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.

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

  • 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

  • Categories


  • Default Versions

    Linux 64 2.8.2
    OS X INTEL 2.8.2

  • Other Available Versions

    Linux 32 2.5.1
    Linux 32 2.6
    Linux 32 2.6.1
    Linux 32 2.7
    Linux 32 2.8
    Linux 64 2.8
    Linux 64 2.9.0b2
    OS X INTEL 2.7
    OS X INTEL 2.8
    powermac 2.4.0b2
    powermac 2.5.1
    powermac 2.6
    powermac 2.6.1

  • Developers

    Geoff Barton, Jim Procter.

  • 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.

    A page from Barton's lab book in around 1988. It shows a multiple sequence alignment produced automatically by his alignment softwstrong textare, 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 ...

    Read More.