+<p>Secondary structure for an RNA aligment</p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
+</ul>\r
+\r
+All these codes including Jronn and AAcon are available at the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+section (registration is required).\r
+\r
+\r
+\r
+<h3><a name="jaba2.1"/>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>\r
+<p>Several new web services are available in this version of JABAWS:</p>\r
+<ul>\r
+ <li>Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object</li>\r
+ <li>RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods</li>\r
+ <li>\r
+ JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting \r
+ Jpred predictions. These predictions are supplied as additional sequences in the aligment\r
+ </li>\r
+</ul>\r
+\r
+<p>Some bugs have been fixed and several improvements have been done:</p>\r
+<ul>\r
+ <li>WS status servlet returns version and some additional information on each web service</li>\r
+ <li>a bug with path to help in the client</li>\r
+ <li>Fix two bug with the Google Analytics library: no-stop due to running thread</li>\r
+ <li>GoogleAnalytics gets proper JABAWS version</li>\r
+</ul>\r
+\r
+\r
+<strong>JABAWS Version 2.0.1 (Released 2nd Jul 2013)</strong><p>JABAWS 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
+<ul>\r
+ <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
+ <li>Jronn failed to process jobs with more than 3 sequences</li>\r
+ <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
+ <li>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 \r
+ in one call</li>\r
+ <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>\r
+ <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>\r
+ <li>Documentation has been updated</li>\r
+ </ul>\r
+ <a name="jaba2"/><strong>JABAWS Version 2 (Released 16th Dec 2011)</strong><p>Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.</p><p>It contains:</p>\r
+<ul><li>updates for all multiple sequence alignment services</li>\r
+ <li>four new protein disorder prediction services</li>\r
+ <li>Clustal Omega multiple sequence alignment web service</li>\r
+ <li>amino acid conservation service</li>\r
+ <li>web services execution statistics visualization </li>\r
+ <li>web services status check from a web page</li>\r
+ <li>VirtualBox support was dropped in favour of VMware</li>\r
+ <li>new WAR package for Mac users</li>\r
+ <li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>\r
+ <li>Improved web services client API</li>\r
+ <li>Simplified WAR package installation</li>\r
+</ul>\r
+\r
+\r
+\r