What's new ?

Jalview 2.8.2 is the first release produced by our new core development team.
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.
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 Jalview 2.8.2 Release Notes.

Annotation visualisation
The alignment window includes a new Annotations menu which provides controls for the layout and display of sequence, group and alignment associated annotation rows. It also now includes the Autocalculated Annotation 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.

Sequence associated annotation
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 via the Add Reference Annotation option.
The Colour by annotation 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.

3D Structural data analysis and display
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 Structures submenu of the sequence ID popup menu. The extraction and display of secondary structure and B-factor column annotation is controlled via a new Structure tab in the Jalview Desktop's Preferences dialog box.

Interoperation with UCSF Chimera
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.
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.
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.

Export of alignment figures as Scalable Vector Graphics
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.