RecombinHunt

RecombinHunt is a data-driven computational tool developed for detecting and characterizing recombinant viral genomes — sequences formed by combining genetic material from two (or more) different viral lineages. It uses statistical analyses of mutations in viral genome sequences to identify contributing parental lineages and the positions (breakpoints) where recombination occurred, doing so with high specificity and sensitivity and relatively fast performance compared with other methods. Originally applied to SARS-CoV-2 and shown to also work with viruses like monkeypox, it helps improve genomic surveillance of evolving viruses and can support early warning systems for future pandemics.