We are quite excited about the release of Jalview 2.11.0!
This major release 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.
Jalview 2.10.5 is a minor release that includes critical patches for users working with Ensembl, RNA secondary structure annotation, and those running Jalview on OSX with Java 10.
The first patch release for Jalview 2.10.4 is now available. It includes the following minor improvments and critical patches:
- HGVS nomenclature used for variant annotation retrieved from Uniprot
- Uniprot import fails for some sequences (Cannot import features with multiple variant elements)
- Clustal files with sequence positions in right-hand column are now parsed correctly
- Wrap view - export to SVG - IDs shown but not alignment area in exported graphic
- F2/Keyboard mode edits work when Overview window has input focus
- Windows specific fixes:
- Annotation panel set too high when annotation added to view
- Updated search paths for Chimera default installation
- Windows File Shortcuts can be dragged onto the Jalview Desktop
- Drag URL from Chrome, Firefox, IE to Jalview desktop on Windows doesn't open file:
Dragging the currently open URL and links from a page viewed in Firefox or Chrome on Windows is now fully supported.
If you are using Edge, only links in the page can be dragged.
With Internet Explorer, only the currently open URL in the browser can be dropped onto Jalview.
If you experience any problems, please let us now via Twitter (@Jalview) or the jalview mailing lists.
This minor release is the last in the 2.10 series. It includes critical patches for maintaining access to public web services and compatibility with Java 10 on OSX. It also includes several efficiency improvements, an improved 3D structure chooser and bug fixes to make SIFTS sequence-structure mappings more reliable.
We are pleased to announce the first Jalview release of 2018!
The Jalview 2.10.3b1 bugfix release is distributed under a new Open Source codesigning certificate ("Open Source Developer, JAMES PROCTER") and includes improvements to the web client for EnsemblGenomes, and fixes the following bugs in the Jalview Desktop:
A bugfix release for 2.10.2 is now available. Version 2.10.2b1 has the following new features:
- Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white)
- Overview tab in Jalview Desktop Preferences
- Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated
Several minor (and not so minor) bugs are also resolved, including problems with retrieval of Ensembl crossreferences for Uniprot sequences, and PDB sequence/structure associations.
This August 2017 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 2.9.0b2 fixes a Desktop bug where group associated consensus and conservation annotation rows are duplicated when an alignment is partitioned by clicking on the tree viewer.