Gemi
PCR primers / probes design from multiple & degenerate sequences
...Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently.
Python source code is available upon request.
Milestone: The tool reached about 3000 downloads sine 2012.
Article
Gemi: PCR primers prediction from multiple alignments. Comparative and functional genomics 2012
PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117
A great review on designing primer, Gemi, and other tools: Designing degenerate primers: Overview, challenges, and computational methods. ...