+ <ul>
+ <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+ been replaced by a single 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>