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sitePath: a visual tool to identify polymorphism clades and help find fixed and parallel mutations
Chengyang Ji1,2, Na Han1,2, Yexiao Cheng1,2,3
1Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
BMC Bioinformatics
|November 26, 2022
Summary
A new R package, sitePath, automates the identification of polymorphism clades on phylogenetic trees. This tool aids in detecting fixed and parallel mutations, crucial for understanding viral evolution and function.
Area of Science:
- * Virology and Bioinformatics
- * Computational Biology and Evolutionary Genetics
Background:
- * Identifying mutations on phylogenetic trees is vital for understanding viral functions.
- * Manual identification of polymorphism clades is time-consuming due to rapid viral sequence accumulation.
- * Automated computational tools are needed for efficient analysis of large viral datasets.
Purpose of the Study:
- * To develop an automated computational tool for identifying polymorphism clades on phylogenetic trees.
- * To enable the inference of fixed and parallel mutations from identified clades.
- * To provide integrated visualization tools for presenting analysis results.
Main Methods:
- * Implementation of a branch-and-bound-like search algorithm.
- * Development of the R package 'sitePath'.
- * Integration of visualization tools for result presentation.
Main Results:
- * The 'sitePath' R package successfully identifies polymorphism clades automatically.
- * Fixed and parallel mutations can be inferred based on identified polymorphism clades.
- * Analysis of an influenza A virus H3N2 dataset showed detected fixed mutations correlating with antigenic shift mutations.
- * 'sitePath' demonstrates high specificity and sensitivity in detecting fixed mutations across various parameters and phylogenetic inference software.
Conclusions:
- * 'sitePath' effectively identifies polymorphism clades at the per-site level.
- * Sequence clustering on phylogenetic trees aids in inferring fixed and parallel mutations.
- * The package generates high-quality figures for visualizing calculated results.
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