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Supported Applications


  • Description

    a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.

  • Usage

    To list all executables provided by Jalview, run: $ sbgrid-list jalview Copy to clipboard
  • Usage Notes

    To use Jalview on OS X, you will need to install Java:

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install jalview Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    A. M. Waterhouse, J. B. Procter, D. M. A. Martin, M. Clamp, and G. J. Barton. 2009. Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics. 25(9): 1189-1191.

    • *Full citation information available through

  • Tales

    Into Alignment

    Into Alignment

    In 1987, when Geoff Barton was a graduate student learning computational structural biology at the University of London, just 6000 protein sequences were known, but their numbers were rising exponentially, and it was becoming clear that they had commonalities. Sequences that yield valuable functions have staying power, so they are conserved throughout evolution. Finding these recurring patterns, however, required painstaking pencil and paper comparisons.

    Barton's lab notebook

    A page from Barton's lab book in around 1988. It shows a multiple sequence alignment produced automatically by his alignment software, printed out then coloured by hand to highlight conserved amino acid positions in the alignment. Secondary structure predictions are shown underneath the alignment and there are other features such as intron/exon boundaries shown for some of the sequences. "Doing things like this all …

    Read the full story here.
  • Webinars


    Topic: Creating and analyzing multiple sequence alignments with the Jalview Desktop Application
    Presenter: Jim Procter, Ph.D., Jalview Coordinator, College of Life Sciences, University of Dundee Scotland, UK

    Host: Jason Key
    Recorded on July 11, 2013

  • Keywords


  • Default Versions

    Linux 64: (773.4 MB)
    OS X INTEL: (594.4 MB)

  • Other Versions

      Linux 64:

      2.10.2b2 (38.5 MB) , 2.10.4b1 (40.1 MB) , (705.7 MB) , (709.3 MB)
    • OS X INTEL:

      2.10.2b2 (213.6 MB) , 2.10.4b1 (215.2 MB) , (504.0 MB) , (563.4 MB)
  • Developers

    Geoff Barton, Jim Procter