sitePath

sitePath identifies polymorphism clades in phylogenetic trees and infers fixed and parallel mutations to analyze viral evolution and adaptation.

Key Features:

• R implementation: Provided as an R package for analysis of phylogenetic trees and sequence-derived polymorphisms.
• Automated identification: Uses a branch-and-bound-like search method to locate polymorphism clades across phylogenetic trees without manual curation.
• Inference of mutations: Analyzes identified clades to infer fixed and parallel mutations associated with evolutionary changes.
• Visualization: Generates figures representing calculated results for interpretation and presentation.
• Robustness: Reported to maintain high specificity and sensitivity across various parameters and phylogenetic tree inference software.

Scientific Applications:

• Virology research: Detects and characterizes genetic variation within virus populations to study evolution and adaptation.
• Antigenic shift analysis: Identifies mutations that align with antigenic shifts relevant to host immune escape.
• Influenza A H3N2 case study: Applied to an influenza A virus H3N2 dataset to identify fixed mutations that align with known antigenic shift mutations.

Methodology:

Implements a branch-and-bound-like search to identify polymorphism clades and analyzes those clades to infer fixed and parallel mutations, with reported high specificity and sensitivity across parameters and phylogenetic tree inference software.