What's new ?

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.
For full details see the Jalview 2.7 release history.

Highlights in Jalview Desktop Version 2.7

- New structure viewer options:
  - Colour and superimpose 3D structures of complexes and multi-domain chains using several different alignments
  - Drag and drop to associate PDB files with sequences that have the same name
  - Open and superimpose all associated structures for the current selection
- New web services for alignment analysis
- Improved graphical user interface for JABAWSservices.
- Sort associated alignment views option in tree viewer
- Default colours for shading alignment by quantitative annotation.
- Jalview Desktop RSS reader - following important updates at http://www.jalview.org/feeds/desktop/rss

Issues Resolved (a select list - see the release history for full details)

Issues in the Jalview Desktop

- Problems viewing associated structures for sequences retrieved from UNIPROT
- Problems viewing Jalview projects from older versions in version 2.6
- Preservation of hidden annotation rows and tree bootstrap values in projects
- Newly added JABAWS servers not always visible in web services menu

Issues specific to the JalviewLite Applet

- Layout problems when lots of annotation rows are displayed
- <= shown as = in annotation row tooltip
- export features raises exception when no features exist
- relative URLs not handled properly when used in parameters and annotation files

Issues affecting both applet and application

- sequence numbering not preserved in MSF alignment output
- sequence associated secondary structure not correctly parsed in interleaved stockholm
- sequences containing lowercase letters are not properly associated with their pdb files
- Jalview PDB file reader does not extract sequence from deoxy nucleotide chains correctly
- Sequence length given in alignment properties window is off by 1