We are very pleased to announce that Jalview version 2.8.2 is now available (just in time for our Jalview course in London on 15th December!).
This release is special for a number of reasons, the most important being that it is the first one produced by our new core development team members Mungo Carstairs and Tochukwu (Charles) Ofoegbu, and also includes features introduced by our 2012 Jalview summer of code student, Anne Menard. The highlights in this release are described below, but please see the Jalview 2.8.2 Release Notes for the comprehensive list of bug fixes and improvements.
A new Annotations menu provides controls for the layout and display of sequence, group and alignment associated annotation rows. New options also control the display of sequence associated annotation such as secondary structure assignments and disorder predictions, for just one or a whole group of sequences. The Colour by annotation function has also been improved, allowing protein sequences to be coloured by secondary structure type, and RNA sequences to be shaded according to stem/helix number.
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.
3D Structural data analysis and display
Jalview now employs Jmol's PDB data API to access secondary structure assignments made by the DSSP algorithm and Fabrice Jossinet's pyRNA web services to obtain secondary structure assignments from RNA structures.
Interoperation with UCSF Chimera
UCSF Chimera is a powerful python-based high-performance molecular graphics and animation system developed by the Resource for Biocomputing, Visualisation, and Informatics at the University of California. Jalview now includes the 'StructureViz' communication mechanism (developed for Cytoscape by Morris et al. 2007) that enables Chimera to be used in place of Jmol for the visualisation of structures associated with alignments. Support for Chimera is experimental, so please let us know if you have any problems via the discussion list, or comment directly at http://issues.jalview.org/browse/JAL-1333