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Unipro UGENE Changelog

What's new in Unipro UGENE 50.0

Apr 14, 2024
  • Changes in the release:
  • 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.

New in Unipro UGENE 49.1 (Nov 26, 2023)

  • Fix crash in genome aligner UI.

New in Unipro UGENE 49.0 (Nov 8, 2023)

  • 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.

New in Unipro UGENE 48.0 (Aug 8, 2023)

  • 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.

New in Unipro UGENE 47.0 (May 21, 2023)

  • Improved bookmark management. An option to update bookmarks has been added.
  • The algorithm from the Primer3 tool is now used by default for melting temperature calculations.
  • The Rebase restriction enzyme database has been updated to the latest version.

New in Unipro UGENE 46.0 (Feb 23, 2023)

  • 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 Msa Editor now supports export of multi-line mode pictures into SVG or regular image formats.

New in Unipro UGENE 45.1 (Dec 31, 2022)

  • This is a bug-fix release. Several major regressions were fixed including error during startup on Windows.

New in Unipro UGENE 45.0 (Nov 20, 2022)

  • 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.

New in Unipro UGENE 44.0 (Aug 21, 2022)

  • 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.

New in Unipro UGENE 43.0 (Jun 6, 2022)

  • 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.

New in Unipro UGENE 42.0 (Mar 7, 2022)

  • 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.

New in Unipro UGENE 41.0 (Dec 3, 2021)

  • A new tool to build phylogenetic trees: IQ-TREE.
  • Stability and performance related improvements.

New in Unipro UGENE 40.1 (Oct 13, 2021)

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

New in Unipro UGENE 40 (Sep 9, 2021)

  • 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.

New in Unipro UGENE 39 (Jun 12, 2021)

  • Changes in the release include:
  • 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.

New in Unipro UGENE 38.1 (Apr 3, 2021)

  • Several important errors have been fixed:
  • Failure on the UGENE opening on Windows;
  • Small font on Linux;

New in Unipro UGENE 38 (Mar 22, 2021)

  • Alignment Editor:
  • New options for copy & paste routines: paste before or after a selection.
  • A new sorting option: "Sort by leading gap size".
  • A new option to select a translation table in DNA-to-protein export.
  • Advanced gap handling options in DNA-to-protein export.
  • Better scaling of text for high-resolution displays.
  • Reworked alignment and phylogenetic tree synchronization logic.
  • The recent "Copy selection" change was reverted to the old simple mode.
  • Sequence Editor:
  • Faster and less resource-consuming auto-annotation mode.
  • Fixed issues with annotation selection in multi-line mode.
  • Better parsing of overlapping circular sequence regions in the annotation creation dialog.
  • Other improvements:
  • Improved BLAST algorithm speed and resource usage when used for NGS.
  • In Sanger Editor a double-click on a read name now centers the read sequence on a screen.
  • Fixed Linux/GTK3 issue with file dialogs in Workflow Designer.
  • A lot of other stability and performance improvements.

New in Unipro UGENE 37 (Dec 15, 2020)

  • Alphabetical order of External Tools:
  • Pay attention that the list of the «External Tools» in the «Application Settings» dialog has become sorted alphabetically.
  • The copy/paste and naming mechanism in the Alignment Editor has been improved:
  • The copy/paste function saves the name of the copied sequence now and also roll this name to make it unique. Besides, the possibility to insert sequence to a certain place (near the current selection) has appeared.
  • Naming in the «Bookmarks» tab has been improved:
  • File and object names writing has become more convenient in the «Bookmarks» window.
  • Other changes:
  • The validation process of External Tools has been improveds.
  • Trimmomatic, BWA, and Bowtie2 have been updated.
  • A large number of bugs and errors, related to working with the database, external tools, and other scripts, have been fixed.

New in Unipro UGENE 36 (Sep 22, 2020)

  • Adding the UGENE launch shortcut on the Desktop:
  • Pay attention to the appeared «Create desktop shortcut» button in the «Help» menu.
  • The «Copy annotations» function is improved in the sequence view:
  • Copying of selected annotated sequences is tied to the strand of the sequence the current annotation is located on. If there are several annotations on both direct and complementary strands are selected, clicking the «Copy» button causes the copying of sequences from the corresponding strands.
  • Other improvements:
  • MySQL 8 is supported.
  • Phylogenetic trees visualization is improved.

New in Unipro UGENE 1.35.0 (Jun 18, 2020)

  • The new version includes a bunch of improvements in Alignment Editor:
  • Sorting sequences in alignment by name and by length: You can sort sequences in alignment using the Sort submenu in the Actions main menu or from the context menu.
  • Also, you can use the General Options Panel tab
  • There are four ways to sort sequences:
  • By name, ascending
  • By name, descending
  • By length, ascending
  • By length, descending
  • Grouping sequences in alignment by sequence names: To search for a pattern(s) in alignment go to the “Search in Alignment” tab of the Options Panel.
  • To group results press the Group button. The results will be selected and grouped to the top after the first click or to the bottom after the second click to the button.
  • Search by sequence names in alignment:
  • To search by sequence names use the Search in Alignment Options Panel tab with the “Sequence Names” search context.
  • “Weak Similarities” color scheme: When there is a choice between two characters and it is not
  • specified by other rules which character to color, following priorities: T>U>G>C>A>B>D>H>K>M>R>S>V>W>Y>N.
  • Coloring rules:
  • Do not color gaps (“-“), i.e. use a black font and white background.
  • Residues should be colored according to their percentage number in the column (use the priorities,
  • described above, in case of equal percentage numbers).
  • Residues with the most frequency/priority in the column.
  • Other modifications include:
  • The ClustalO tool is updated to the latest version.
  • “Navigation” and “Appearance” menus in Alignment Editor were restructured for better usability.
  • “Edit” menu in Sequence View got a new structure.

