ExcaliBAR: a simple and fast software utility to calculate intra- and interspecific distances from DNA barcodes

Author:

Aliabadian Mansour12,Nijman Vincent3,Mahmoudi Ahmad1,Naderi Mehdi4,Vonk Ronald5,Vences Miguel6

Affiliation:

1. 1 Department of Biology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran

2. 6 E-mail: aliabadi@um.ac.ir

3. 2 Oxford Brookes University School of Social Sciences and Law, Department of Anthropology and Geography OX3 0BP Oxford United Kingdom

4. 3 Department of Computer Engineering, Faculty of Engineering Ferdowsi University of Mashhad Mashhad Iran

5. 4 Naturalis Biodiversity Center Darwinweg 2 2333 CR Leiden The Netherlands

6. 5 Zoological Institute Technical University Braunschweig Mendelssohnstr. 4 38106 Braunschweig Germany

Abstract

In the context of DNA Barcoding, sequences of standard marker genes for thousands and potentially millions of individuals and species are becoming available, requiring ever more efficient bioinformatic environments and software algorithms for analysis. We here present ExcaliBAR (Extraction, Calculation, Barcoding), a user-friendly software utility to facilitate one important initial step in DNA barcoding analyses, namely the determination of the barcoding gap between pairwise genetic distances among and within species, based on original distance matrices computed by MEGA software. In addition, the software is able to rename sequences downloaded via the standard user interfaces of public databases such as GenBank, without the need of developing and applying specific scripts for this purpose.

Publisher

Brill

Subject

Animal Science and Zoology,Ecology, Evolution, Behavior and Systematics

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