- <strong>Enhancements and new features</strong>
- <ul>
- <li>Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred works</li>
- <li>allow import of data from gzipped files</li>
- <li>Improved per-sequence 'colour-by-annotation' performance</li>
- <li>Support '' style escaping of quotes in Newick files</li>
- <li>group options for JABAWS service by command line name</li>
- <li>Select primary source when selecting authority in database
- fetcher GUI</li>
- <li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF
- scope to group annotation rows</li>
- <li>add .mfa to FASTA file extensions recognised by Jalview</li>
- <li>groovy scripting for headless jalview operation</li>
- <li>Output in Stockholm format</li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- <li>Uniprot and PDB database cross-reference fetching works
- properly</li>
- <li>'View all structures' in the desktop is more reliable</li>
- <li>Web services parameter dialog box shows the options enabled
- for different presets</li>
- <li>Interactive creation of RNA secondary structure works more
- smoothly</li>
- <li>Keyboard mode 'P' command jumps to the right place</li>
- <li>Improved support for parsing database cross-references via
- Stockholm and Rfam database</li>
- <li>Improved semantics in annotation files for grouping
- annotation rows associated with particular sequences and groups</li>
- <li>More robust DNA->Amino acid translation</li>
- <li>Improved Headless-mode operation for DAS annotation
- retrieval, groovy script execution and alignment figure generation</li>
- <li>annotation label tooltip text needs to be wrapped</li>
- </ul>
+ <p>
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
+ </p>
+ <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+ been replaced by a single 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>
+ <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>
+ <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>
+ </ul>