New in Unipro UGENE 1.34.0 (Mar 23, 2020)

  • A new option for realigning a sequence to other sequences of an alignment
  • Advanced search options
  • Appearance of a selected region in an alignment

New in Unipro UGENE 1.32.0 (Feb 27, 2019)

  • The new version includes update of the NGS data analysis framework:
  • MetaPhlAn2 tool for metagenomic data classification and other minor improvements.

New in Unipro UGENE 1.31.1 (Oct 17, 2018)

  • Exporting consensus in the Sanger Reads Editor
  • Downloading a sequence from the Ensembl database

New in Unipro UGENE 1.31 (Aug 17, 2018)

  • The new version introduces a lot of major features for NGS data analysis:
  • Quality control: a new tool Trimmomatic was integrated for quality control of NGS reads. It allows one to cut Illumina adapters, trim reads ends by quality, trim reads by length, etc.
  • The tool is available as a workflow element and included into several sample workflows (see below, for example).
  • Trimmomatic is a java application. Install Java Runtime Environment and configure it in the UGENE Application Settings to use the tool.
  • De novo assembly: SPAdes was updated to version 3.12.0. Graphical interface for the tool in UGENE was updated. It is now possible to input hybrid data, for example, assemble Illumina and Oxford Nanopore reads.
  • Begin with sample workflows available from “Tools > NGS data analysis > Reads de novo assembly (with SPAdes)” item in the UGENE main menu.
  • Modify the SPAdes input type, if required. SPAdes requires at least one library of the following types: Illumina paired-end/high-quality mate-pairs/unpaired reads; IonTorrent paired-end/high-quality mate-pairs/unpaired reads; PacBio CCS reads
  • Additionally, one can provide PacBio CLR, Oxford Nanopore, Sanger reads or contigs.
  • See “Input data” parameter of the SPAdes workflow element.
  • Metagenomics: a new infrastructure for taxonomy classification of whole-genome shotgun sequencing data was developed. This includes tools Kraken, CLARK, DIAMOND, WEVOTE and other. Reference data for the tools are also provided: NCBI taxonomy information; RefSeq data for viruses, bacteria, human; etc. It is recommended to use the Online Installer UGENE package to install and configure the data, check required items in the “NGS additions: metagenomics classification” item.
  • Several sample workflows with the tools are available from “Tools > NGS data analysis > Metagenomics classification” item in the main menu. In particular, the following workflow executes Kraken, CLARK, and DIAMOND tools in parallel. After that, the results are merged by WEVOTE.
  • Besides classification, building of a custom database is supported for each tool (see, for example, “Build Kraken Database” workflow element).
  • Note that the computer should be powerful enough to run the workflows (at least 8Gb of RAM is required). The whole package requires about 230-240 Gb of disk space (see details here). Trimmomatic and FastQC tools, included into the sample workflows, require Java Runtime Environment to be installed and configured in the UGENE Application Settings. The other tools are provided for macOS and 64-bit Linux operating systems only.
  • Transcriptomics: a new tool StringTie for transcript assembly was integrated as a workflow element. Also, another element “StringTie Gene Abundance Report” was implemented. It allows one to get a common report for several input samples.
  • A sample workflow with the elements is available from the main menu “Tools > NGS data analysis > RNA-Seq data analysis”.
  • Create a new dataset for each sample (a sample here may be a pair of FASTQ files, for example)!
  • Note that StringTie and TopHat tools are available on macOS and 64-bit Linux operating systems only. Trimmomatic and FastQC tools, included into the sample workflow, require Java Runtime Environment to be installed and configured in the UGENE Application Settings.

New in Unipro UGENE 1.30 (Jun 1, 2018)

  • The new version is majorly a bug-fix release.
  • However, several usability improvements were also added, for example, modification of the selection in the Sequence View.

New in Unipro UGENE 1.29 (Dec 30, 2017)

  • A new mode for a sequence editing in the Sequence View.
  • A new mode for amino acid translations visualization in the Sequence View.
  • Usability improvements.
  • Bug fixes.

New in Unipro UGENE 1.28.1 (Nov 20, 2017)

  • Tweaking of the Sanger reads mapping feature, based on feedback received
  • Fix of a critical issue of searching in amino acid translations of a nucleotide sequence
  • Other minor bug fixes and improvements

New in Unipro UGENE 1.28.0 (Oct 30, 2017)

  • Support of Vector NTI/AlignX format
  • Improvement of the Sanger reads mapping algorithm
  • Bug fixes and minor improvements

New in Unipro UGENE 1.27.0 (Aug 24, 2017)

  • Sanger Reads Editor:
  • A brand new framework for analysis of Sanger sequencing results:
  • Reads mapping to a reference sequence
  • Browsing of the result alignment with trace chromatograms
  • Editing of reads
  • Exporting of the results
  • See this introductory video for the quick start.
  • Bug fixes and minor improvements

New in Unipro UGENE 1.26.3 (Jun 20, 2017)

  • Change in the release includes:
  • Fix of a critical error with project files (.uprj) and workflows (.uwl): backward compatibility with previous version of Unipro UGENE is restored.

