SlackBuildsOrg/academic/amplicon

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.