Jalview 2.11.1.1

Jalview 2.11.1.1 is the first patch release for Jalview version 2.11.1. In addition to fixes for some critical bugs, it also contains a handful of new features suggested by the Jalview community.

• Shift+arrow keys navigate to next gap or residue in cursor mode (enable with F2)
• Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
• Improved recognition of GZipped files from local disk or retrieved via the web
• EMBL and EMBL CDS database records retrieved from the European Nucleotide Archive's Data API as 'EMBL Flatfile' records
• Improved Java Console and logging to help track down problems
• Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)

Critical bug fixes include

• Jalview runs correctly when launched with Turkish language settings
• Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig (such as viral genomes)
• Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console
• Count of features not shown can be wrong when there are both DNA and Protein features mapped to the position under the cursor
• Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
• Find doesn't report matches that span hidden gapped columns
• Jalview ignores file format parameter specifying output format when exporting an alignment via the command line

For the full release notes, see the Jalview 2.11.1.1 release notes.

Known Issues

• We've had reports from a small number of windows 10 users who see a warning dialog pop up when Jalview tries to save a new version of an existing file. If you are affected by this bug and this latest version of Jalview doesn't fix it, please let us know!
• Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
• Drag and drop of alignment file onto alignment window when in a HiDPI scaled mode in Linux only works for the top left quadrant of the alignment window