zol

zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances, performing functional annotation and computing evolutionary statistics for each inferred ortholog group.

Key Features:

• Ortholog group inference: Performs reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances at large scale across broad taxonomic contexts and thousands of genomes.
• Functional annotation: Performs functional annotation for each inferred ortholog group.
• Evolutionary statistics: Computes a variety of evolutionary statistics for each inferred ortholog group.
• Table report generation: Creates table reports showing ortholog group conservation, annotation, and evolutionary stats for gene clusters or loci of interest.
• Scalability: Scales to handle thousands of gene cluster instances and produce detailed reports.

Scientific Applications:

• Longitudinal virus tracking: Enables longitudinal tracking of a virus in metagenomes.
• Population genetic investigation of BGCs: Supports population genetic investigations of biosynthetic gene clusters (BGCs) for a fungal species.
• Evolutionary trend analysis of virulence clusters: Uncovers evolutionary trends for virulence-associated gene clusters across thousands of genomes from diverse bacterial genera.
• Comparative analysis of mobile-genetic elements: Enables large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses.

Methodology:

zol operates on orthologous instances of a query gene cluster of interest identified among a database of target genomes, performing context-specific orthology inference for individual protein-encoding genes across gene cluster instances.