The ad hoc distance threshold (see Virgilio et al. 2012) can be calculated for each particular reference library of DNA barcodes. Using this distance threshold in the "best close match method" (a method where a species name assignment is rejected when the distance between the query and its best match in a reference dataset is above the threshold) will provide identifications with an estimated relative error probability that is fixed by the user (e.g. 5%).
adhocTHR
(Package: adhoc) :
Calculation of an ad hoc distance threshold for DNA barcoding identification
This function utilises the output of checkDNAbcd to quantify the relative identification errors obtained for a particular reference library at set of arbitrary distance thresholds. It then performs linear (or polynomial) regression and calculates the ad hoc distance threshold corresponding to an expected relative identification error. The method is described by Virgilio et al. (2012).
checkDNAbcd
(Package: adhoc) :
Evaluation of a reference library of aligned DNA barcodes
This function provides an overview of the content of a reference library of aligned DNA barcodes (Sonet et al. 2013). It calculates all pairwise distances and delivers an output that can be used by the function adhocTHR.
providing 
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