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.
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