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shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals.
Zhan, Li; Luo, Xiao; Xie, Wenqin; Zhu, Xuan-An; Xie, Zijing; Lin, Jianfeng; Li, Lin; Tang, Wenli; Wang, Rui; Deng, Lin; Liao, Yufan; Liu, Bingdong; Cai, Yantong; Wang, Qianwen; Xu, Shuangbin; Yu, Guangchuang.
Afiliación
  • Zhan L; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Luo X; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Xie W; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Zhu XA; 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.
  • Xie Z; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Lin J; Ubigene Biosciences Co., Ltd., Guangzhou, Guangdong 510530, China.
  • Li L; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Tang W; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Wang R; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Deng L; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Liao Y; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Liu B; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory
  • Cai Y; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Wang Q; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China.
  • Xu S; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China. Electronic address: xshuangbin@163.com.
  • Yu G; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China. Electronic address: gcyu1@smu.edu.cn.
J Genet Genomics ; 51(7): 762-768, 2024 Jul.
Article en En | MEDLINE | ID: mdl-38417547
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Filogenia / Programas Informáticos Idioma: En Revista: J Genet Genomics Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: China
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Filogenia / Programas Informáticos Idioma: En Revista: J Genet Genomics Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: China