Alignment of Biological Sequences with Jalview

James B. Procter (Lead / Corresponding author), G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton, Lauren Lui, Anne Menard, Natasha Sherstnev, David Roldan-Martinez, Suzanne Duce, David M. A. Martin, Geoffrey J. Barton

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review

50 Citations (Scopus)
109 Downloads (Pure)


In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview's core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from the command line. The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis, and publication of alignments on the web.

Original languageEnglish
Title of host publicationMultiple Sequence Alignment
Subtitle of host publicationMethods and Protocols
EditorsKazutaka Katoh
Place of PublicationNew York
PublisherHumana Press
Number of pages22
ISBN (Electronic)9781071610367
ISBN (Print)9781071610350 (hbk), 9781071610381 (pbk)
Publication statusPublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Multiple sequence alignment visualization
  • Interactive analysis
  • Web application
  • Desktop application
  • Functional site inference
  • Web services

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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