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使用MIGRATE进行群体遗传推断。

Population Genetic Inference With MIGRATE.

作者信息

Beerli Peter, Mashayekhi Somayeh, Sadeghi Marjan, Khodaei Marzieh, Shaw Kyle

机构信息

Department of Scientific Computing, Florida State University, Tallahassee, Florida.

Department of Mathematics, Kennesaw State University, Marietta, Georgia.

出版信息

Curr Protoc Bioinformatics. 2019 Dec;68(1):e87. doi: 10.1002/cpbi.87.

DOI:10.1002/cpbi.87
PMID:31756024
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9286049/
Abstract

Many evolutionary biologists collect genetic data from natural populations and then need to investigate the relationship among these populations to compare different biogeographic hypotheses. MIGRATE, a useful tool for exploring relationships between populations and comparing hypotheses, has existed since 1998. Throughout the years, it has steadily improved in both the quality of algorithms used and in the efficiency of carrying out those calculations, thus allowing for a larger number of loci to be evaluated. This efficiency has been enhanced, as MIGRATE has been developed to perform many of its calculations concurrently when running on a computer cluster. The program is based on the coalescence theory and uses Bayesian inference to estimate posterior probability densities of all the parameters of a user-specified population model. Complex models, which include migration and colonization parameters, can be specified. These models can be evaluated using marginal likelihoods, thus allowing a user to compare the merits of different hypotheses. The three presented protocols will help novice users to develop sophisticated analysis techniques useful for their research projects. © 2019 The Authors. Basic Protocol 1: First steps with MIGRATE Basic Protocol 2: Population model specification Basic Protocol 3: Prior distribution specification Basic Protocol 4: Model selection Support Protocol 1: Installing the program MIGRATE Support Protocol 2: Installation of parallel MIGRATE.

摘要

许多进化生物学家从自然种群中收集遗传数据，然后需要研究这些种群之间的关系，以比较不同的生物地理假说。MIGRATE是一种用于探索种群间关系和比较假说的有用工具，自1998年以来就已存在。多年来，它在所用算法的质量和执行这些计算的效率方面都稳步提高，从而能够评估更多的基因座。随着MIGRATE被开发为在计算机集群上运行时可同时执行许多计算，其效率得到了提高。该程序基于合并理论，并使用贝叶斯推断来估计用户指定的种群模型所有参数的后验概率密度。可以指定包括迁移和殖民化参数在内的复杂模型。这些模型可以使用边际似然性进行评估，从而允许用户比较不同假说的优缺点。所介绍的三个方案将帮助新手用户开发对其研究项目有用的复杂分析技术。© 2019作者。基本方案1：MIGRATE的初步步骤 基本方案2：种群模型规范 基本方案3：先验分布规范 基本方案4：模型选择 支持方案1：安装程序MIGRATE 支持方案2：并行MIGRATE的安装。

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4
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