The probability of erroneous DNA barcoding identification is higher when identification is based on a large distance between the query (the barcode sequence of the specimen to identify) and its best match in a reference barcode library. Yet, the number of these incorrect identifications can be reduced by setting a distance threshold above which identification is considered unreliable. To this end, it has been proposed to use an ad hoc distance threshold producing identifications with a user-defined error probability (e.g. 5%). Here, we propose two R scripts to automate the calculation of ad hoc distance thresholds for reference libraries of DNA barcodes. Both scripts, a user manual and an example file are freely available upon request on the JEMU website (http://jemu.myspecies.info).