What's new ?

Jalview Version 2.08

Editing can be locked to the selection area so that any edits made within the locked area do not unexpectedly shift other parts of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list of keyboard controls, look here.

Create sequence features from searches. Previously, the regions of sequences highlighted as the result of searches were added as new regions in the alignment. Now, the sequence region selected by a search can be used to define named sequences features attached to the sequence, rather than the alignment.

Sequence feature display and rendering has also been enhanced, with the addition of sequence feature groups (which can be used to show or hide a set of features en masse) and user defined feature colours as well as transparency controls, using the Sequence Feature Settings window. The Features file has also been extended to accomodate these enhancements.

Alignment annotation and colouring is also considerably enhanced. Precalculated symbolic and quantitative annotations (text labels, secondary structure symbols and multiple scalar graphs) can now be loaded onto alignments via the Annotation File. Additionally, the Annotation Colouring dialog box allows an alignment to be coloured based on any of the graphed quantities with which it is annotated.

Rendering speed has been improved by disabling anti-aliasing via the Smooth Fonts option in the View menu (its default set in Preferences). In addition, response times when editing alignments can be reduced by turning off the automatic calculation of amino acid property Consensus (which has been reintroduced to the Calculate menu as Autocalculate Consensus).

Issues Resolved

• Drag & Drop now works on common Linux desktops (at least KDE and Gnome)
• Jalview XML Archive Input/Output is now faster (using an internal Jalview schema), and sequence description strings are now preserved in the archive.
• Jalview can now correctly read and write MODELLER style PIR files.

See the Release History page for details of all new features and resolved issues.