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Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
Bioinformatics ( IF 5.8 ) Pub Date : 2020-12-29 , DOI: 10.1093/bioinformatics/btaa820
Jose Barba-Montoya 1, 2 , Qiqing Tao 1, 2 , Sudhir Kumar 1, 2, 3
Affiliation  

As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates.

中文翻译:

当违反平稳性和时间可逆性假设时,使用 GTR+Γ 替代模型确定序列发散的年代

随着当代数据集中物种和基因的数量和多样性的增长,所有分子测年方法中的两个共同假设,即替代过程的时间可逆性和平稳性,变得站不住脚。没有任何用于分子测年的软件工具允许研究人员在他们的数据分析中放宽这两个假设。通常,跨谱系的相同通用时间可逆 (GTR) 模型以及跨站点的伽马 (+Γ) 分布速率用于松弛时钟分析,该分析假设替代过程的时间可逆性和平稳性。许多报告量化了违反这些基本假设对分子系统发育的影响,但没有一个系统分析它们对分歧时间估计的影响。
更新日期:2020-12-31
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