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

作     者：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 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

作者机构：Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of ComputersGuangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co.Ltd.GuangzhouGuangdong 510530China State Key Laboratory of Applied Microbiology Southern ChinaGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China 

出 版 物：《Journal of Genetics and Genomics》 (遗传学报（英文版）)

年 卷 期：2024年第51卷第7期

页      面：762-768页

核心收录：

学科分类：0710[理学-生物学] 08[工学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：supported by the National Natural Science Foundation of China(32270677) 

主　　题：Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal 

摘      要：The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,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 *** a relaxed molecular clock model better aligns with the complexities of *** 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 *** its utility,there remains a lack of corresponding software implementations for broader *** 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://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** 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.