New in Unipro UGENE 1.26.1 (Feb 23, 2017)

  • Fix of a critical error with project files (.uprj) and workflows (.uwl): backward compatibility with previous version of Unipro UGENE is restored.

New in Unipro UGENE 1.26.0 (Feb 9, 2017)

  • General:
  • Support of high-resolution Retina displays
  • By default, all documents are opened in tabs instead of windows. To change this parameter go to the Application Settings
  • NGS: All databases, supported by SnpEff, are now available for prediction of variant effects
  • Bug fixes and minor improvements

New in Unipro UGENE 1.25.0 (Oct 25, 2016)

  • NGS:
  • New parameter for reads mappers (BWA, Bowtie2, etc.) to remove “unpaired” reads from quality-filtered paired-end FASTQ files before the mapping
  • Support of different options for CutAdapt parameters in the “Raw NGS data processing” wizards (5′ adapters, 3′ adapters, 5′ and 3′ adapters)
  • Optimization of the coverage calculation in the Assembly Browser
  • Bug fixes and minor improvements

New in Unipro UGENE 1.24.2 (Oct 25, 2016)

  • This is a patch release that contains several major bug fixes

New in Unipro UGENE 1.24.1 (Sep 6, 2016)

  • This is a patch release that contains several major bug fixes

New in Unipro UGENE 1.24.0 (Aug 12, 2016)

  • WORKFLOW DESIGNER:
  • New element: “Convert SnpEff Variations to Annotations”. Element converts variations with SnpEff information into standard annotations, so you can observe them in the Sequence View.
  • NGS workflows improvements.

New in Unipro UGENE 1.23.1 (Jul 8, 2016)

  • This is a patch release that contains several major bug fixes

New in Unipro UGENE 1.23.0 (Jun 25, 2016)

  • Major changes in this release include:
  • Auto-update: there is no need to download a new version manually anymore. As soon as the new version released, UGENE will ask your permission to update and with your consent the program will be updated automatically.
  • Performance:
  • Opening of large Genbank files was improved.
  • The visualisation of restriction sites was improved.
  • Minor interface improvements and bug fixes.

New in Unipro UGENE 1.22.0 (Apr 6, 2016)

  • MAJOR CHANGES:
  • In silico PCR:
  • Degenerate primers were supported.
  • Sequence View:
  • Annotations editing was improved.
  • Configuration of translation frames visibility was simplified.
  • NGS:
  • Extracting of an assembly region in BAM/SAM/UGENE database formats was supported.

New in Unipro UGENE 1.21.0 (Feb 17, 2016)

  • One of the improvements worth mentioning is enhancement of the clipboard support in the Sequence View and the Alignment Editor.

New in Unipro UGENE 1.20.0 (Feb 17, 2016)

  • Multi-line Sequence View: A new mode for wrapping sequences in the Details View was added.
  • Multiple Alignment: Replacing of characters was added. Click Shift+R on a character to enter the replacement mode, input another character.
  • Proteins: Loading of chain names from PDB files was corrected.
  • Usability: Inversion of annotations selections was improved.
  • Distributed Annotation System (DAS) features were removed, as DAS services are going to retire at the end of the year.
  • Windows XP support was restored.

New in Unipro UGENE 1.19.0 (Nov 3, 2015)

  • Major changes in this release include:
  • Usability: Pasting of data into UGENE was further improved. In particular, you can now paste file using its URL (see video below).
  • Sequence View: Visibility of the Sequence View subviews (Overview, Zoom View, Details View) can be configured using new buttons on the Sequence View toolbar.
  • Multiple Alignments: A region of an alignment can now be copied in the RichText (HTML) format.
  • Phylogeny: The Build Phylogenetic Tree dialog interface was improved.
  • NGS: Setting of a reference for an assembly became much easier.
  • NGS: The SPAdes de novo assembler was updated to 3.6.0 version.
  • NGS: Partially valid BED files can now be opened. A warning notification is shown for lines that can’t be parsed.
  • Workflows Automation: The Multiplexer workflow element was simplified. Check out its documentation.
  • UGENE appearance on HiDPI displays was improved.
  • Chinese and Czech languages are no more supported since this UGENE version.

New in Unipro UGENE 1.18.0 (Sep 22, 2015)

  • Important changes in this major release include:
  • Usability: Ctrl+V in the Project View was supported.
  • For example, if you have a sequence in the FASTA format, opened in a text editor, try to:
  • Select the text of the sequence. Press Ctrl+C.
  • Open UGENE and activate the Project View. Press Ctrl+V.
  • You should see that a new document has been created with the corresponding data.
  • Note that this feature is supported for other formats as well.
  • In silico PCR: a possibility to include annotations to the extracted PCR product was added.
  • Sequence View: exporting of a sequence image was improved. It is now possible to export the Details View and the Zoom View separately in different formats, including SVG.
  • NGS: partially valid VCF files can now be opened. A warning notification is shown for lines that can’t be parsed.
  • Usability: some buttons from a toolbar of the Sequence View were moved to the left toolbars of the sequence sub-views: Zoom View, Details View, etc.
  • Usability: a new icon for a circular sequence was added to the Project View.
  • When you work with a circular sequence, don’t forget to check “Mark as circular” in the Project View. In this case all algorithms in the Sequence View will take into account that the sequence is circular.
  • Optimizations of big data processing in UGENE.

