pyani

pyani computes whole-genome similarity measures for draft or complete prokaryote genomes (bacteria and archaea) to provide quantitative metrics for genomic comparison and taxonomic analysis.

Key Features:

• Whole-Genome Similarity Calculation: Computes similarity measures across entire genomes to quantify genetic relatedness between prokaryotic isolates.
• Support for Draft and Complete Genomes: Accepts draft and complete prokaryotic genome assemblies as input for comparative analyses.
• Quantitative, Objective Metrics: Produces reproducible numerical metrics that support objective genome-to-genome comparisons and downstream classification.
• Taxonomic Classification Support: Provides genome similarity results that can be used to inform taxonomic assignment of bacterial and archaeal genomes, including pathogen identification.

Scientific Applications:

• Taxonomic Classification: Supports quantitative classification and identification of bacterial pathogens and other prokaryotes, with relevance to studies including food-security–related organisms.
• Genomic Research: Enables investigation of genetic diversity, evolutionary relationships, and genomic variation within and between prokaryotic species.

Methodology:

Calculates whole-genome similarity measures using algorithms that generate objective, reproducible metrics for genome-to-genome comparisons.