X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=297233de91dd97a110bee36910d925156a9e8441;hb=9ee29162e3f41c2a60c50f1fda2f3d045adb658f;hp=d908cda70785ed4636a6911d805974d54883a93c;hpb=5b05749cab04092671551fbbcdc80406b53da7d0;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 2.6 introduces new web services, and includes an updated
-version of the Jmol molecular graphics visualization system. See the release history for the full
-details.
-Highlights in Jalview Version 2.6
-
- - JABA Web Services for
- multiple alignment using:
-
- - ClustalW
- - MAFFT
- - Muscle
- - ProbCons
- - T-COFFEE
-
-
- - User modifiable alignment service parameters
- - Visualization of superposed structures associated with protein
- or nucleotide sequence alignments.
- - Export coordinates and projection as CSV from PCA viewer
-
+
+ Jalview 2.10.2b1 bugfix release
+
+
+ This is patch release for 2.10.2. See the release notes for full
+ details bugs addressed in this version, which also introduces
+ additional improvements to the overview panel, and patches for
+ several minor issues including the ability to correctly recover
+ cross-references for Uniprot protein sequences from Ensembl.
+
+
+ What's new in Jalview 2.10.2 ?
+
+
+ Version 2.10.2 was released in August 2017, and introduced new user
+ interface features, improved and more extensible tree and PCA
+ analysis, more robust 3D structure viewing with UCSF Chimera and an
+ updated service client for JABAWS. The full list of bug fixes and
+ new features can be found in the 2.10.2 Release Notes, but
+ the highlights are below.
+
+
+ - New dialog and faster and more
+ configurable Tree and PCA calculations
Menu entries for
+ calculating PCA and different types of tree have been replaced by
+ a single Calculations
+ dialog box. The underlying implementation for the PCA and tree
+ calculations have been made faster and more memory efficient.
+ - Extensible score models
A new
+ framework has also been created for the score models used to
+ calculate distances between sequences and shade alignments. This
+ framework allows import of substitution matrices in NCBI and
+ AAIndex format.
PCA Bug Fixes. Jalview's
+ implementation of PCA differed in its treatment of gaps and
+ non-standard residues. The BLOSUM62 matrix also included a typo
+ that affected results. See the 2.10.2 release note
+ about score model bugs for details and how to reinstate legacy
+ behaviour.
+ - Update to JABAWS 2.2
Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by JABAWS 2.2.
+ Several of the programs provided as JABAWS 2.2 services have been
+ updated, so their options and parameters have changed.
+ - URL linkouts to other bioinformatics
+ databases
New preferences for opening web pages for
+ database cross-references via the UK Elixir's EMBL-EBI's MIRIAM
+ database and identifiers.org services.
+ - Showing and hiding regions
Hide insertions in the
+ PopUp menu has changed its behaviour. Prior to 2.10.2, columns
+ were only shown or hidden according to gaps in the sequence under
+ the popup menu. Now, only columns that are gapped in all selected
+ sequences as well as the sequence under the popup menu are hidden,
+ and column visibility outside the selected region is left as is.
+ This makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove) without
+ affecting the rest of the hidden columns.
+ - Gap count - a.k.a. the Occupancy
+ Annotation Row
Another way to filter columns according to
+ the presence of gaps is to enable the Occupancy
+ Annotation row via Jalview's Preferences. This annotation row
+ shows a histogram of the number of aligned residues at each
+ column. The Select
+ By Annotation dialog now also includes a percentage threshold
+ mode, to make it easy to filter alignments to show only those
+ columns with a particular fraction of aligned sequences.
+ - Recent search history for Find, PDBe and
+ Uniprot
Easily repeat a previous search for Find and the free
+ text search system (for querying Uniprot and the PDBe).
+ - Improved Overview Window
The alignment overview is now easier
+ to use when working with alignments of more than 5000 rows and
+ columns, and features a new pop-up menu that allows hidden regions
+ to be excluded from the overview. It also works with CDS/Protein
+ alignments and MSA views in wrapped mode.
+ - 3D Structure
Jalview's communication
+ with UCSF Chimera has been made more robust, particularly when
+ working with many structures and long sequences. Regions in
+ structures that correspond to hidden regions in an alignment view
+ are now left un-coloured, making it easier to highlight specific
+ features in 3D. See below for experimental
+ features for exchanging annotation between Chimera and Jalview.
+
+
+ Scripting
New groovy examples
+ demonstrate Jalview 2.10.2 APIs for creation of data-driven
+ colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker
+ introduced in Jalview 2.10 has also been refactored to allow
+ efficient counting across multiple feature types. Please be aware
+ that feature counter scripts created for earlier versions will not
+ execute in Jalview 2.10.2.
+
+
+ Experimental Features
+
+
+ This release of Jalview introduces an Experimental Features
+ option in the Jalview Desktop's Tools menu that allows you
+ to try out features that are still in development. To access the
+ experimental features below - first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
+
+
-Issues Resolved (a select list - see release history for details)
-
- - clustalx colourscheme colours Ds preferentially when both D+E
- are present in over 50% of the column
- - Prevent sequence fetcher from replacing ',' for ';' when querying DAS sequence sources
- - InstallAnywhere builds fail to launch on OS X java 10.5 update
- 4 (due to apple Java 1.6 update)
-
-See the Release History page for
-details of all new features and resolved issues.