Amplicon is a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. Other useful features that are not common in other PCR primer design software are handling of gapped sequences and degenerate sites in aligned DNA. Amplicon can import aligned DNA sequences produced by Clustal, or aligned sequences in MEGA or Fasta format. For details and citation: Jarman SN (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20: 1644-1645.