Efficient ancestry and mutation simulation with msprime 1.0.
Genetics
; 220(3)2022 03 03.
Article
em En
| MEDLINE
| ID: mdl-34897427
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.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Modelos Genéticos
Idioma:
En
Revista:
Genetics
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Alemanha