Efficient ancestry and mutation simulation with msprime 1.0
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 develope...
| Glavni autori: | , , , , , , , |
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| Format: | Journal article |
| Jezik: | English |
| Izdano: |
Oxford University Press
2021
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| _version_ | 1826307832489705472 |
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| author | Baumdicker, F Bisschop, G Goldstein, D Zhu, S Jeffery, B Wohns, AW Wong, Y Kelleher, J |
| author_facet | Baumdicker, F Bisschop, G Goldstein, D Zhu, S Jeffery, B Wohns, AW Wong, Y Kelleher, J |
| author_sort | Baumdicker, F |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T07:08:58Z |
| format | Journal article |
| id | oxford-uuid:3f43e3b5-48a0-43fc-9600-c676a1d0ad57 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:08:58Z |
| publishDate | 2021 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:3f43e3b5-48a0-43fc-9600-c676a1d0ad572022-06-09T10:09:20ZEfficient ancestry and mutation simulation with msprime 1.0Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:3f43e3b5-48a0-43fc-9600-c676a1d0ad57EnglishSymplectic ElementsOxford University Press2021Baumdicker, FBisschop, GGoldstein, DZhu, SJeffery, BWohns, AWWong, YKelleher, JStochastic 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. |
| spellingShingle | Baumdicker, F Bisschop, G Goldstein, D Zhu, S Jeffery, B Wohns, AW Wong, Y Kelleher, J Efficient ancestry and mutation simulation with msprime 1.0 |
| title | Efficient ancestry and mutation simulation with msprime 1.0 |
| title_full | Efficient ancestry and mutation simulation with msprime 1.0 |
| title_fullStr | Efficient ancestry and mutation simulation with msprime 1.0 |
| title_full_unstemmed | Efficient ancestry and mutation simulation with msprime 1.0 |
| title_short | Efficient ancestry and mutation simulation with msprime 1.0 |
| title_sort | efficient ancestry and mutation simulation with msprime 1 0 |
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