New in Unipro UGENE 1.17.0 (Jul 10, 2015)

  • SEQUENCE VIEW:
  • recalculation of regions in qualifiers after sequence editing
  • ALIGNMENT EDITOR:
  • Aligning of sequences to an existent alignment
  • Exporting of multiple alignments to SVG format
  • Copying of an alignment region in a chosen format (Ctrl+Shift+C)
  • New workflow: In silico PCR
  • New workflow: Searching for annotations intersections
  • Usability: options panel resizing

New in Unipro UGENE 1.16.1 (Mar 24, 2015)

  • This is a patch release that contains several major bug fixes and minor interface improvements requested by users

New in Unipro UGENE 1.16.0 (Feb 21, 2015)

  • Important changes in this major release include:
  • Advanced and comfortable search in a project
  • Usability:
  • Sequence Viewer resizing
  • Regrouping of the Tools menu items
  • Workflow Designer: generating of output file names
  • Sanger reads quality control and alignment
  • NGS:
  • Reads quality control with FastQC
  • Variations annotation with SnpEff
  • Alignment Viewer: conservation level highlighting
  • Vector NTI sequence format

New in Unipro UGENE 1.15.1 (Dec 29, 2014)

  • This is a patch release that contains several major bug fixes and minor interface improvements requested by users:
  • Bug UGENE-3900: Disappeared selection in chromatogram view
  • Bug UGENE-3896: Several small problems with Project View
  • Bug UGENE-3894: Problem opening trees created from some alignments
  • Bug UGENE-3886: Extract MSA consensus wizard crash
  • Improvement UGENE-3868: Vector NTI GenBank format: support labels
  • Sub-task UGENE-3850: UGENE-3841 SAFE_POINT triggers on creating annotations from find results loaded from file
  • Bug UGENE-3835: Circular view draw huge annotations incorrectly
  • Bug UGENE-3834: Annotations that intersect a junction point are drown over each other in Circular View
  • Bug UGENE-3833: Relations are broken when sequence is renamed
  • Bug UGENE-3829: DAS annotating crash
  • Bug UGENE-3824: BWA-MEM status on Windows is not clear
  • Bug UGENE-3823: Verify tests for raw NGS worfklow samples
  • Bug UGENE-3822: Shared database can not be initialized
  • Bug UGENE-3821: Error message in Primer3 search should contain more information
  • Bug UGENE-3819: Reads for assembly in a shared database are not drawn
  • Improvement UGENE-3818: Common wizard of the raw RNA-seq data processing workflow sample
  • Bug UGENE-3817: The "Region" combobox switches incorrectly in the Find Pattern OP tab
  • Bug UGENE-3816: UGENE fails on a phy tree file opening
  • Bug UGENE-3815: SAFE_POINT on a short sequence translation export
  • Bug UGENE-3813: UGENE crashes on auto-annotating
  • Bug UGENE-3812: UGENE crashes on setting new sequence origin
  • Bug UGENE-3809: UGENE crashes on opening chromatogram
  • Improvement UGENE-3805: Creating reverse and complement sequence in the Sequence View
  • Bug UGENE-3788: Incorrect annotation handling on the sequence crop
  • Bug UGENE-3780: Selection marks unexpectedly disappear on the Chromatogram view
  • Bug UGENE-3779: Zoom in assembly view works incorrectly
  • Bug UGENE-3778: Circular view cannot be exported as image
  • Bug UGENE-3767: Fix tab order on the Find Pattern widget
  • Bug UGENE-3762: "Delete selected annotations" action works wrong
  • Bug UGENE-3757: UGENE crashes on opening PDB
  • Bug UGENE-3753: Renaming of objects exported from the DB hangs UGENE
  • Bug UGENE-3749: Incorrect right click processing in MSA Editor
  • Bug UGENE-3738: CAP3 result file cannot be opened in Assembly Browser
  • Sub-task UGENE-3736: UGENE-3841 Find pattern with regexp doesn't allow to find patterns like "A{4,6}"
  • Bug UGENE-3733: files in .ace format are not imported to database
  • Improvement UGENE-3728: Fix shared object order in the Project View
  • Bug UGENE-3718: Tophat: wrong Bowtie path is detected
  • Bug UGENE-3669: Some cistrome and tuxedo tools throw errors
  • Bug UGENE-3668: Bad layout in cistrome wizard
  • Bug UGENE-3643: Wrong behavior of database tree selector
  • Improvement UGENE-3618: Find patter widget: "Use pattern name" option change shouldn't run a new find task
  • Bug UGENE-3459: Descriptions and versions of external tools
  • Improvement UGENE-3449: Add "Edit annotation" item to menus
  • Improvement UGENE-3390: Annotation regions order unification
  • Bug UGENE-3359: Peaks on a chromatogram are shifted
  • Bug UGENE-3342: Dotplot view can't be closed
  • Improvement UGENE-3221: Limit 15 bases for length of pattern name
  • New Feature UGENE-2938: Drag'n'drop documents
  • Improvement UGENE-2633: Copy/paste in Crash Reporter window
  • Bug UGENE-2510: Fix the MAFFT task progress
  • Improvement UGENE-2004: External tools settings should be saved on the preferences closing.
  • Improvement UGENE-1505: Get sequence by annotation: add region in source sequence in result names

New in Unipro UGENE 1.15.0 (Dec 2, 2014)

  • Important changes in this major release include:
  • Quick search in a sequence without creation of annotations
  • PCR in silico
  • NGS:
  • Spades de novo assembler
  • Export of a short reads assembly coverage
  • Raw NGS filtering workflow samples
  • Circular View and circular sequences:
  • Support of all algorithms for circular sequences: ORF, restriction sites, BLAST, etc.
  • Circular View visualisation settings
  • Shared database:
  • Support of shared databases in the UGENE Workflow Designer
  • Usability improvements:
  • Welcome page:
  • Remembering of Options Panel setting within one

