R in DNA Barcoding
DNA barcoding bloomed as a routine application in biodiversity assessment and species identification. Several improvements have occurred in the DNA sequence analysis approaches. Recently, R language and environment for statistical computing and graphics emerged as powerful tool in sequence and phylogenetic analysis. Bioinformaticians have written several specialized packages for R to provide reading and writing data and manipulating sequence analysis, as well as several advanced DNA barcode sequence-based analysis. SeqinR package is mainly used to retrieve and analyze biological sequences, and APE packages are for construction of phylogenetic and evolutionary tree-based molecular data. However, SPIDER and BarcodingR packages are completely devoted to analyze for DNA barcode sequences. The purpose of this chapter is to provide a quick reference for DNA barcode associate researcher in sequence and phylogenetic analysis.
KeywordsR language DNA barcoding APE SPIDER BarcodingR
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