NLM-DIR/vadr

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Local version of the virus identification and analysis web server (tool set)

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

viral-ngs: command line tools and wrappers for processing raw viral genomic data

geNomad: Identification of mobile genetic elements

A listing of software, tools and databases useful for virome analysis

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.