New in Unipro UGENE 1.14.1 (Sep 10, 2014)

  • This is patch release that contains several major bug fixes and minor interface improvements requested by users

New in Unipro UGENE 1.14.0 (Aug 1, 2014)

  • Important changes in this major release include:
  • Help system:
  • Help buttons were added into all UGENE dialogs.
  • The documentation was moved to the Atlassian Confluence system, this makes it easier to search for required information in it.
  • Shared storage: sharing of bioinformatics data in a lab. For details, see this page.
  • Alignment Editor:
  • Overview for a multiple alignment was added, a lot of configuration options are available.
  • A multiple alignment consensus can now be exported.
  • Phylogenetic Trees:
  • PhyML Maximum Likelihood was integrated.
  • It is now possible to re-root a tree.
  • Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
  • Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
  • Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)
  • NGS:
  • BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
  • Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
  • UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
  • A splash screen was added on the UGENE startup.

New in Unipro UGENE 1.13.0 (Dec 12, 2013)

  • DAS: you can now annotate an unknown amino acid sequence using annotations of its homologs. First, you search for homologs using the Uniprot BLAST. Second, you load the annotations of the selected homologs to your sequence using the Distributed Annotation System (DAS).
  • NCBI Genbank search interface: search for DNA and protein sequences in the GenBank database directly from UGENE.
  • Bowtie2: use sequencing reads aligner "Bowtie2" from UGENE GUI.
  • Codon table: a new help view "Codon table" was added into the Sequence View. Click "Ctrl+T" to open it there.
  • Multiple Alignment Format: a new format PHYLIP is now supported.
  • Assembly Format: ACE format is now opened in the Assembly Browser.
  • NGS pipelines: "Call variant with SAMtools" pipeline was optimized.
  • Workflow Designer:
  • Usage of a common workflow output directory
  • Storing history of a workflow execution (in dashboards)
  • Managing of different workflows output
  • Re-running of a workflow from a dashboard
  • Debugging of a workflow execution and investigation of an intermediate data state.
  • "Workflow schemas" were renamed to "workflows"

New in Unipro UGENE 1.12.3 (Oct 9, 2013)

  • Task:
  • MrBayes needs preinstalled libraries on Mac
  • Update QT to 4.8.x on Linux and check windows DLLs
  • Return removed external tools
  • fix genome aligner test suite
  • Update mafft on test server
  • Reconfigure build process of full packages.
  • Improvement:
  • Fix determination of VCF format
  • Make "Backspace" remove smaller gap regions
  • ClustalO for nucleotide sequences
  • Tuxedo validation: no "accepted_hits" output of TopHat
  • Bug:
  • Scribbling does not work when selection includes alignment start
  • Change hint style in "Fetch Data from Remote Database" dialog
  • Fix t_coffee start script.
  • src/muscle/muscle_context.cpp:558: bad call to memset
  • Fix "Create Annotation Widget" appearence
  • Bug UGENE-2188 Assert is triggered on reloading a file containing sequence(s)
  • Find tandems finds wrong results
  • Crash on shifting in MSA Editor
  • Opening certain files causes UGENE crash.
  • Muscle worker triggers assert on subtask canceling
  • Try to reproduce crash on UGENE startup
  • UGENE crashes while exporting assembly to SAM file
  • If an msa contains both amino and DNA sequences, the msa alphabet should be amino
  • "Can't find a row in alignment" error when a sequence name contains space character(' ')
  • Some visual noise is in the color scheme dialog on Mac
  • Fix scribbling mode in MSA
  • Incorrect starting selection motion
  • MSA: Custom color schemes menu item dissapears
  • Color Scheme dialog layout
  • Crash when create MSA file with bigs size.
  • No plugins folder in zip snapshot builds
  • Wrong format of statistical report
  • Loading scheme button on dashboard doesn't work
  • Incorrect result of the current sequence deleting in MSA Editor.
  • Incorrect behavior of MSA Editor with one-lined msa.
  • Selection in MSA doesn't move when backspace is pressed
  • Incorrect layout of the "ORF marker" dialog on Mac
  • Incorrect reference sequence selection behavior in MSA Editor
  • Incorrect behavior of selection with an empty line in it in the MSA Editor
  • WD: fix remote blast worker with cdd bases
  • Progress management in MAFFT alignment task is incorrect.
  • REBASE Info url is out of date in find restriction sites dialog
  • WD Elements such as "Write sequence" have incorrect output document formats
  • Task waits for memory resource which will never be released instead of fail task run
  • UGENE cmdline: update schemes and parameters
  • Incorrect MAFFT task progress
  • no-return-in-nonvoid-function in U2AbstractDbi.h
  • BioStruct3D bug: Ball-and-Stick render style doesn't work

New in Unipro UGENE 1.12.2 (Aug 20, 2013)

