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.
- 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
based on Three Rings' Getdown system.
- Backup files
Jalview will automatically
create backups when overwriting existing files, and - unlike with
earlier versions, should Jalview crash during a save, the original
file will be unaffected.
- PCA plots stored in Jalview Projects
The PCA
viewer has also been enhanced and the user interface revised.
-
The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
Jalview and Java 11, 13, and onwards
The Jalview application comes bundled with its own independent
Java installation which will be updated automatically from
www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
runtime, but installations will be migrated to the latest Java
release once remaining issues have been addressed.