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

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The molecular clock model is fundamental for inferring species divergence times from molecular se-quences.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,shinyTemp-Signal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

Molecular clockRoot-to-tip regressionTemporal signalPhylogenetic signal

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

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Department of Bioinformatics,School of Basic Medical Sciences,Southern Medical University,Guangzhou,Guangdong 510515,China

Faculty of Computers,Guangdong University of Technology,Guangzhou,Guangdong 510006,China

Ubigene Biosciences Co.,Ltd.,Guangzhou,Guangdong 510530,China

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

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National Natural Science Foundation of China

32270677

2024

10.1016/j.jgg.2024.02.004

遗传学报
中国遗传学会 中国科学院遗传与发育生物学研究所

遗传学报

CSTPCD
影响因子：0.821
ISSN：1673-8527
年,卷(期)：2024.51(7)