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+
What's new ?
-What's new ?
+
+ What's new ?
+
+
+ Jalview 2.9 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 full list of changes, see the
+ Jalview 2.9 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.
+
-Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for
-one alignment
-Easily add, amend and delete sequence features
-"Reload" alignment from File or URL to revert to
-original
-"Save" to current filename or "Save As" to
-new filename
-New "New Window" button on the
-"Output To Textbox" opens output window for quick 'sequence
-editing'.
-Set different text colour for dark or light background
-Right align sequence ids
-Set colour of lower case residues in a user defined colour scheme
-
-Menu Rearrangements: New Format for alignment
-layout and Select for region selection.
-
-Menu item accelerator keys added
-Control-V pastes sequences to active window, Control-Shift-V
-pastes to a new window.
-Raise/Minimise alignment and all associated windows from desktop
-window's window menu
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.
-Issues Resolved
-
-Optimisations for large alignments: faster multithreaded
-calculations and Undo/Redo system.
-Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-DAS feature fetching slowed down, doesn't overload DAS servers
-DAS feature fetching can be cancelled
-Correct display of > and < symbols for feature descriptions
-without explicit <html> tags.
-Zoom working in PCA viewer
-Sequence Descriptions retained after running a web service
-
-See the Release History page for
-details of all new features and resolved issues.