Welcome to the JABAWS 2.2 website

JABAWS is free software which provides web services conveniently packaged to run on your local computer, server or cluster.

Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, T-Coffee, ProbCons, MSAProbs, and GLProbs. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and GlobPlot; and calculation of amino acid alignment conservation with AACon. The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the Vienna RNA package.

JABAWS web-services can be accessed through the Jalview desktop graphical user interface (GUI) (version 2.8 onwards) or the JABAWS Command Line Interface (CLI) client. In this way you can perform computations on your sequences using the publicly available servers running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis limited only by your own computing resources, by running it in your local computer, server or cluster.

The public server based on JABAWS 2.1 at the University of Dundee has been in production since October 2013 and serviced over 442,000 jobs for users worldwide.

Jalview: Sequence Alignment

Public JABAWS Server

You can access our public JABAWS web services with Jalview, JABAWS CLI, or with your own program. The latest versions of Jalview (version 2.9 or later) are fully compatible with JABAWS 2.2 and are configured to use the public JABAWS server by default.

These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy, then you can download and run the JABAWS WAR on your own hardware.

New in JABAWS 2.2

The current JABAWS version is 2.2 released on 18 August 2017. Among the new developments in JABAWS 2.2 are:

  • Several programs included in JABAWS, including Clustal Omega, ClustalW, Mafft and T-coffee, were updated.
  • AACon was also updated to the latest release, version 1.1.
  • Service Status and Usage Statistics are now cached and refreshed asynchronously for improved Website loading times.
  • We now provide a Docker image which allows for JABAWS to be run in Docker containers.
  • The website looks were updated to use the Twitter Bootstrap CSS framework, and documentation pages are now generated with Sphinx.

More information about the changes introduced in the latest release can be found in the changelog pages.


Peter V Troshin, James B Procter, Alexander Sherstnev, Daniel L Barton, Fábio Madeira and Geoffrey J. Barton (2018) JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure Bioinformatics bty045. doi: 10.1093/bioinformatics/bty045.

Peter V. Troshin, James B. Procter and Geoffrey J. Barton (2011) Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS Bioinformatics 27 (14): 2001-2002. doi: 10.1093/bioinformatics/btr304.


JABAWS and AACon are part of the "Dundee Resource for Protein Sequence analysis and structure prediction", which is an ELIXIR-UK resource.

Site Last updated: 27 March 2018 by Fábio Madeira. This site was built using the Bootstrap framework.