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- What's new in Jalview 2.10.2 ?
-
-
- This August 2018 release of Jalview introduces 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.
+ Jalview 2.11 - major and minor new features
+ Jalview 2.11 introduces support for loading VCF files, and new
+ filters and shading models for sequence features. Under the hood,
+ we've addressed many bugs, and also made some important changes in
+ the way the Jalview desktop is installed and launched.
- - 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- calculating PCA and different types of tree have been replaced by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.
+ - VCF Support. Proteins and genomic contigs with
+ chromosomal location annotation (such as protein coding genes
+ retrieved from Ensembl) can be annotated with variants imported
+ from a local VCF file.
+ - The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to
+ download and install Jalview once. After installation, Jalview
+ will automatically keep itself up to date. The launcher also sets
+ Jalview's memory automatically, so you'll never again have to
+ manually configure Java's memory settings.
We are grateful to
+ Install4J who provided us with a free license for their
+ installation system, and Jalview's over the air update system is
+ via Getdown.
- 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
+ The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
- 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.
+ Jalview and Java 11, 13, and onwards
+ Java 11 provides improved performance and better OS
+ integration, so we now recommend users select our Java 11 Jalview
+ distribution rather than the legacy Java 8 build.
+ Known Issues - update for 211
- - Annotation transfer between Chimera and Jalview
Two
- new entries in
- the Chimera viewer's Chimera menu allow positional annotation to
- be exchanged between Chimera and Jalview.
+ - OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file
+ to load yields a FileNotFound exception.The workaround is to first
+ clear the 'Untitled' filename before selecting the file you wish
+ to load.
+
+ - OSX: Links don't open when clicked on or via the Sequence
+ or Alignment window popup menu.
+ - OSX (Webstart): Jalview only displays old news feed items
-