  • Set in tracker that new version released.
  • FindSingleEnzymeTask operating with sequence chunks works incorrect
  • Excess warning message when editing substring
  • Fix export highligtning in MSA editor
  • Enzymes task gets whole sequence from db
  • Configure Teamcity precommit suits not to trigger build when updated only scenarios folder
  • Focus is not cleared from ADVSequence widget when you click on project tree view
  • Add export highligtning in MSA editor
  • Create workflow schema by user request
  • There is no validation for cistrome tools
  • Switch off the cistrome validation on the UGENE start.
  • Not enought checks in export consensus task
  • Change the Teamcity build agent settings for the hot-fix snapshot build
  • CUDA validation tasks error durins the first UGENE start
  • Del key does not work in the overview
  • UGENE triggers assert
  • Set up external tools on Win7-i7 machine for testing
  • Elements on the edge of the dotplot are not shown in the maximum zoom.
  • "Remove columns of gaps" dialog appearance
  • WD: cannot change resolution of an image to be exported
  • Problems when getting access to remote database
  • Dotplot: code refactoring
  • Save annotations names when use "Align" action in Sequence View
  • Failure when building genome aligner index with UGENE

New in Unipro UGENE 1.12.1 (Jul 12, 2013)

  • Several major bug fixes and minor interface improvements requested by users

New in Unipro UGENE 1.12.0 (Jun 22, 2013)

  • Search TFBS with matrices algorithm creates invalid annotation qualifiers
  • Assertion fails after selecting region in sequence graphs
  • Progress for "Generete distance matrix" task is incorrect
  • Errors during UGENE installation and uninstallation on Windows
  • Call Variants pipeline cannot be stoped on big files
  • Linux 64bit full package snapshot does not work
  • Identity columns in MSA shows incorrect data
  • Graphs in sequence viewer work slow
  • MACS and seqpos output
  • Memory leak during logging
  • When external tool pack path is selected in settings not all the tools are found
  • MacOS: temporary switch off running workflows in separate process
  • Error when loading a remote document but the document is in the project
  • Workflow sample wizards
  • Crash on simultaneous loading many files in UGENE
  • Access remote database window resize
  • UGENE crashes when trying to open Geneious application.lock
  • Crash during clicking undo in msa
  • Crash on selecting python external tool
  • Worfklow Designer dashboard
  • TaskScheduler must try to lock resources without blocking calls
  • ugeneui fails to link
  • Improve WD validation messages
  • Undo after align 'eats' sequences
  • Solve 'disk space' problem on test servers
  • Trace to log UGENE memory usage to be able to have that information in crash reports
  • UGENE cannot save/read Pfam annotations
  • AppResource needs to be thread-safe
  • Crash on x32 because of BioStruct3DPlugin memory leak
  • Crash on loading large FASTQ file containing short reads on x32
  • WD crashes when using pipelines
  • Last saved value of the consensus threshold is incorrect
  • Crash on loading large FASTA file containing short reads on x32
  • MSA Editor: reference hint
  • Assert stop triggered during shifting the selected region in a msa.
  • Support Tuxedo simplified pipelines
  • Shift+arrows selection doesn't work in the name list of the MSA Editor.
  • Paired reads in wizards
  • Genome Aligner binary find optimization and refactoring
  • Only one tab at a time on the Options Panel
  • Incorrect result of distance algorithm
  • MSAEditor: double enter for sequence choose widget
  • MSAEditor: capital letters for sequence choose widget
  • MSAEditor: text alignment of sequence choose widget
  • MSA Editor: save chosen sequences for PWA
  • GTFFormat: file with multiple sequence ids are not recognized
  • Undo for renaming sequence works wrong
  • Crash during modifying an msa selection with a keyboard.
  • Shift+arrow shifts selection on Mac.
  • TopHat: one run for one dataset when input files are used
  • German Grekhov German Grekhov Major Tested Tested Fixed 16/May/13 05/Jun/13

New in Unipro UGENE 1.11.3 (Jun 22, 2013)

  • Find Pattern: stack overflow when remove a symbol from sequence in FASTA input
  • FindPattern allow using sequence names as annotation names when FASTA format is provided
  • Find Pattern: search button is not disabled if there are errors in parameters
  • Find Pattern. No validation on annotation creation
  • Find Pattern: cannot rename annotation/annotation group sometimes
  • WD: bind all avaiable incoming slots to the destination slot
  • Investigate the problem of schemas with a script
  • Change behaviour of "Find restrictions sites" for enzymes with unknown sequence field
  • Thresholds of Align short reads dialog are too tight
  • Export 3 translated frames function has artifucts
  • Annotation Selection. Shift+Ctrl modifiers
  • DNA statistics error: negative Molar ext. coef.
  • Renamed sequences keep old names when exported as multiple alignment
  • Replace UWL header
  • Circular molecules are not saved properly
  • Edit sequence usability and shortcuts
  • UGENE crashes on repeated find pattern launch
  • Crash when selecting sequence regions on UGENE 1.11.2
  • WD: samples preview shows wrong schema
  • UGENE hangs up/crashes on region selection (Linux only)
  • Crash while reading FASTQ
  • "Entrez Query" option for the remote BLAST
  • Wrong cuts from enzymes with blunt ends
  • Ugene crashes on displaying options panel in assembly browser
  • Support multiple patterns in Find Patterns
  • UGENE-1139 PhyTreeObject::clone() - PhyTree has not a copy constructor
  • UGENE doesn't detect when a file from the opened project is deleted
  • WD: minimal style setting does not work
  • A gff file with blank lines in the middle crashes UGENE
  • Add 64/32-bit info to Ugene version
  • OpenCL Binary Search: Division by zero
  • Bad deserialization of database attribute of fetch-sequence worker
  • Scheme with remote BLAST + marker + filter fails
  • Import BAM destination dir
  • "Save Schema" button works incorrectly in the QD
  • New document from text url bug
  • Set focus to the search pattern field and listen to Enter
  • Ghost slider on scrollbars in PanView without zoom

