Softpedia >Windows >Portable Software >Education >Portable UGENE >  Changelog

Portable UGENE Changelog

What's new in Portable 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 Portable UGENE 49.1 (Nov 26, 2023)

  • Fix crash in genome aligner UI.

New in Portable 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 Portable 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.
  • Many small issues related to the usability and stability of UGENE on all platforms have been fixed.

New in Portable UGENE 47.0 (May 21, 2023)

  • 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.

New in Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable UGENE 41.0 (Dec 3, 2021)

  • 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.
  • Version 40.1

New in Portable UGENE 40.1 (Oct 12, 2021)

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

New in Portable 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 Portable UGENE 1.33.0 (Sep 22, 2020)

  • Import of your tool into UGENE external tools: the list of external tools is available in the UGENE Application Settings dialog. Here for each tool you can provide a path to the tool executable file. Since UGENE version 33 you can also specify your own tools. See documentation for details.
  • Enhanced wizard for creating a workflow element for the tool: to use a custom tool in the UGENE Workflow Designer graphical interface, create a workflow element that specifies the tool input/output, parameters, and the command. To start the wizard click ['Create element with external tool' button on the WD toolbar] on the WD toolbar. See details here. [The first page of the 'Configure Element with External Tool' wizard]
  • Tighter integration with the WD dashboard: a file or a folder, produced by a parameter of type “Output file URL” or “Output folder URL”, automatically appears on the dashboard. [Result on the WD dashboard]
  • Another improvement in UGENE version 33 is a new color scheme “Percentage Identity (colored)” in the Alignment Editor, see description in the documentation.

New in Portable UGENE 1.32.0 (Sep 30, 2019)

  • The new version introduces a bunch of improvements for adding a custom tool into UGENE, in particular:
  • Import of your tool into UGENE external tools: the list of external tools is available in the UGENE Application Settings dialog. Here for each tool you can provide a path to the tool executable file. Since UGENE version 33 you can also specify your own tools. See documentation for details.
  • Enhanced wizard for creating a workflow element for the tool: to use a custom tool in the UGENE Workflow Designer graphical interface, create a workflow element that specifies the tool input/output, parameters, and the command. To start the wizard click ['Create element with external tool' button on the WD toolbar] on the WD toolbar
  • Tighter integration with the WD dashboard: a file or a folder, produced by a parameter of type “Output file URL” or “Output folder URL”, automatically appears on the dashboard.

New in Portable 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 Portable UGENE 1.31.1 (Oct 17, 2018)

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

New in Portable UGENE 1.31.0 (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 Portable UGENE 1.30.0 (Aug 17, 2018)

  • The new version is majorly a bug-fix release.
  • However, an approach for selection in the Sequence View was also modified. Selection of an annotation was detached from selection of a sequence region. Thus, one mouse click on an annotation selects the annotation only. To select both the annotation and the corresponding sequence region double-click on the annotation.
  • The selection appearance was also improved

New in Portable UGENE 1.29.0 (Dec 30, 2017)

  • A new mode for a sequence editing appeared in the Sequence View. To switch on the editing mode click the Edit sequence button on the left toolbar of the Details View. Settings for handling the corresponding annotations are available through Actions – > Edit – > Annotations settings on sequence editing item in the main menu.
  • Editing in the Sequence View
  • A new mode for amino acid translations visualization in the Sequence View.
  • Translating selected region of a nucleotide sequence
  • Handy resizing of a selected region in the Sequence View and the Alignment Editor
  • Resizing of an alignment region
  • The default appearance of a sequence in the Details View has changed: translation frames are hidden.
  • Possibility to decrease the Detail View vertical size has been added.
  • Highlighting of the extended alphabet characters in the Sanger Reads Editor has been corrected.
  • Other bug fixes.

New in Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable UGENE 1.25.0 (Feb 9, 2017)

  • 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 Portable UGENE 1.24.1 (Aug 22, 2016)

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

New in Portable 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 Portable UGENE 1.23.1 (Jul 8, 2016)

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

New in Portable 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 Portable 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 Portable 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 Portable UGENE 1.20.0 (Feb 17, 2016)

  • Major changes in this release include:
  • 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 Portable UGENE 1.19.0 (Nov 3, 2015)

  • 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 Portable 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 Portable UGENE 1.17.0 (Jul 9, 2015)

