Release 45.0

• New visualization mode in MSA Editor: Wrap Mode.
• Phylogenetic tree visualization improvements: hiding nodes, copying of tree image to clipboard, branch curvature.
• Primer 3 tool is updated to the latest version.
• Experimental features: a new Genecut tool.
• Other stability and usability fixes.

Release 44.0

• Fixed issues with visualization of cladogram and phylogram phy-trees in circular and unrooted modes.
• Improved support for Unicode symbols in file paths for BAM and SAM files used by Samtools module.
• GL2PS library to export vector images of 3D structures was upgraded to the latest version.
• Performance and stability improvements in GFF and ASN format readers.
• MrBayes algorithm now uses the same seed by default and produces repeatable results with the default settings.
• Other stability and usability fixes.

Release 43.0

Changes in UGENE v.43

• Assembly browser for a multi-contig reference sequence automatically selects and shows the contig with mapped reads.
• Improved support of MSA alignments with duplicate row names: all phy-tree algorithms integrated into UGENE were fixed.
• MrBayes phy-tree tool integration uses 'random seed' parameter correctly and produces repeatable tree results.
• Zoom-to-selection in MSA Editor fits the selected area into view correctly.
• Dotplot view region selection by mouse clicks was improved.
• Experimental shared MySQL database support is removed from UGENE.
• Many small interface improvements and stability fixes.

Release 42.0

Changes in UGENE v.42

• A new widget in MSA Editor: Exclude List.
• Custom algorithm selection support in 'Re-align selected sequences to the alignment' action.
• MSA Overview was optimized and is ON by default for any alignment sizes.
• MSA Editor performance while browsing huge alignment files is improved.
• New dedicated controls for popular options in IQ-TREE dialog.
• Double click on a sequence name in MSA Editor scrolls between start and end of the sequence into the view.
• Fixed order of joined and complemented annotation sequences during the export.
• Create Annotations widget uses standard Genbank feature names by default.
• Map reads to reference" algorithm is optimized to handle a large count of reads.
• Regression with a new MySQL database connection is fixed.
• Newick file format support is improved.
• Many other bug fixes and improvements.

Release 41.0

Changes in UGENE v. 41

• A new tool to build phylogenetic trees: IQ-TREE.
• Opening of very large alignments does not block UGENE anymore.
• A double-click in Sequence Viewer does not produce an unexpected selected region.
• Stockholm format parser now supports Unicode correctly.
• FASTA files with a very large number of sequences now can be opened as a multiple sequence alignment.
• ABIF files with incorrect dates do not cause a crash anymore.
• A search by a long list of patterns in Sequence Viewer is not disabled anymore.
• Stability and memory consumption of PCR and Smith-Waterman algorithms are improved.

A complete list of changes can be found on the UGENE website.

Release 40.1

This release includes fixes for several major regressions introduced by version 40.0 in MSA and Sanger editors.

Release 40.0

Changes in UGENE v. 40

Alignment Editor

• Multi-row selection support.
• The "Build Tree" dialog now has all PhyML algorithms listed.
• A new option to move selected sequences from one document to another.
• The grouping mode: sorting by the size of a group and showing group sizes in the name list.

Sanger Editor

• A new visualization mode: show alternative mutations.
• Several vertical scrolling bugs have been fixed.

Sequence Viewer

• Speed, memory usage, and precision of sequence graphs have been improved.
• Stability problems of auto-annotation routines have been fixed.
• Bugs, which appear while working with sequences larger when 2Gb, have been fixed.

Other improvements

• The "Smith-Waterman" algorithm support for CUDA has been improved.
• The Unicode support has been added for Newick, Plain text, Diff, VCF, SNP file formats.
• The "Random Sequence Generator" memory footprint and generation speed have been improved.

A complete list of changes can be found on the UGENE website.

Release 39.0

Changes in UGENE v. 39

• Phylogenetic tree viewer now allows setting custom colors and fonts for subtree branches and labels.
• The "Align to alignment" option got support for algorithm selection: ClustalO, MAFFT, Muscle, or UGENE.
• Alignments with the RAW (undefined) alphabet can be converted to the DNA, RNA, or Amino alphabets.
• Improved Unicode support for FASTA, MSF, and CLUSTALW formats.
• Sequence Viewer got a new option to show codons or protein statistics for selected regions.
• UGENE now speaks Turkish. Use menu Settings/Preferences to update the language.

A complete list of changes can be found on the UGENE web site.

Release 38.1

Critical fixes for UGENE platform styles on Windows and Linux.

Release 38.0

Changes in UGENE v. 38

Alignment Editor

1. New options for copy & paste routines: paste before or after a selection.
2. A new sorting option: "Sort by leading gap size".
3. A new option to select a translation table in DNA-to-protein export.
4. Advanced gap handling options in DNA-to-protein export.
5. Better scaling of text for high-resolution displays.
6. Reworked alignment and phylogenetic tree synchronization logic.
7. The recent "Copy selection" change was reverted to the old simple mode.

Sequence Editor

1. Faster and less resource-consuming auto-annotation mode.
2. Fixed issues with annotation selection in multi-line mode.
3. Better parsing of overlapping circular sequence regions in the annotation creation dialog.

Other improvements

1. Improved BLAST algorithm speed and resource usage when used for NGS.
2. In Sanger Editor a double-click on a read name now centers the read sequence on a screen.
3. Fixed Linux/GTK3 issue with file dialogs in Workflow Designer.
4. A lot of other stability and performance improvements.