New in Unipro UGENE 1.11.2 (Oct 6, 2012)

  • Enlarge the maximum number of hits for remote BLAST results
  • Genome aligner dead lock
  • Crash on removing the PDB document in the debug mode
  • Correct physical memory size info for Win, Linux
  • Genome aligner don't work if run from command-line (ugenecl)
  • Genome aligner: "memory leak" in OpenCL mode
  • Genome aligner: use GPU optimization checkbox enabled if no gpus are enabled in the settings
  • Genome aligner: memory leak after "build index only" mode finished or cancelled
  • Crash on aligning with Genome Aligner
  • Crash on aligning with Genome Aligner when the first big part of reference sequence contains N's only
  • Crash handler: send report win x64 information
  • Crash on aligning with Genome Aligner
  • WD: after copying element, copy parameters different
  • Crash if wrong bowtie tool path used while starting bowtie aligning
  • Problem displaying consensus in the Assembly Browser
  • GFF file is not visualized right
  • Ugene crashes on T-Coffee alignment start
  • Ugene crashes on removing sequence from alignment editor
  • Ugene crashes on unloading file *.ugenedb from assembly browser
  • Notification about failed task appears after canceling document loading
  • Problems with writing gff file with a sequence.
  • Collocalion search worker: save original annotations
  • Digest Into Fragments: add missing option
  • WD: wrong output path fails UGENE
  • Genome aligner wrong statistics
  • Find Pattern: load patterns from a file
  • Improve "Save a copy" functionality to "Export document"
  • U2SequenceObject::clone() - not all sequence attributes are copied
  • Russian translation does not work on Linux
  • Create the task for "Save a copy"
  • Review: GObject::clone()
  • AssemblyObject error

New in Unipro UGENE 1.11.1 (Aug 18, 2012)

  • UGENE crashes on document unloading
  • Crash on closing a project with MSA
  • Showing sequence from BLAST database for BLAST results
  • "QObject: Cannot create children for a parent that is in a different thread" errors in log when running tests
  • UGENE-1060 WD Samples: "Convert UQL schema results to alignment" sample does not work
  • UGENE-1060 WD samples: Temporary exclude "Create alignment" sample
  • UGENE-1060 WD Samples: Quality filter scheme crashes
  • Genome Aligner: strange error
  • UGENE-1060 Samples with groupers do not work
  • UGENE-1060 Samples with filters do not work
  • UGENE-1060 Script samples do not work
  • Convert to SAM crash while import is not finished
  • UGENE-1060 Query Designer Worker: orf finder crash
  • UGENE Genome Aligner doesn't work with GPU optimization
  • crash on deleting dna sequence
  • Cannot open a FASTA file (Ubuntu 12.04)
  • Temporary switch off remote run of WD schemes
  • Search elements in WD usability improvements
  • Create a "Read Annotations" workflow element
  • Errors in log during opening an assembly
  • UGENE crashes when an annotation is edited
  • Dotplot crash while navigating using minimap on max zoom in
  • Type "D" of optional field while reading a BAM file
  • Text Qualifier Marker fales UGENE
  • WD: duplicated Smith-Waterman elements remain linked when modifying the content
  • Delete ugene.ini file option
  • Memory limit in 64-bit version
  • UGENE hangs up/crashes while deleting auto-annotations
  • Auto-annotation update task is not canceled when view is already closed
  • Save any file to tmp file first, then rename
  • Export project fails when contains repeated names
  • Converting to amino doesn't work when performing multiple alignment
  • T-Coffee doen't work
  • WD: Converting Huge FASTQ
  • KAlign can't align COI.aln from samples
  • Problems with Find Pattern tool
  • Dotplot crash when deleting sequence from project tree view
  • Crash on UGENE close after double dotplot creation
  • Revise multiple alignment similarity/dissimilarity measure
  • Dotplot crash
  • Dotplot: wrong dotplot
  • Bad "Go To" dialog in the MSA Editor
  • "Custom elements with scripts" do not have scripts
  • UGENE hangs on "Auto-annotations update task"
  • Dotplot crash
  • Secondary structure prediction: algorithms use different reporting for small regions
  • Create document from text: replacement symbol is not checked
  • WD schemes work slowly when they are run in separate process
  • Incorrect "Undo" behavior when a sub-alignment is dragged and dropped
  • Artifact on changing a qualifier of an annotation

New in Unipro UGENE 1.9.4 (Jul 13, 2011)

  • Fixed reported crashes with ORF auto-annotations
  • Assembly Browser: better & faster coverage
  • Integrated new tool: CAP3
  • New plugin: DNA flexibility

New in Unipro UGENE 1.9.0 (Jan 25, 2011)

  • Cloning in silico: digest into fragments
  • Cloning in silico: construct molecule
  • Query Designer tool introduced
  • External tool support: BLAST+
  • External tool support: TCoffee
  • OpenCL support added on Linux and Windows
  • Logging system improvements
  • Popup notification system added
  • Fixed several "Export from annotation features"
  • "Fetch by ID from Annotation" feature added
  • Fixed sequence viewer behavior
  • Improved circular sequence detection
  • "Replace sequence" feature added
  • MSAEditor: export to aminoacids
  • MSAEditor: reverse-complement sequence
  • Genome Aligner: save index in external file
  • Workflow editor: new human-readable schema format
  • Dotplot plugin: zooming options added
  • Dotplot plugin: selection improvements
  • Crash handler improvements
  • Project view: active document is highlighted
  • Fixed 3'-5' annotations export
  • Fixed BLAST annotation result reporting
  • Fixed external tools managment issues
  • and much more bugfixes...

