[Jalview-discuss] Jalview 2.5 Release

[Jim Procter]

Dear Jalviewers.

Once again, I am pleased to announce that a new version of Jalview is 
now available from the website.

Jalview version 2.5 integrates features that been developed over the 
last two years, since version 2.4's release in 2008. The major 
improvements in this release are described below.

Sequence Feature Visualization
------------------------------
A new feature colour model has been introduced that enables features of 
a particular type to be shaded according to their score, or associated 
label text. Features may also be excluded according to score, enabling 
low or high scoring annotations to be easily revealed, and new buttons 
enable them to be used for re-ordering the alignment.

Alignment Annotation
--------------------
Sequence logos have been added to the consensus annotation in The 
Jalview Desktop. The jalview 2.5 alignment annotation model aslo 
includes a number of improvements, including support for group 
associated annotation rows, which can also be enabled from the Jalview 
desktop.

ENFIN Services in the Jalview Desktop
-------------------------------------

The Jalview Desktop's 'Web Services' menu now provides the option to 
submit sequences and sequence IDs to the Envision2 system for further 
analysis. Envision2 is a web application hosted at the European 
Bioinformatics Institute, which provides access to EnCORE services 
developed by research groups within the ENFIN European Network of 
Excellence (www.enfin.org). Envision2 is aimed at systems biologists, 
and enables them to execute workflows that access a range 
of databases and analysis services to gather experimental data and 
predictions about a set of proteins.

The next Jalview Release
------------------------
Jalview 2.6 is scheduled for release in the middle of this year. The 
major changes that are planned for this release are as follows:

   * Upgrade the embedded instance of Jmol used by Jalview
   * Introduce a new Alignment Web Services framework
   * Extend the JalviewLite javascript API with mouse over and selection 
events

That's all for now! Watch out for a new Jalview update newsletter in the 
next few months.

Happy Jalviewing
Jim Procter.

-- 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.