- <li><strong>Virtual Features</strong><br />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
- <a href="features/splitView.html#virtualfeats">Sequence
- Features dialog</a>. This allows more analyses of nucleotide and
- peptide sequence features on alignments in a more flexible and
- memory efficient way than in earlier versions.<br />
- <em>Note: Virtual features work best when variants are
- annotated with CSQ fields. Please <a
- href="features/importvcf.html#computepepvariants">see this
- Groovy script workaround</a> if you are working with VCF files
- without CSQ fields.
- </em></li>
- <li><strong>Improved VCF data import</strong><br /> <a
- href="features/importvcf.html#attribs">Standard attributes for
- filtering variants</a> (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.</li>
- <li><strong>Extended feature attributes are exported
- in GFF3</strong><br />Complex attributes from VCF files can be exported
- and imported via GFF3</li>
- <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
- installation packages are now built with Install4j 8, which brings
- better support for Linux and improved control of file
- associations. New <a href="memory.html#jvm">parameters on the
- Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
- a Jalview launch file, to prevent it from hogging your system.</li>
+ <li>Jalview runs correctly when launched with Turkish language
+ settings</li>
+ <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+ products shown for a single contig (such as viral genomes)</li>
+ <li>Errors encountered when processing variants from VCF files
+ yield "Error processing VCF: Format specifier '%s'" on the console</li>
+ <li>Count of features not shown can be wrong when there are
+ both DNA and Protein features mapped to the position under
+ the cursor</li>
+ <li>Sequence ID for reference sequence is clipped when Right
+ align Sequence IDs enabled</li>
+ <li>Find doesn't report matches that span hidden gapped columns</li>
+ <li>Jalview ignores file format parameter specifying output
+ format when exporting an alignment via the command line</li>