New in Unipro UGENE 1.8.0 (Oct 22, 2010)

  • New features & plugins:
  • Support for external Blast: build and search
  • New format is supported: MEGA
  • New improved plugin system
  • Support for large (over 1 GB) files analisys in DNA Assembly
  • Improvements:
  • Crash handler is improved: now you can send us report is something unexpected happend
  • Command line interface improvements: comprehensive help-system and verbose error diagnostics
  • Editing script workers in workflow designer
  • Deleting and hiding script workers
  • Drag and drop from Project View
  • Task report in Primer 3
  • Application supressed exit
  • Disabiling unused ports in Workflow Designer
  • Bugfixes:
  • Fixed crash when calculating surface for large proteins
  • Workflow designer fixes in GUI and usability
  • Fixed crash while opening project
  • Fixed crash with alignments consisting only of gaps
  • Fixed crash with MUSCLE region alignment
  • Fixed data formats: srfasta, sam
  • Multiple designer workers fixed
  • Remote tasks in Muscle and HMM are converted to Workflow schemas

New in Unipro UGENE 1.7.2 (Aug 25, 2010)

  • New features & plugins:
  • New plugin: cloud support. Running computational workflow on Amazon EC2;
  • New plugin: external tool support. Multiple alignment with Mafft and clustal;
  • New format supported: Nexus (read & write)
  • Advanced scripting capabilities in Workflow Designer;
  • Minor improvements:
  • Added capability to change name of sequence and set name when creating new sequence from text
  • Added capability to cancel the insertion of workflow sample
  • Items "Lock document for editing" and "Unlock document for editing" are not shown for documents wich can't be changed
  • Documents with unknown type (i.e. workflow schema) are not loaded in project
  • If during loading of document error occures, document is deleted from project
  • Added capability to export sequence with annotations
  • Added capability to open several files
  • Added capability to remove columns with certain amount of gaps(absolute or relative) in alignment editor
  • When annotations are imported from CSV file, they are automatically added to active sequence view (if possible)
  • When creating connection between blocks in workflow, to port by default added data from nearest block
  • Automatic creation of the new project before the construction of the new Dotplot
  • Added feature to search inverted repeats, search simultaneously both types of repeats
  • Added feature "Lock dotplots" for simultaneous viewing several dotplots built on the same sequences
  • Synchronization with PanViews of the sequences
  • Bugfixes:
  • Annotations highlight enable/disabled fixed
  • Incorrect sequence reading in Find repeats in Workflow
  • Issue with saving a copy of document
  • Crash when deleting three ot more documents from project
  • Incorrect search in Alignment Editor
  • Crash when opening incorrect file to build HMM2 profile
  • Issue with creating new annotation when selected nonexistent document for storage of annotations
  • Bug when call --help for nonexistent parameter in command line
  • Reading alignment file with non-alignment extention for build weight matrix
  • Incorrect removing of region in alignment
  • Incorrect offset values in alignment editor
  • Issue with reading alignment with gaps in SAM format
  • Incorrect adding gaps to alignment
  • Counter for annotations in annotation group
  • Wrong behavior of "zoom to range"
  • Toolbar disappearance after removal of the document
  • Creation of cyclic schemas in workflow designer
  • Fixed a bug related to incorrect positioning of the cursor
  • Crash after deleting sequences from the project with opened circular view bug fixed
  • Crash after selecting sequences in the locked mode with builded circular view
  • Resizing circular view bug fixed
  • Hidden sequence view bug fixed
  • Exporting circular view as image bug fixed
  • Anaglyph view option is disabled if the rendering device doesn’t support it.

New in Unipro UGENE 1.7.1 (Jul 12, 2010)

  • New features & plugins:
  • Dot plot view: effective sequence visual comparison method;
  • SAM format support and PHRED quality scores import;
  • Advanced chromatogram analysis. Find out details in the tutorial;
  • BowTie assembly options integration, new modes for UGENE Genome Aligner. Now available from Workflow Designer!
  • Weight matrix based analisys improvements;
  • New Workflow Designer samples and built-in command line schemas;
  • Circular view: support for annotations with virtual gap.

New in Unipro UGENE 1.7.0 (May 20, 2010)

  • Major renaming: congene -> ugene, ugene -> ugeneui
  • New plugin: genome aligner;
  • New plugin: bowtie;
  • Dna assembly to reference functionality added;
  • Poistion-weight matrix advanced support added;
  • MSAEditor: new zooming mode added;
  • Circular view improved.
  • Overview added to Sequence View;
  • Integration with JASPAR and UniProbe.
  • Alignment logo added.
  • Command line interface improved.
  • Command line version Workflow designer support added.
  • Remote request re-worked.
  • Scripting framework introduced in CSV import.
  • Tree viewer re-worked, new modes added.

New in Unipro UGENE 1.6.2 (Mar 30, 2010)

  • New plugin: sequence circular view;
  • Workflow designer: support for launching tasks remotely;
  • MSA Editor: consensus mode added, usability improvements;
  • Phylogenetic tree viewer: zooming, normalization, export to SVG;
  • Export plugin: reverse protein translation;
  • Support for import annotation tables from CSV files;
  • Enzymes plugin: support for creation of custom enzyme databases in BAIROCH format;