X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=0cf5661b1143ce17b00aba690d18e3b6a8288807;hb=a7f28f3acaa5f8d94a3d412d01df432447c793cd;hp=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hpb=cfcd397b19f70fb39d6d21437db8eb6ffcac3914;p=jalview.git
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- Jalview 2.11.1.0
+ Welcome to Jalview Version $$Version-Rel$$ !!
+
Please take a
+ look at the release
+ notes for this build. Read on for the highlights.
- Jalview 2.11.1.0 is the first minor release for the 2.11 series.
- Along with a number of critical bug fixes and improvements it brings
- new functionality for mapping sequence features between CDS and
- Protein alignments. It is also the first release made under a new four
- number versioning scheme, which will allow us to keep track of
- patches and bug fixes.
+ Highlights in 2.11.2
+
+ New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities:
- Linked viewing with ChimeraX and PyMol
Simply configure your prefered viewer for 3D molecular data in Jalview's structure preferences, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!
+ - View predicted protein structures via 3D-Beacons
+ Jalview 2.11.2's Structure Chooser includes a client for the 3D-Beacons Network, a new service that allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources.
+
+ Retrieval
-
- - Virtual Features
In previous
- versions of Jalview, specific nucleotide sequence features such as
- genomic variants and exons were transferred to protein products on
- import. Jalview 2.11.1 instead provides 'virtual features' that
- can be enabled and overlaid on linked CDS/Protein views via their
- Sequence
- Features dialog. This allows more analyses of nucleotide and
- peptide sequence features on alignments in a more flexible and
- memory efficient way than in earlier versions.
- Note: Virtual features work best when variants are
- annotated with CSQ fields. Please see this
- Groovy script workaround if you are working with VCF files
- without CSQ fields.
-
- - Improved VCF data import
Standard attributes for
- filtering variants (e.g. position, QUAL field etc) are now
- extracted from VCF files. This new feature was suggested by a user
- at the Jalview booth during ISMB 2019.
- - Extended feature attributes are exported
- in GFF3
Complex attributes from VCF files can be exported
- and imported via GFF3
- - Updated Jalview Installer and Launcher
Jalview's
- installation packages are now built with Install4j 8, which brings
- better support for Linux and improved control of file
- associations. New parameters on the
- Jalview launcher allow an upper memory limit to be specified via
- a Jalview launch file, to prevent it from hogging your system.
-
- See the 2.11.1.0
- release notes for full details of bugs fixed and new known issues.
+ For the full release notes, see the Jalview 2.11.1.4
+ release notes.
- JalviewJS News
With the release of Jalview 2.11.1.0,
- the team are now focused on bringing JalviewJS to full production.
- To follow our progress take a look at http://www.jalview.org/jalview-js/
- and follow updates on our new JalviewJS
- Releases github repository.
+ Known Issues
+ New known issues in this release affect recovery of CDS/Protein
+ relationships from project files, and interactive selection of
+ protein sequences from a tree built on linked nucleotide sequences.
+ We will provide patches for these issues as soon as possible.
+