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JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance.

Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, T-Coffee, ProbCons, MSAProbs, and GLProbs. Analysis services allow prediction of the protein secondary structure with Jpred and protein disorder with DisEMBL, IUPred, Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and GlobPlot; and calculation of amino acid alignment conservation with AACon.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 2.1 installation can be accessed from the Jalview desktop application (version 2.8 onwards) and the JABAWS command-line client.
JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own computing resources.

For Users

The Server: JABAWS Virtual Appliance: (440M) or JABAWS on Amazon Webservices Cloud
The Main Client: Jalview (18M)

To use JABAWS web services on most operating systems, just download and install the JABAWS Virtual Appliance (VA).
Or even easier - just start JABAWS machine on the cloud and point Jalview at it!

For System Administrators

The Server: JABAWS Web Application aRchive (55M)

JABAWS requires a Servlet 2.4 compatible servlet container like Apache Tomcat to run. Please check the quick start guide for installation instructions.

For Bioinformaticians/Developers

The Server: JABAWS Web Application aRchive (55M)
The Client: Command Line Client binary | source

You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public server (see below) with the command line client or you own script. Check out the quick start guide for further details.

Public JABAWS Server

You can access our public JABAWS web services with our command line client, Jalview, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1. The latest versions of Jalview are configured to use public JABAWS server by default.

  • The JABAWS public web services address is http://www.compbio.dundee.ac.uk/jabaws
  • A detailed web services description is available from here: WSDL List

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 or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.

Previous versions of JABAWS

We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains some important bug fixes. Please consult the manual for more information on compatibility between versions.


Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.