tinselR

tinselR annotates and visualizes phylogenetic trees from whole-genome sequencing data to support confirmation of pathogen outbreaks and inference of transmission routes.

Key Features:

• Visualization: Renders phylogenetic trees to display relationships among pathogen sequences.
• Annotation: Adds labels and annotations to tree nodes and branches to highlight genetic similarities and differences relevant to outbreak investigations.
• Phylogenetic analysis: Implements methods to infer evolutionary relationships among pathogen genomes.
• Whole-genome sequencing integration: Accepts and uses whole-genome sequencing data for phylogenetic and annotation analyses.

Scientific Applications:

• Outbreak confirmation: Identifies clusters of related pathogen sequences to confirm suspected outbreak events.
• Transmission inference: Maps genetic relationships to support reconstruction of transmission routes.
• Public health laboratory investigations: Supports laboratory analyses aimed at interpreting pathogen genomic data during outbreak response.

Methodology:

Performs phylogenetic analysis of pathogen genomes and applies tree annotation tools within an R Shiny framework.