shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals

Li Zhan; Xiao Luo; Wenqin Xie; Xuan-An Zhu; Zijing Xie; Jianfeng Lin; Lin Li; Wenli Tang; Rui Wang; Lin Deng; Yufan Liao; Bingdong Liu; Yantong Cai; Qianwen Wang; Shuangbin Xu; Guangchuang Yu

doi:10.1016/j.jgg.2024.02.004

Volume 51 Issue 7

Jul. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(7): 762-768

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shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals

doi: 10.1016/j.jgg.2024.02.004

a. Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China;
b. Faculty of Computers, Guangdong University of Technology, Guangzhou, Guangdong 510006, China;
c. Ubigene Biosciences Co., Ltd., Guangzhou, Guangdong 510530, China;
d. State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, China

Funds:

This study was supported by the National Natural Science Foundation of China (32270677).

Received Date: 2023-12-14
Accepted Date: 2024-02-22
Rev Recd Date: 2024-02-20

Available Online: 2025-06-06

Publish Date: 2024-02-26

Abstract

Abstract

The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately labeled sampling times. Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences. Furthermore, while not all branches of a phylogenetic tree may exhibit a clear temporal signal, specific branches may still adhere to the assumptions, with varying evolutionary rates. Supporting a relaxed molecular clock model better aligns with the complexities of evolution. The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals. Despite its utility, there remains a lack of corresponding software implementations for broader applications. To address this gap, we present shinyTempSignal, an interactive web application implemented with the shiny framework, available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal. This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models. By extending the root-to-tip regression method to diverse signals, shinyTempSignal helps in the detection of evolving features or traits, thereby laying the foundation for deeper insights and subsequent analyses.
- Molecular clock,
- Root-to-tip regression,
- Temporal signal,
- Phylogenetic signal

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References

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