JAva Bioinformatics Analysis Web Services (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prediction of protein disorder with DisEMBL, IUPred, Jronn (a Java implementation of Ronn by P. Troshin and G. Barton, unpublished), and GlobPlot; and calculation of amino acid alignment conservation with AACon.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 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.
Server: Public JABAWS server or the JABAWS Virtual Appliance (VA)
Client: Jalview
--%> <%--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!--%> <%--
--%>Server: Public JABAWS server, the JABAWS Virtual Appliance (VA) or the JABAWS Web Application aRchive (WAR)
Client: Jalview or the Command Line Interface (CLI) Client
--%> <%--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.--%> <%--
--%>Server: JABAWS Web Application aRchive (WAR)
Client: Command Line Interface (CLI) Client
--%> <%--JABAWS requires a Servlet 2.4 compatible servlet container like Apache Tomcat--%> <%--to run. Please check the quick start guide for installation instructions.--%> <%--
--%>You can access our public JABAWS web services with the command line client, Jalview, 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 or on an unreliable network connection, then you can download and run the JABAWS Server on your own hardware.
--%> <%--The current JABAWS version is 2.2.0 released on XX March 2017. We advise you to update to JABAWS 2.2 as this version is fully backward compatible with JABAWS v1.0, v2.0 and v2.1.--%> <%--Please consult the documentation pages--%> <%--for the changelog and more information on compatibility between versions.
--%> <%--<%–Should you require them, however, old versions of JABAWS are available here:
–%>--%> <%--<%–Peter V. Troshin, James B. Procter and Geoffrey J. Barton - Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS Bioinformatics 2011. 27 (14): 2001-2002. doi: 10.1093/bioinformatics/btr304.