highlights are below.
</p>
<ul>
- <li>
+ <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+ Menu entries for calculating PCA and different types of tree have
+ been replaced by a single <em>Calculations</em> dialog box. The
+ underlying implementation for the PCA and tree calculations have been
+ made faster and more memory efficient. A new framework has also been
+ created for the score models used to calculate distances between
+ sequences. This framework allows import of substitution matrices in
+ NCBI and AAIndex format, and custom score models to be created via a
+ groovy script.</li>
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.</li>
<li>New preferences for <a href="webServices/urllinks.html">opening
web pages for database cross-references</a> via the UK Elixir's
EMBL-EBI's MIRIAM database and identifiers.org services.
</li>
+ <li><em>Showing and hiding regions</em>
+ <ul>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</li>
+ </ul></li>
</ul>
<p>
<strong><a name="experimental">Experimental Features</a></strong>
</p>
- <p>This release of Jalview includes a new option in the Jalview Desktop
- that allows you to try out features that are still in development. To
- access the features described below, please first enable the
- <strong>Tools→Enable Experimental Features</strong> option, and then restart Jalview.
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
</p>
<ul>
<li><em>Annotation transfer between Chimera and Jalview</em><br />Two
- <a href="features/chimera.html#experimental">new entries in the Chimera viewer's Chimera menu</a> allow positional
- annotation to be exchanged between Chimera and Jalview.
- </li>
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
</ul>
</body>
</html>