Gemi
PCR primers / probes design from multiple & degenerate sequences
...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. Methods in Microbiology. Vol 57, 2025, Pages 73-89; DOI: 10.1016/bs.mim.2025.01.002