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: 使用...估计种群树上迁移边的最佳数量。

: estimating the optimal number of migration edges on population trees using .

作者信息

Fitak Robert R

机构信息

Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA.

出版信息

Biol Methods Protoc. 2021 Sep 16;6(1):bpab017. doi: 10.1093/biomethods/bpab017. eCollection 2021.

Abstract

The software has become extensively used to estimate the number of migration events, or edges (), on population trees from genome-wide allele frequency data. However, the appropriate number of edges to include remains unclear. Here, I show that an optimal value of can be inferred from the second-order rate of change in likelihood (Δ) across incremental values of . Repurposed from its original use to estimate the number of population clusters in the software (Δ), I show using simulated populations that Δ performs equally as well as current recommendations for . A demonstration of an empirical dataset from domestic dogs indicates that this method may be preferable in large, complex population histories and can prioritize migration events for subsequent investigation. The method has been implemented in a freely available R package called "OptM" and as a web application (https://rfitak.shinyapps.io/OptM/) to interface directly with the output files of .

摘要

该软件已被广泛用于根据全基因组等位基因频率数据估计种群树中的迁移事件数量或分支数量()。然而,合适的分支数量仍不明确。在这里,我表明可以从似然性(Δ)随 增量的二阶变化率推断出 的最优值。从其最初用于估计软件 (Δ)中的种群簇数量的用途重新调整后,我使用模拟种群表明,Δ 的表现与当前关于 的建议相当。对家犬实证数据集的演示表明,该方法在大型复杂种群历史中可能更可取,并且可以优先考虑迁移事件以便后续调查。该方法已在一个名为 "OptM" 的免费可用 R 包中实现,并作为一个网络应用程序(https://rfitak.shinyapps.io/OptM/)直接与 的输出文件接口。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bc8a/8476930/8e09382dcae9/bpab017f1.jpg

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