barcoding.spe.identify2 {BarcodingR}R Documentation

Species Identification Based on Fuzzy-set Method and kmer


Species identification based on fuzzy-set method (Zhang et al. 2012)and kmer.


barcoding.spe.identify2(ref, que, kmer = kmer, optimization = TRUE)



object of class "DNAbin" used as a reference dataset, which contains taxon information.


object of class "DNAbin", whose identities (species names) need to be inferred.


a numeric to indicate the length of maximum kmer to try in the range of 1 to kmer in case of optimization = TRUE, otherwise, only a certain length of kmer is used.


a character string, indicating whether different length of kmer (up to kmer) will be used or just a specified length of kmer will be used.


a list indicating the identified species.


read.dna() from package ape was used to obtain DNAbin object for unaligned non-coding barcodes.


Ai-bing ZHANG, Cai-qing YANG, Meng-di HAO, CNU, Beijing, CHINA, contact at zhangab2008 (at) mail. cnu. edu. cn.


Zhang, A. B., M. D. Hao, C. Q. Yang, and Z. Y. Shi. (2017). BarcodingR: an integrated R package for species identification using DNA barcodes. Methods Ecol Evol. 8(5):627-634.

Jin,Q., H.L. Han, X.M. Hu, X.H. Li,C.D. Zhu,S. Y. W. Ho, R. D. Ward, A.B. Zhang . (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One 8: e644.

Zhang, A. B., C. Muster, H.B. Liang, C.D. Zhu, R. Crozier, P. Wan, J. Feng, R. D. Ward.(2012). A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 21(8):1848-63.

Zhang, A. B., D. S. Sikes, C. Muster, S. Q. Li. (2008). Inferring Species Membership using DNA sequences with Back-propagation Neural Networks. Systematic Biology, 57(2):202-215.


que<-ref<-barcoding.spe.identify2(ref,que, kmer = 1, optimization = FALSE)

[Package BarcodingR version 1.0-3 Index]