Misassembly due to the presence of repetitive DNA sequences often complicates the contig assembly stage of genome sequencing. Accurate physical representations of chromosomes, such as restriction maps or contig maps, provide a means for validating the sequence assembly and clarifying alignment ambiguity. The Contig Assembly Verifier (CAVe) software tool allows the researcher to automatically reconcile a sequence assembly with a physical representation, and, if needed, to modify the assembly using an intuitive graphical user interface.