Version 2.2 (Released 18 August 2017)

The website and documentation were improved:

  • Sphinx is now used to generate our documentation pages.
  • Documentation was updated to reflect the latest changes introduced in the project.
  • Usage Statistics are now cached and refreshed every hour for improved website loading times.
  • Service Status are now similarly cached and monitored every 10 minutes.
  • We now provide a Docker image which allows for JABAWS to be run in Docker containers.
  • Downloading the JABAWS distributions no longer require ‘sign in’ or ‘sign up’ to a user account.
  • The pre-configured JABAWS Amazon Machine Image (AMI), which allowed for JABAWS to be run in the Amazon EC2 cloud, is no longer provided due to very limited use by the scientific community peers.

The versions of several application programs provided by JABAWS were bumped to the latest available.

  • Clustal Omega was updated to version 1.2.4
  • ClustalW was updated to version 2.1
  • Mafft was updated to version 7.3.10
  • T-Coffee was updated to version 11.00.8cbe486
  • AACon was updated to version 1.1
  • Protein secondary structure prediction with Jpred (version 3.0.3) was dropped from the list of provided services, as the use of the dedicated Jpred REST API (Jpred 4) is encouraged and recommended. This is the version that is currently provided within Jalview 2.9 or later.


JABAWS version 2.2 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0, 2.0, 2.0.1 and 2.1 clients should also be able to use JABAWS 2.2 services.

Version 2.1 (Released 1st Oct 2013)

Several new web services are available in this version of JABAWS:

  • Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object
  • RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods
  • JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting Jpred predictions. These predictions are supplied as additional sequences in the aligment

Some bugs have been fixed and several improvements have been done:

  • WS status servlet returns version and some additional information on each web service
  • a bug with path to help in the client
  • Fix two bug with the Google Analytics library: no-stop due to running thread
  • GoogleAnalytics gets proper JABAWS version

Version 2.0.1 (Released 2nd Jul 2013)

JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0. These are listed below:

  • Disembl returned swapped strings for HOTLOOPS and REM465
  • Jronn failed to process jobs with more than 3 sequences
  • JABAWS could not deal with FASTA records with ‘>’ symbols in the record identificator
  • Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon’s conservation scores in one call
  • JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in
  • Default web security has been incompatible with Tomcat 7.0.31 and newer
  • Documentation has been updated

Version 2 (Released 16th Dec 2011)

Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.

It now contains:

  • Updates for all multiple sequence alignment services
  • Four new protein disorder prediction services
  • Clustal Omega multiple sequence alignment web service
  • Amino acid conservation service
  • Web services execution statistics visualization
  • Web services status check from a web page
  • VirtualBox support was dropped in favour of VMware
  • New WAR package for Mac users
  • Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud
  • Improved web services client API
  • Simplified WAR package installation


To access the analysis web services introduced in JABAWS 2.0, clients that were designed for JABAWS v1.0 must be updated.