-<p><strong>What's new ?</strong> </p>
-<p>If you are reading this then you will already have seen some of the recent changes
- made to Jalview.<br>
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window. </p>
-<p>If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:</p>
-<ul>
- <li>Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.</li>
- <li>To insert or edit the gaps in one sequence in alignment, the
- "Shift" key must be held down when dragging the mouse.</li>
- <li>To insert or edit gaps for a group of sequences, the
- "Alt" key (or in X windows the "Control"
- key) must be held down.</li>
- <li>Selecting colour schemes in the colour menu either sets just the
- "background" colourscheme for the alignment, or - when
- the tickbox "Apply colour to all groups" is ticked,
- applies the scheme to the background and all groups defined on the alignment.</li>
- <li>Use the right mouse button (apple and click on the Mac) whilst
- the pointer is within the selection area to access the "define" region menu to
- define a new region, give it a name, and change its colourscheme and display
- properties.</li>
- <li>Conservation is automatically updated whenever the alignment is edited</li>
- <li>There is no "quick draw" option</li>
- <li>Edits can be undone, and redone!</li>
-</ul>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ The Jalview 2.7 release features new web services, and important
+ improvements to the way in which Jalview handles alignments and
+ associated PDB structures, as well as numerous minor improvements and
+ bug fixes. Version 2.7 of the JalviewLite applet also features a
+ significantly enhanced Javascript API enabling it to be more easily
+ integrated with javascript based web applications. <br /> For full
+ details see the <a href="releases.html#Jalview2.7">Jalview 2.7
+ release history</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Desktop Version 2.7</strong>
+ </p>
+ <ul>
+ <li>New <a href="features/viewingpdbs.html">structure viewer
+ options</a>:
+ <ul>
+ <li>Colour and superimpose 3D structures of complexes and
+ multi-domain chains using several different alignments</li>
+ <li>Drag and drop to associate PDB files with sequences that
+ have the same name</li>
+ <li>Open and superimpose all associated structures for the
+ current selection</li>
+ </ul>
+ <li>New web services for <a href="webServices/shmr.html">alignment
+ analysis</a></li>
+ <li>Improved graphical user interface for <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
+ </li>
+ <li>Sort associated alignment views option in tree viewer</li>
+ <li>Default colours for <a
+ href="colourSchemes/annotationColouring.html">shading alignment
+ by quantitative annotation</a>.
+ </li>
+ <li><a href="webServices/newsreader.html">Jalview Desktop RSS
+ reader</a> - following important updates at <a
+ href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
+ </ul>
+
+ <p>
+ <strong>Issues Resolved (a select list - see the <a
+ href="releases.html#Jalview2.7">release history</a> for full details)
+ </strong>
+ </p>
+ <p>
+ <strong>Issues in the Jalview Desktop</strong>
+ <ul>
+ <li>Problems viewing associated structures for sequences
+ retrieved from UNIPROT</li>
+ <li>Problems viewing Jalview projects from older versions in
+ version 2.6</li>
+ <li>Preservation of hidden annotation rows and tree bootstrap
+ values in projects</li>
+ <li>Newly added JABAWS servers not always visible in web services
+ menu</li>
+ </ul>
+ <strong>Issues specific to the JalviewLite Applet</strong>
+ <ul>
+ <li>Layout problems when lots of annotation rows are displayed</li>
+ <li><= shown as = in annotation row tooltip</li>
+ <li>export features raises exception when no features exist</li>
+ <li>relative URLs not handled properly when used in parameters
+ and annotation files</li>
+ </ul>
+ <strong>Issues affecting both applet and application</strong>
+ <ul>
+ <li>sequence numbering not preserved in MSF alignment output</li>
+ <li>sequence associated secondary structure not correctly parsed
+ in interleaved stockholm</li>
+ <li>sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ <li>Jalview PDB file reader does not extract sequence from deoxy
+ nucleotide chains correctly</li>
+ <li>Sequence length given in alignment properties window is off
+ by 1</li>
+ </ul>