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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
What's new ?
-
- What's new ?
-
-
- The Jalview 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications.
For full
- details see the Jalview 2.7
- release history.
-
-
- Highlights in Jalview Desktop Version 2.7
-
-
+
+ What's new ?
+
+
+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
+ to a multitude of bug fixes and minor improvements (both small, and
+ rather big!), it also brings major new capabilities for codon-level
+ analysis of protein alignments and the retrieval and manipulation of
+ structural data.
For the patches since version 2.9 was release, see the
+ Jalview 2.9.0b1 Release Notes.
+
+
+ Highlights in Jalview 2.9
+
+ - Visualisation, editing and analysis of
+ cDNA and Protein alignments
A new Split View window allows linked
+ protein and nucleotide sequence alignments to be viewed, edited,
+ and analysed as one.
cDNA alignments can also be
+ reconstructed from protein alignments calculated by Jalview's web
+ services, and update in response to edits in the amino acid view.
To
+ start experimenting with cDNA/Protein analysis, jut drop a file
+ containing cDNA sequences which code for proteins in an existing
+ alignment, and Jalview will do the rest.
+ - Enhanced Integration of UCSF Chimera
Jalview
+ 2.9 provides full support for the use of Chimera to view 3D
+ structures linked to alignment views in the Jalview Desktop. We've
+ also included support for saving Chimera sessions in Jalview
+ project files.
Jalview and Chimera communicate using local
+ web server connections, which may cause firewall alerts on some
+ systems, but has the advantage of allowing bidirectional
+ communication. Communication between Jalview and Chimera is now
+ much more responsive, and selected regions in Chimera are now
+ shown as highlighted regions in the Jalview desktop.
+ - Interactive querying of the PDBe
Jalview
+ users can now browse and retrieve 3D structure data from the PDB
+ via the PDBe
+ Search API (Gutmanas
+ et al 2014). Developed in collaboration with the PDBe group at
+ EMBL-EBI, the interface allows both structured and free-text
+ queries to be performed, and allows automatic selection of the
+ most relevant structures for an alignment acording to a variety of
+ criteria.
+ - Improved support for RNA visualisation
Jalview
+ 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
+ can also now be stored in Jalview projects. We've also dealt with
+ a number of lingering bugs in the VARNA/Jalview interface,
+ including the loss of pseudoknots when RNA secondary structure is
+ shown VARNA.
+ - Protein Secondary Structure predictions
+ with JPred4
Jalview includes a number of new features for
+ working with secondary structure predictions from the JPred4
+ server. These include new popup menu actions to automatically hide insertions and highlight
+ mutations in an alignment with respect to a Reference
+ Sequence. Jalview 2.9's new scrollable
+ SVG HTML export was also developed specifically for the JPred4
+ server.
+
-
- Issues Resolved (a select list - see the release history for full details)
-
-
-
- Issues in the Jalview Desktop
-
- - Problems viewing associated structures for sequences
- retrieved from UNIPROT
- - Problems viewing Jalview projects from older versions in
- version 2.6
- - Preservation of hidden annotation rows and tree bootstrap
- values in projects
- - Newly added JABAWS servers not always visible in web services
- menu
-
- Issues specific to the JalviewLite Applet
-
- - Layout problems when lots of annotation rows are displayed
- - <= shown as = in annotation row tooltip
- - export features raises exception when no features exist
- - relative URLs not handled properly when used in parameters
- and annotation files
-
- Issues affecting both applet and application
-
- - sequence numbering not preserved in MSF alignment output
- - sequence associated secondary structure not correctly parsed
- in interleaved stockholm
- - sequences containing lowercase letters are not properly
- associated with their pdb files
- - Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly
- - Sequence length given in alignment properties window is off
- by 1
-