X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d8ae02d413744351f8fb6da957d5a38d1b8ccfd7;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=7fa98068aeb4b86d2713b5985d58fa64e8061ba5;hpb=4e377b5c02352a12537100dddd2f8a2b84536205;p=jalview.git
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-
-What's new ?
-
-What's new ?
-Jalview Version 2.08
- Editing can be locked to the selection area.
- Any edits made within the locked area do not affect the rest of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously results from searches were added as alignment positions, which was
- wrong. Now the search results are saved as sequence features and their visibility
- and colour can be modified using the Sequence
- Feature Settings window.
- Precalculated annotations can be loaded onto alignments. The Annotation
- File format is a tab delimited set of values.
- Features file allows grouping of
- features. The Sequence Feature Settings
- window then makes it very easy to set the visibility of groups of features.
-
- Annotation Colouring
- scheme added. A new colour scheme which colours columns on a per-column value.
- Smooth fonts off by default - faster rendering. Toggle on / off from the View
- menu, or can be set in Preferences.
- Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.
-
-Issues Resolved
- Drag & Drop fixed on Linux
- Jalview Archive file faster to load/save, sequence descriptions saved.
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+What's new ?
+
+
+
+ What's new ?
+
+
+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
+ The release of Jalview 2.9 in September 2015 included
+ 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 released, see the
+ Jalview 2.9.0b2 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.
+
+
+
+