VIRIDIC

VIRIDIC calculates nucleotide-based intergenomic similarities among viruses infecting prokaryotes (bacteria and archaea) to support viral taxonomy and phylogenetic relationship analysis.

Key Features:

• ICTV algorithm implementation: Implements the traditional nucleotide-based algorithm used by the International Committee on Taxonomy of Viruses (ICTV) Bacterial and Archaeal Viruses Subcommittee to compute intergenomic similarities.
• Benchmark performance: Demonstrated superior performance in benchmarking versus other software by avoiding overestimation of relatedness for distantly related phages.
• Additional similarity indicators: Provides three additional indicators to assess alignment capability, including aligned fractions for each genome and the length ratio between genomes being compared.
• Integrated heatmap output: Produces a heatmap that integrates intergenomic similarity values with genome lengths and aligned genome fractions for visual inspection of relationships.

Scientific Applications:

• Phylogenetic analysis: Supports construction and refinement of phylogenetic relationships among viruses based on nucleotide similarity metrics.
• Taxonomic classification: Assists classification of viral strains using ICTV-consistent intergenomic similarity criteria.
• Large-scale genomic analyses: Enables inclusion in genomic research workflows that require comparative intergenomic similarity assessments across many genomes.
• Application to eukaryotic viruses: Can be applied to eukaryotic viruses, particularly those with monopartite genomes, for intergenomic similarity assessment.

Methodology:

Computes nucleotide-based intergenomic similarities using the traditional ICTV algorithm, calculates aligned fractions per genome and length ratios for genome pairs, and generates a heatmap integrating similarity values with genome lengths and aligned genome fractions.