Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification

By

Sonet, Gontran
Jordaens, Kurt
Nagy, Zoltan T
Breman, Floris C., 1977-
De Meyer, Marc
Backeljau, Thierry
Virgilio, Massimiliano

Type

Article

Date of Publication

2013

Original Publication

ZooKeys

Volume

365

Pages

329-336

Subjects

accuracy , COI , precision , reference library , relative error , species identification

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers

Identifiers

DOI: https://doi.org/10.3897/zookeys.365.6034

 

Abstract

Identification by DNA barcoding is more likely to be erroneous when it 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. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has to be rejected. To this end, we proposed recently to use an ad hoc distance threshold producing identifications with an estimated relative error probability that can be fixed by the user (e.g. 5%). Here we introduce two R functions that automate the calculation of ad hoc distance thresholds for reference libraries of DNA barcodes. The scripts of both functions, a user manual and an example file are available on the JEMU website (http://jemu.myspecies.info/computer-programs) as well as on the comprehensive R archive network (CRAN, http://cran.r-project.org).