*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<head><title>Home Page</title></head>
+<head><title>Jalview Documentation</title></head>
<body>
<IMG src="align.jpg"><font size="4">
Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It
features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,
for the analysis of sub-families and the prediction of functional sites, but is
-fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a>).
+fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a> at www.jalview.org).
<p></p>
<p> If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
<association extensions="pfam" mime-type="application-x/ext-file"/>
<association extensions="aln" mime-type="application-x/ext-file"/>
<association extensions="pir" mime-type="application-x/ext-file"/>
+ <association extensions="stk" mime-type="application-x/ext-file"/>
<offline-allowed/>
</information>
<security>
</security>
<resources>
<!-- <em>the additional memory parameters are here</em> -->
- <j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/>
- <jar href="jalview.jar"/>
+ <j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
+ <jar href="jalview.jar"/>
<jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/>
- <jar href="Jmol-11.0.2.jar"/>
+ <jar href="Jmol-12.1.13.jar"/>
<jar href="activation.jar"/>
<jar href="axis.jar"/>
<jar href="castor-1.1-cycle-xml.jar"/>
<jar href="jhall.jar"/>
<jar href="log4j-1.2.8.jar"/>
<jar href="mail.jar"/>
+ &jt;jar href="min-jaba-client.jar"/>
<jar href="regex.jar"/>
<jar href="saaj.jar"/>
<jar href="vamsas-client.jar"/>
<jar href="wsdl4j.jar"/>
<jar href="xercesImpl.jar"/>
<jar href="xml-apis.jar"/>
- <property name="jalview.version" value="2.5"/>
+ <property name="jalview.version" value="2.6"/>
</resources>
<application-desc main-class="jalview.bin.Jalview"/>
</jnlp>
</pre>
-<address>
-<a
-href="http://www.jalview.org/mailman/listinfo/jalview-discuss">If you have problems, send an email to jalview-discuss</a>
-</address>
+<address><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss">If
+you have problems, send an email to jalview-discuss</a></address>
</body>
</html>
</head>
<body>
<p><strong>What's new ?</strong></p>
-<p>Jalview 2.6 introduces new web services, and includes an updated version of the Jmol molecular graphics visualization system. See the <a href="releases.html#Jalview2.6">release
-history</a> for the full details.</p>
-<p><strong>Highlights in Jalview Version 2.5</strong></p>
-<ul>
-</ul>
-<em>Jalview Desktop:</em>
-<ul>
-</ul>
-<em>JalviewLite:</em>
-<ul>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
+<p>Jalview 2.6 introduces new web services, and includes an updated
+version of the Jmol molecular graphics visualization system. See the <a
+ href="releases.html#Jalview2.6">release history</a> for the full
+details.</p>
+<p><strong>Highlights in Jalview Version 2.6</strong></p>
<ul>
+ <li><a href="webServices/JABAWS.html">JABA Web Services</a> for
+ multiple alignment using:
<ul>
+ <li>ClustalW</li>
+ <li>MAFFT</li>
+ <li>Muscle</li>
+ <li>ProbCons</li>
+ <li>T-COFFEE</li>
</ul>
- <em>Desktop Issues</em>
- <ul>
- </ul>
+ </li>
+ <li>User modifiable alignment service parameters</li>
+ <li>Visualization of superposed structures associated with protein
+ or nucleotide sequence alignments.</li>
+ <li>Export coordinates and projection as CSV from PCA viewer</li>
</ul>
-<p> </p>
+<p><strong>Issues Resolved (a select list - see release history for details)</strong></p>
+<ul>
+ <li>clustalx colourscheme colours Ds preferentially when both D+E
+ are present in over 50% of the column</li>
+ <li>Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources</li>
+ <li>InstallAnywhere builds fail to launch on OS X java 10.5 update
+ 4 (due to apple Java 1.6 update)</li>
+</ul>
<p>See the <a href="releases.html">Release History</a> page for
details of all new features and resolved issues.</p>
</body>
git://source.jalview.org / jalview.git / commitdiff