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.
Highlights in Jalview Version 2.8
- Improved JABAWS
client and new JABAWS 2.0 Services
- 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