GL-UVAB

GL-UVAB classifies genomic lineages of uncultured viruses of Archaea and Bacteria from nearly 200,000 viral nucleotide sequences to characterize viral diversity and lineage-specific gene content.

Key Features:

• Phylogenomic analysis: Identifies protein-coding genes with Prodigal and performs all‑versus‑all protein searches using Diamond.
• Dice distance calculation: Computes Dice distances between sequences for genomic-content comparison.
• Dice tree construction: Constructs a Dice phylogenetic tree in R to represent evolutionary relationships among viral genomes.
• Lineage identification: Supports defining user-specified criteria to identify and classify viral lineages.
• Pan-genome analysis: Analyzes pan-genome content of identified viral lineages to assess shared and lineage-specific genes.
• Reference database for metagenome annotation: Provides lineage references for annotating metagenomes and assessing habitat distribution.
• Automation: Automates the analysis workflow via a Perl script.

Scientific Applications:

• Infection strategies and host interaction: Pan-genome analysis of lineages provides insights into potential infection strategies, mechanisms to modulate host physiology, and viral mechanisms to escape host resistance systems.
• Ecological insights: Enables investigation of habitat distribution patterns of viral lineages and environmental factors influencing community composition through metagenome annotation.

Methodology:

The workflow identifies protein-coding genes with Prodigal, performs all-versus-all protein searches with Diamond, computes Dice distances, constructs a Dice phylogenetic tree in R, and is automated via a Perl script.