gANI

gANI computes genome-wide Average Nucleotide Identity and alignment fraction to quantify genomic relatedness for prokaryotic species classification.

Key Features:

• Whole-Genome Analysis: Evaluates entire genome sequences rather than single marker genes to represent evolutionary relationships among prokaryotes.
• Alignment Fraction (AF): Incorporates an alignment fraction metric alongside ANI to refine assessments of genomic similarity.
• Scalability: Applied to over 86.5 million genome pairs across 13,151 prokaryotic genomes assigned to 3,032 species, demonstrating capacity for large-scale analyses.
• Identification of Taxonomic Anomalies: Uses complete linkage clustering of genome clusters and comparison to existing taxonomy to identify that approximately 18% of prokaryotic species show anomalies in species definitions.

Scientific Applications:

• Species Definition and Classification: Provides an objective genome-based metric (gANI and AF) to support redefinition and assignment of microbial species.
• Exploration of Genetic Diversity: Enables examination of the continuum of genetic diversity to assess whether distinct species boundaries exist or variation is continuous.

Methodology:

Calculates Average Nucleotide Identity between genome pairs and assesses alignment fraction, uses complete linkage clustering to compare genome clusters with existing taxonomy, and applies the proposed MiSI (Microbial Species Identifier) approach combining AF and gANI metrics.