PopNetD3

PopNetD3 visualizes population structure and identifies chromosomal regions with conserved genetic patterns from single nucleotide polymorphism (SNP) diversity data using network-based PopNet clustering.

Key Features:

• Data submission and processing: Accepts tab-delimited files of SNP diversity data and processes them to define chromosomal regions with conserved genetic patterns via PopNet clustering.
• D3.js visualization: Generates dynamic D3.js visualizations of population structure to examine chromosomal regions predicted to share ancestry.
• Scalability: Handles population datasets comprising hundreds of individuals for large-scale genomic analyses.

Scientific Applications:

• Population genomics and evolutionary biology: Analyzes population structure and genetic conservation to infer ancestry and evolutionary relationships.
• Epidemiology and pathogen diversity: Applied to study bacterial diversity and evolution, demonstrated on 16 strains of Neisseria gonorrhoeae.

Methodology:

Integrates tab-delimited SNP diversity data with network-based PopNet clustering to identify chromosomal regions of conserved genetic patterns and produces D3.js-based visualizations.