RecMpox is a command-line tool that flags potential recombination events in monkeypox viruses. It identifies recombination tract breakpoints within your own provided consensus genomes. It does not confirm recombination; it flags genomes that may be recombinant for further investigation. RecMpox takes two references (e.g. Clade Ia vs Ib, or IIa vs IIb), aligns them with Squirrel, finds diagnostic SNP positions where the references differ, then classifies each consensus genome at those positions. Genomes where both refs contribute at least 5% are flagged as potential recombinants. Recombination tracts and breakpoints are inferred along the genome.