Ugene Versions Save

Changes

Primer3 can be run without a target sequence.

Primer-BLAST has been implemented in UGENE.

The hairpin visualization tool mfold has been integrated into UGENE.

The PlasMapper plasmids annotation database has been updated to the latest version.

Python, included in the UGENE package, has been upgraded to version 3.

The list of presets for Primer3 has been expanded.

Improved compatibility with theme settings in macOS.

Fixed issues related to the stability and usability of UGENE.

Demo

See also a new video about the recent improvements in UGENE.

• Fix crash in genome aligner UI.

• The "Presets" feature has been developed for Primer3, that allows you to select a set of preset settings to run the tool. At the moment, two presets are available - default settings and Recombinase Polymerase Amplification.
• Primer3 has received the function of filtering the resulting primer pairs depending on their homo/heterocomplementarity.
• Annotation selection has been corrected in the Sequence Editor.
• Various minor interface fixes and enhancements.

• Fixed a crash on project view filtering with hundreds of objects.

• Improved macOS support: Dozens of minor interface issues have been fixed.
• Revamped interface for working with restriction sites: New filters and enzyme details have been added.
• Most external tools shipped with UGENE have been updated to their latest versions.
• Enhanced support for PDB and ClustalW file formats.
• Many small issues related to the usability and stability of UGENE on all platforms have been fixed.

• Improved bookmark management. An option to update bookmarks has been added.
• Improved support for large SAM and BAM files.
• The algorithm from the Primer3 tool is now used by default for melting temperature calculations.
• Improved parameter descriptions and functionality in the Primer3 tool.
• Fixed focus issues in several dialogs on macOS.
• The Rebase restriction enzyme database has been updated to the latest version.
• Added the ability to choose commercial suppliers for restriction enzymes.
• Fixed bugs related to annotations and multiline mode in multiple sequence alignment editor.

• Introducing a new external tool for building phylogenetic trees: FastTree.
• A new built-in oligonucleotide melting temperature algorithm provided by the Primer3 tool.
• The Phy-tree Viewer has been improved with better scrolling, zooming, preservation of collapse and selection states when switching between different layout types, and more..
• The Assembly Browser has been improved to ensure that the navigational coverage overview does not miss regions for very large references.
• The Msa Editor now supports export of multi-line mode pictures into SVG or regular image formats.
• Improved sequence alphabet detection for extended DNA/RNA alphabets, and enhancements in support for different file formats.

This is a bug-fix release.

Several major regressions were fixed including error during startup on Windows.

• 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.

• 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.