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, finds diagnostic sites, and classifies each genome along the alignment to infer recombination tracts and breakpoints. Optionally, RecMpox can build a phylogeny of the inferred tract sequences alongside outbreak references, to help confirm true recombination and reduce false positives caused by ancestral population structure.