X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=dd536b10e9d2a48ebc4d2f6104455c8d89ea8f55;hb=db49817596814aee5d269aabdf640f5bc5ed2363;hp=e6ab69520eb599fea0ced93a73e300673f272971;hpb=c43a1ee36b2679fd972599186e4d6e45fda87623;p=jalview.git
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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 ?
-Jalview 2.5.1 is a bug fix release for the 2.5 version of
-Jalview. See the release
-history for the bugs that this release resolves.
-Highlights in Jalview Version 2.5
-
- Linked viewing of nucleic acid sequences and structures
- Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.
- Order an alignment by sequence length, or using the average score or total feature count for each sequence.
- Shading features by score or associated description
- Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
- New hide/show options including Shift+Control+H to hide everything but the currently selected region.
-
-Jalview Desktop:
-
- Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources
- Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.
- Group-associated consensus, sequence logos and conservation
- plots
- Symbol distributions for each column can be exported and
- visualized as sequence logos
- Jalview Java Console
- New webservice for submitting sequences and IDs to Envision2 Workflows
- Improved VAMSAS synchronization and sharing of selections.
-
-JalviewLite:
-
- Middle button resizes annotation row height
- New Parameters - including default tree display settings.
- Non-positional features displayed in ID tooltip
-
-Issues Resolved (a select list)
-
-
- Source field in GFF files parsed as feature source rather
- than description
- Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).
- URL links generated for all feature links (bugfix)
- Codons containing ambiguous nucleotides translated as 'X' in
- peptide product
- Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.
- Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)
- Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.
-
- Desktop Issues
-
- Better handling of exceptions during sequence retrieval
- PDB files retrieved from URLs are cached properly
- Sequence description lines properly shared via VAMSAS
- Sequence fetcher fetches multiple records for all data
- sources
- Ensured that command line das feature retrieval completes
- before alignment figures are generated.
- Reduced time taken when opening file browser for first time.
- User defined group colours properly recovered from Jalview projects.
-
-
-
-
-See the Release History page for
-details of all new features and resolved issues.
+
+ What's new ?
+
+ Jalview 2.8.1 includes new features for group creation, RNA secondary
+ structure prediction and a host bug fixes. It also includes support
+ for version 2.1
+ of JABA and includes a Spanish translation of its user interface.
+ The highlights are detailed below, and the full list is given in the Jalview 2.8.1 Release Notes.
+
+ The Desktop and web based applet include new keystrokes for
+ defining and undefining groups, and PAM250 has been added to the range
+ of score models available for use by the tree and PCA calculations.
+ The Jalview project file format has also been extended for handling
+ RNA and protein secondary structure annotation, in anticipation for
+ new structure based secondary structure support in Jalview 2.8.2.
+ Internationalisation
+ Jalview 2.8.1 is the first release to include support for
+ displaying Jalview's user interface in different languages. In August
+ 2013, David Roldán-Martinez took on the task of
+ internationalising Jalview's user interface. He also recruited Sara
+ Hernández Díaz and Laura Ferrandis Martinez who created
+ Jalview's first spanish user interface translation.
+
+ If you notice any problems, or would like to help translate Jalview's
+ user interface into other languages, head over to issues.jalview.org and put in a
+ feature request describing the translations you can provide to the i18n
+ component. David has also documented
+ the process of creating i18n translations to help you get started.
+
+ RNA Secondary Structure Prediction with JABA 2.1
+
+ This version of Jalview includes a client to access the new services available in JABA v2.1 , which
+ provides services for RNA consensus secondary structure prediction and
+ two new alignment programs (GLProbs and MSAProbs).
+
+ To see how to perform RNA secondary structure predictions like the one below, take a look at the RNAAliFold
+ client documentation.
+
+
+
The RNAalifold client was implemented by Jalview's 2013
+ summer student, Dan Barton.
+