Jalview 2.3

Hello Jalview users,

We are packaging together the latest new features added and issues resolved and writing documentation for the next Jalview release, which will be Version 2.3.

New Features:

Jmol 11 integrated in Application.

    * Jmol is an opensource structure viewer written in Java, so fits
      naturally with Jalview. The integration allows all the features
      from the original Jalview Structure viewer, such as colouring
      structures from alignment colours and mouse over structure /
      alignment highlighting.
    * For the first time you will be able to save the structure view
      along with your alignments within the Jalview file format.
    * Jalview 11 is not Java 1.1 compatible, but there are steps being
      made to allow Jmol to run in all browsers. For this reason, the
      Jmol applet will only run in Web Browsers with Java 1.4 plugin or
      greater. If the web browser uses Java 1.1 only, the original
      Jalview Structure viewer is still available.

Slide sequences with cursor keys - very useful editing feature which has been missing from Jalview.

Edit sequence in place - another highly requested editing feature, allows residues/sequences to be altered in place.

Feature / Annotation editing in Applet - Previously only available in the application, but has proven to be very useful in web alignment editing tools.

Sequence fetcher parses EMBL codon records - CDS regions marked on sequences retrieved using WsDBFetch sequence fetcher from EBI.

Feature fetcher maps Uniprot features onto EMBL sequence.

Feature display optimization - layering of features on the alignment can be optimized by a button on the Feature Settings window.

Alignment Properties - View simple alignment statistics and predefined alignment properties.

Annotation file - extensions have been made to add alignment properties and scores to sequence and alignment annotations.

Sort by score - if scores exist in the alignment, Jalview will recognise them and allow the user to sort the sequences by the available scores.

Issues Resolved :

Headless state 2.2.1 - small bug in 2.2.1 prevented this release from running in a truely headless state.

Applet 2.2.1 no transparency for features - compilation error lead to omission of feature transparency.

DNA pairwise alignment will now run with non - GCTA symbols.

Cut & paste of sequences with associated alignment annotation works

Coming soon!!!