Title
Adhoc : an R package to calculate ad hoc distance thresholds for DNA barcoding identification Adhoc : an R package to calculate ad hoc distance thresholds for DNA barcoding identification
Author
Faculty/Department
Faculty of Sciences. Biology
Publication type
article
Publication
Subject
Biology
Source (journal)
ZooKeys
Volume/pages
(2013) :365 , p. 329-335
ISSN
1313-2989
ISI
000329206600019
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
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).
Full text (open access)
https://repository.uantwerpen.be/docman/irua/0ecc54/6668.pdf
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