CapsID Screenshots. The top panel illustrates the input page of CapsID. Inputs allowed are the desired enzymes to be used for the CAPS markers, and a multiple sequence alignment(s) of sequences from the reference organisms. The bottom panel shows the CapsID output page summarizing the number of potential CAPS markers found, as the most parsimonious set to use to genotype organisms not in the reference set. Clicking on a given CAPS marker results in a page containing 'virtual' gel images for that CAPS marker in each reference organism to be generated, as well as the primers and the exact cut locations of the indicated enzyme.