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R in DNA Barcoding

  • Asim Kumar Mahadani
  • Pradosh Mahadani
  • Goutam Sanyal
Chapter

Abstract

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.

Keywords

R language DNA barcoding APE SPIDER BarcodingR 

References

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Asim Kumar Mahadani
    • 1
  • Pradosh Mahadani
    • 2
  • Goutam Sanyal
    • 1
  1. 1.Department of Computer Science & EngineeringNational Institute of TechnologyDurgapurIndia
  2. 2.Crop Improvement DivisionICAR-National Rice Research InstituteCuttackIndia

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