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Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task. Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data. Availability: PrimerProspector is open-source software available atdoi:10.1093/bioinformatics/btr087 pmid:21349862 pmcid:PMC3072552 fatcat:5hjzj2h6wfccxanexj2mkyksse