MPprimer
a program for reliable multiplex PCR primer design
...These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility.
Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization.