The JAva Bioinformatics Analysis Web Services system (JABAWS)
Jalview includes a client for interacting with programmatic (SOAP) web services for the JABAWS service model, developed at the University of Dundee by Peter Troshin and Geoff Barton. This is an open source system that provides a framework for wrapping command line bioinformatics analysis programs that enables them to be executed locally or on a cluster using data and analysis parameters provided by a program linked with the JABA engine directly or accessing it remotely via its web services interface.

The list of JABAWS servers known to the Jalview desktop is shown in the Web Services Preferences Panel, and detailed information about a particular service is available from the help text and web pages accessible from its job parameters dialog box.

Obtaining JABAWS
One of the aims of JABAWS is to enable you to easily perform computationally intensive bioinformatics analysis tasks using your own computational facilities. It can be installed on a workstation to provide stand-alone execution of analysis programs, or as a job submission engine - enabling larger numbers of jobs to be handled. If you would like to download and install JABAWS for your own use, please go to http://www.compbio.dundee.ac.uk/jabaws for more information.

Configuring your own JABAWS services for use by Jalview
Once you have downloaded and installed JABAWS, and verified it is working, all that is needed is to add the URL for your JABAWS server(s) to the list in the Web Services Preferences Panel. After adding your service and saving your preferences or hitting the 'refresh web services' button, you should be able to submit jobs to the server via the alignment window's web services menu. Your JABAWS servers list is stored in your Jalview preferences, so you will only have to configure Jalview once for each new server.

Support for accessing JABAWS servers was introduced in Jalview 2.6.