Jalview 2.11.1.0
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.
- 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.
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.