-"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. <span style="color:black; font-weight:normal; text-align:left;">Unlike other web services you can run JABAWS services from your own computer. This puts you in control of the web services - they will be where and when you need them, have no restrictions and your data privacy is guaranteed. JABAWS scales well from the single user single computer to the cluster with hundreds of users. Finally, you do not have to be an expert to use JABAWS - the installation is simple and you can use the services from the comfort of your desktop via <a href="http://www.jalview.org">Jalview</a>.</span></p>\r
-<h3>Public JABAWS Server</h3>\r
-<p> You can access our public JABA Web Services with our <a href="download.html">command line client, </a>the <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a>, or write your own program. To guarantee a level service for everyone our public services impose some restrictions on the size and the number of the jobs you can submit. Currently we do not process tasks that exceed 1000 sequences per 1000 letters on average. Should you find this to be insufficient for your needs you can download and run JABAWS Server on your own hardware. This also applies if the privacy is a concern or an Internet connection is a problem. </p>\r
+"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. \r
+<span style="color:black; font-weight:normal; text-align:left;">JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.<br />\r
+<br />\r
+</span>Please note that JABAWS 2 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012). In the meantime you can access all JABAWS2 services through the JABAWS command-line client.</p>\r
+<div id="mainpagefeatures">\r
+<table>\r
+<tr><td>\r
+ <div class="brick"> \r
+ <div class="brick_header"><h2>For Users</h2></div>\r
+ <div class="brick_content">\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance:</a> (520M)\r
+ or <a href="man_awscloud.html">use JABAWS on Amazon Webservices Cloud</a><br/>\r
+ <strong>The Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
+ <p>To use JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
+ </div>\r
+ </div>\r
+ </td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For System Administrators</h2></div>\r
+ <div class="brick_content">\r
+ <p><strong>The Server: </strong><a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M) </p>\r
+ <p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
+ </div>\r
+ </div></td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
+ <div class="brick_content">\r
+<strong>The Server: </strong><a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
+ <br/>\r
+ <strong>The Client: </strong>\r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.0.jar">source</a> \r
+ <!-- <li><a href="http://www.jalview.org/download.html">Jalview</a> (18M)</li> -->\r
+ \r
+ \r
+<p>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 just script against our public server (see below) with the command line client or you own script. \r
+Check out the <a href="manual_qs_client.html#qsc">quick start guide</a> for further details.</p>\r
+\r
+ </div>\r
+ </div></td>\r
+ </tr>\r
+</table>\r
+</div>\r
+\r
+<h3 style="margin:0;">Public JABAWS Server</h3>\r
+<p> You can access our public JABA Web Services with our <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">command line client</a>, <a href="http://www.jalview.org/download.html">Jalview</a>, or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2. The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r