<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5.0" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
\r
<!-- panel end-->\r
<div id="content">\r
-<h2 id="headtitle">JABAWS 2.5</h2>\r
+<h2 id="headtitle">JABAWS 2.1</h2>\r
<p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> \r
is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment \r
include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. \r
</p><p> \r
<span style="color:black; font-weight:normal; text-align:left;">\r
-JABA 2.5 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r
+JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r
and sequence analysis calculations limited only by your own computing resources.<br />\r
</span></p>\r
<div id="mainpagefeatures">\r
<strong>The Server: </strong><a href="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-2.5.jar">binary</a> | <a href=\r
-"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.5.jar">source</a> \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.1.jar">source</a> \r
\r
<p>\r
You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. \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-2.5.jar">command line client</a>, \r
- <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 2.5.\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-2.1.jar">command line client</a>, \r
+ <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 2.1.\r
The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
<ul>\r
<li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>\r
or if you are concerned about privacy or on an unreliable network connection, then you can \r
<a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
<h3>Previous versions of JABAWS </h3>\r
-<p>We advise you to update to JABAWS 2.5 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
- contains <a href="man_about.html#jaba2.5">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
+<p>We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
+ contains <a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p><ul><li>\r
<strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> \r
<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li></ul> \r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<li><a href="#wisjaba">What is JABAWS?</a></li>\r
<li><a href="#wjaba">JABAWS Benefits</a></li>\r
<li><a href="#alprog">JABA Web Services Programs </a></li>\r
- <li><a href="#jaba2.5">What is new in JABAWS 2?</a> </li>\r
+ <li><a href="#jaba2.1">What is new in JABAWS 2.1?</a> </li>\r
<li><a href="#jabaclient">What is JABAWS Client</a>?</li>\r
<li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>\r
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>\r
\r
\r
\r
-<h3><a name="jaba2.5"/></a>What is new in JABAWS 2.5? </h3>\r
-<strong>JABAWS Version 2.5 (Released 2nd Jul 2013)</strong><p>JABAWS 2.5 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2</a>. These are listed below:</p>\r
+<h3><a name="jaba2.1"/></a>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong><p>JABAWS 2.1 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
\r
<h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
<p>\r
- JABAWS version 2.5 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
- v2.0 clients should also be able to use JABAWS 2.5 services. To access the analysis web services introduced in\r
+ JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
+ v2.0 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in\r
JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
</p>\r
\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<table>\r
<tr>\r
<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+ <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
<div id="banner">\r
<table>\r
<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.5" title="Java Bioinformatics Analysis Web Services version 2.5"/></td>\r
+<td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r