- <p>
- This bug fix release includes numerous minor enhancements made over
- the last 12 months. Importantly, it is also the first release that
- provides Jalview as a trusted application, signed with a certificate
- donated to us by <a href="certum.eu">Certum</a>.
- </p>
- <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>
+ Jalview 2.8.2 is the first release produced by our new core
+ development team.<br /> It incorporates many minor improvements and
+ bug-fixes, and new features for working with 3D structure data,
+ shading alignments by secondary structure and generation of alignment
+ figures as Scalable Vector Graphics. <br />The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the <a
+ href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Annotation visualisation</strong> <br /> The alignment window
+ includes a new <em>Annotations</em> menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the <em>Autocalculated
+ Annotation</em> submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+ </p>
+ <p>
+ <strong>Sequence associated annotation</strong><br /> New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+ The <strong>Colour by annotation</strong> function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+ </p>
+ <p>
+ <strong>3D Structural data analysis and display</strong><br />
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the <em>Structures</em>
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled <em>via</em>
+ a new <strong>Structure</strong> tab in the Jalview Desktop's
+ Preferences dialog box.
+ </p>
+ <p>
+ <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.<br />Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+ </p>
+ <p>
+ <strong>Export of alignment figures as Scalable Vector
+ Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+ </p>
+