barcoding.gap: Barcoding Gap Calculation

In BarcodingR: Species Identification using DNA Barcodes

Description

Calculation of DNA barcoding gap. Besides K2P distance, raw distance and euclidean could also be used for calculation DNA barcoding gap.

Usage

barcoding.gap(ref, dist = dist)

Arguments

ref	object of class "DNAbin" used as a reference dataset, which contains taxon information.
dist	a character string which takes one of ("raw","K80","euclidean").

Value

a list indicates the summary statistics of interspecific and intraspecific genetic distance, such as k2P distance.

Note

the current version of the function can only be used for protein-coding barcodes, such as, COI. The futuren version may incorporate calculation for non-coding barcodes,for instance, ITS1, ITS2.

Author(s)

Ai-bing ZHANG, PhD. CNU, Beijing, CHINA, contact at zhangab2008(at)mail.cnu.edu.cn

References

Meyer, Christopher P., and Gustav Paulay. (2005). ”DNA barcoding: error rates based on comprehensive sampling.”.PLoS biology 3.12: e422.

F.Jiang, Q. Jin, L. Liang, A.B. Zhang,and Z.H. Li.(2014). Existence of Species Complex Largely Reduced Barcoding Success for Invasive Species of Tephritidae: A Case Study in Bactrocera spp. Mol Ecol Resour. 14(6):1114-1128 DOI: 10.1111/1755-0998.12259.

Examples

data(TibetanMoth)
TibetanMoth<-as.DNAbin(as.character(TibetanMoth[1:20,]))
b.gap<-barcoding.gap(ref=TibetanMoth,dist="K80")
b.gap

BarcodingR documentation built on April 14, 2020, 6:04 p.m.