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-
-
What's new ?
-
-What's new ?
-If you are reading this then you will already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.
- - To insert or edit the gaps in one sequence in alignment, the "Shift"
- key must be held down when dragging the mouse.
- - To insert or edit gaps for a group of sequences, the "Alt" key
- (or in X windows the "Control" key) must be held down.
- - Selecting colour schemes in the colour menu either sets just the "background"
- colourscheme for the alignment, or - when the tickbox "Apply colour to
- all groups" is ticked, applies the scheme to the background and all groups
- defined on the alignment.
- - Use the right mouse button (apple and click on the Mac) whilst the pointer
- is within the selection area to access the "define" region menu
- to define a new region, give it a name, and change its colourscheme and display
- properties.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone, and redone!
-
-
-
- Release |
- New Features |
- Issues Resolved |
-
-
- 2.05b
- 15/9/05 |
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
- |
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
- |
-
-
- 2.05
- 30/8/05 |
-
- - Edit and annotate in "Wrapped" view
- |
-
- - Several GUI bugs resolved
- |
-
-
- 2.04
- 24/8/05 |
-
- - Hold down mouse wheel & scroll to change font size
- |
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
- |
-
-
- 2.03
- 18/8/05 |
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
- |
-
- - InstallAnywhere download for Sparc Solaris
- |
-
-
- 2.02
- 18/7/05 |
- |
-
- - Copy & Paste order of sequences maintains alignment order.
- |
-
-
- 2.01
- 12/7/05 |
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at launch of Jalview.
- |
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key will initiate
- a search.
-
- |
-
-
- 2.0
- 20/6/05 |
- |
- |
-
-
-
-
-
+
+
+
+What's new ?
+
+
+
+ Jalview 2.10.2b1 bugfix release
+
+
+ This is patch release for 2.10.2. See the release notes.
+
+
+ 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.
+
+
+
+
+