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利用 msprime 1.0 进行高效的祖先和突变模拟。

Efficient ancestry and mutation simulation with msprime 1.0.

机构信息

Cluster of Excellence "Controlling Microbes to Fight Infections", Mathematical and Computational Population Genetics, University of Tübingen, 72076 Tübingen, Germany.

Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK.

出版信息

Genetics. 2022 Mar 3;220(3). doi: 10.1093/genetics/iyab229.

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.

摘要

随机模拟是群体遗传学的一个关键工具,因为所涉及的模型通常在分析上难以处理,而模拟通常是获得真实数据以评估推断的唯一方法。正因为如此,已经开发了大量专门的模拟程序,每个程序都填补了一个特定的空缺,但功能基本重叠,并且大量重复工作。在这里,我们介绍 msprime 版本 1.0,它基于简洁的树序列数据结构和 tskit 库高效地实现了祖先和突变模拟。我们总结了 msprime 的许多功能,并展示了它的性能非常出色,通常比专门的替代方案快得多,内存效率也高得多。这些高性能特性已经经过了彻底的测试和验证,并使用协作的、开源的开发模型构建,通过社区参与减少了工作重复并提高了软件质量。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e39f/9176297/464d32355f44/iyab229f1.jpg

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