What's new ?
Jalview 2.8 includes a number of enhancements and new features that have been in development since July 2010. It is also the first Jalview release to incorporate RNA visualization features developed by Lauren Lui and Jan Engelhart during their Google Summer of Code projects (http://code.google.com/soc/). As usual you can find the highlights below, but to see the comprehensive list take a look at the look at the Jalview 2.8 Release Notes.

• Improved JABAWS client and new JABAWS 2.0 Services
  • AACon alignment conservation
  • Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
  • Clustal Omega for creating huge protein alignments
• RNA
  • Import sequence and alignment associated WUSS or VIENNA dot-bracket notation from files and the RFAM database
  • Interactive editing of RNA secondary structure annotation
  • Colour scheme for purine/pyrimidine and to highlight RNA helices
  • RNA canonical base pair consensus score and sequence logo
  • Embedded VARNA RNA secondary structure viewer in the Desktop
• Parse and display T-COFFEE alignment quality scores (thanks to Paolo di Tomasso of the Notredame Group)
• Per sequence alignment annotation shading
• Enhanced PCA viewer: more export options, and switch between different PCA modes and residue score models
• New Jalview Desktop database fetcher GUI
• Support for DAS 1.6 and DAS 2.0 sources (thanks to the new JDAS Distributed Annotation client library (see http://code.google.com/p/jdas))
• Export sequence database annotation as an HTML report
• Normalised Sequence Logo Display

Issues resolved in the Jalview Desktop

• PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service
• Stop windows being moved outside desktop on OSX
• Jnet job queues forever if a very short sequence is submitted for prediction
• Structure view highlighting doesn't work on windows 7
• Jalview desktop fails to launch with exception when using proxy
• DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
• Cannot close news reader when JABAWS server warning dialog is shown
• Edited sequence not submitted to web service
• Jalview 2.7 InstallAnywhere installer doesn't unpack and run on OSX Mountain Lion
  • If you use webstart then you may need to go into the Security panel (a.k.a the gatekeeper) in your System Settings, and select the 'allow any code to run' option.

Issues specific to the JalviewLite Applet

• Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
• loading features via javascript API automatically enables feature display
• scrollToColumnIn javascript API method doesn't work

Issues affecting both applet and application

• Redundancy removal fails for rna alignment
• PCA window shows grey box when first opened on OSX
• Letters coloured pink in sequence logo when alignment coloured with clustalx