JSpecies

JSpecies calculates average nucleotide identity (ANI) and tetranucleotide signature correlation indices to assess genomic similarity and support prokaryotic species delineation.

Key Features:

• Average Nucleotide Identity (ANI): Computes ANI between two prokaryotic genomes and uses an approximate 95-96% ANI boundary for species delineation.
• Tetranucleotide Signature Correlation Index: Calculates an alignment-free tetranucleotide signature correlation index that correlates with ANI to assess genomic relatedness.
• Partial-genome analysis: Supports taxonomic analyses using partial genome sequences, with reliable classification achievable from at least 20% random coverage of query genomes.

Scientific Applications:

• Prokaryotic species delineation: Determines whether two strains should be classified within the same species based on genomic similarity metrics.
• Modern microbial taxonomy: Provides genomic-based metrics to construct and update taxonomic classifications for prokaryotes.
• Alternative to DNA-DNA hybridization (DDH): Acts as a genomic alternative to traditional DDH for species-level classification of prokaryotic organisms.

Methodology:

Computes ANI between genomes, calculates an alignment-free tetranucleotide signature correlation index, compares ANI to an approximate 95-96% threshold, and supports analyses using partial genome sequences with ≥20% random coverage.