- <li><strong>More memory efficient</strong><br />We've slimmed
- down the consensus analysis data structures used by Jalview so
- even wider alignments can be worked with.</li>
- <li><strong>Select highlighted region</strong><br />Press 'B'
- or use the new menu option in the alignment window's Select menu
- to mark columns containing highlighted regions generated from
- structure selections, mouse-overs, or resulting from a Find
- operation.</li>
- <li><strong>New custom link mechanism for opening URLs
- for database cross references.</strong><br /> If you have customised URL
- links in your Jalview preferences, then you may already have seen
- the <a href="#warning"> warning dialog (see below).</a></li>
- <li><strong>New command line export option for BioJS
- MSAviewer</strong><br />A number of small bugs with the HTML export
- functions from the Jalview desktop were also fixed.</li>
- <li><strong>Small but significant changes to the
- physicochemical properties and consensus calculations</strong><br />Threonine
- is no longer considered a non-hydrophobic residue in the protein
- conservation calculation, and minor bugs addressed in PID and
- consensus colouring.</li>
- <li><strong>Correct display of disulphide bond
- features</strong><br /> In linked structure views, Jalview would
- highlight all residues between in addition to the two linked
- cysteines. The 'select columns by feature' function in the feature
- settings would also select all intermediate columns.
+ <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>