskit library. We summarise msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised 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.Competing Interest StatementThe authors have declared no competing interest. ER -