eDNAprimer

eDNAprimer is a software program that facilitates the selection of primer and probe sets for quantitative PCR (qPCR) reactions. In essence, eDNAprimer uses the core functionality of Primer3 to produce a list of potential primer sets based on efficiency, but allows the user to incorporate specificity against a list of non-target sequences in the primer selection process. Multiple target sequences may also be used as input, with primer selection directed towards regions that are consistent across target sequences. eDNAprimer was developed with environmental DNA studies in mind, where one may wish to detect the DNA of a target species (with multiple haplotypes) via qPCR while failing to amplify the DNA of closely related species in the same environment.