Phylotyper

Phylotyper predicts gene subtypes from whole genome sequencing (WGS) data using phylogenetic methods for public health surveillance and outbreak analysis.

Key Features:

• In silico subtype prediction: Predicts gene subtypes from whole genome sequencing (WGS) gene sequences.
• Phylogeny-based classification: Employs a phylogenetic framework to model evolutionary trajectories of subtypes rather than relying solely on sequence similarity.
• WGS pipeline integration: Operates within whole genome sequencing pipelines and supports multiple subtype schemes.
• Annotation-independent inference: Infers subtypes for sequences that lack existing annotation.
• Phenotypic and strain-level inference: Supports phenotypic inference and strain differentiation for epidemiological analyses.
• Implementations: Provided as Python and R packages.

Scientific Applications:

• Public health surveillance: Enables subtype assignment from WGS data to inform surveillance activities.
• Outbreak analysis: Facilitates identification and differentiation of strains during outbreak investigations.
• Genomic epidemiology: Supports reconstruction of subtype relationships to contextualize pathogen spread and diversity.
• Phenotype prediction: Aids inference of phenotypic traits from subtype assignments.

Methodology:

Uses phylogenetic methods to predict subtypes from gene sequences derived from whole genome sequencing (WGS) data.