  • Fixed:
  • Undo action becomes disabled after exporting an msa to SVG
  • Crash: export of a big alignment to SVG
  • UGENE crashes on undo changes for large alignment
  • Overview is not recalculated when alignment is edited with mouse
  • DAS Search OP tab layout is broken
  • Label text is empty in the "Weight Matrix Search" dialog
  • Assert on HMM dialog opening
  • Incorrect UGENE version in crash report
  • ORIGDB comment in Vector NTI sequence format is not parsed properly
  • Concurrent work with assemblies is impossible in Shared DB
  • Align sequences to an existing alignment not working some times
  • Shorten long file names in the recent files list
  • The "View matrix" dialog has incorrect constraints
  • Two typos in the crash handler
  • The "Help" button is in focus in the "Primer Designer" dialog
  • Annotation name can be cut in Circular View
  • Crash on the subsequence removing while a restriction site is selected in a circular view
  • Remove "Assembly Information" toolbar button and the dialog
  • UGENE crashes on shutdown cancellation
  • UGENE isn't restarted after crash
  • UGENE crashes on copying sequence to clipboard
  • Crash on short reads alignment on cancelling on 40%
  • PhyML tree building hangs for large alignments
  • PCR In Silico workflow trims result sequence
  • Fix several bugs in align sequences to an existing alignment
  • Crash on remove loading file
  • UGENE crashes on deleting MSA with active task
  • Auto-annotations cannot be removed
  • UGENE can't process very long qualifiers
  • Missed scrollbar in the Circular View
  • Objects shown in AB aren't highlighted in Project view
  • Crash on a creation of a custom cmdline element in WD
  • BWA index algorithm setter works wrong
  • Read-write annotations in WD
  • Search qualifier works incorrectly
  • Wrong position of restriction site arrows
  • Problems with opening specific .fa file
  • Assert on workflow run
  • Errors in log when running SnpEff
  • FreeBSD build problems
  • Bad performance for opening bed files
  • Annotation comments are displayed incorrectly
  • Find Pattern Widget: wrong annotation names
  • UGENE crashes on closing when "Import SAM" task is active
  • Optimize UGENE for opening GenBank files with ~1 million annotations
  • snpEff does not work when input file path contains spaces
  • Wrong folder order in shared DB
  • UGENE fails on safe point when deleting object
  • UGENE crashes in Query Designer
  • MSA simple overview: conservation level highlighting
  • Wrong scroll for sequence zoom view
  • Wrong association between sequence and annotation
  • BWA: UGENE does not check external tool availability
  • Incorrect layout in the Options panel Statistics tab
  • Unexpected new window shows up in MSA editor
  • Wrong names highlighting when tree view is shown with msa
  • Incorrect focus policy in consensus area
  • Annotation names from search pattern results can't contain some symbols
  • UGENE crashes on finding ORFs
  • Export primers: raw sequence format error
  • Import primers: not ACGT sequence
  • Import primers from database error
  • Import primers dialog errors
  • Error during importing assembly to a shared DB
  • Relation is lost between local sequence object and shared annotations
  • Correct misprint in the format name
  • Sequence view isn't updated after number of strands has changed
  • MSA Editor doesn't allow to select sequences that are not visible
  • Marker + filter worker elements work incorrectly
  • Can't find "reset settings" in the documentation
  • Annotation objects are imported incorrectly to a shared DB
  • Back slashes are used as word separators in qualifier values
  • Incorrect writing of the comment section in Vector NTI sequence format
  • Incorrect exporting sequences as alignment
  • Sequence reverse transformation doesn't work
  • "Add object to selected document" action copies the object in the main thread
  • Wrong annotation coordinates on the Zoom View
  • The first created annotation item in the group is duplicated
  • No space for upper labels on the Circular View
  • Correct labels on the "Annotations Highlighting" tab
  • Inactive scrollbars are always visible in MSA
  • Documents without objects can cause crashes
  • BAM importer ignores prebuilt index in some cases
  • "Delete" key doesn't work in the Query Designer
  • SAFE_POINT on opening text document
  • UGENE crashes on rendering overview
  • Broken dashboard
  • Active wizard button without an opened sample
  • Unnecessary 'note' qualifier in new annotation
  • SAFE_POINT on auto-annotations search auto-launch
  • No "Preferences" in the Russian UGENE localization
  • New annotation dialog: wrong line edit state
  • UGENE fails on safe point when opening some .uwl files
  • UGENE crashes on insertion sequence into "Create document" dialog
  • Can't see name column of input data in the WD
  • Exporting consensus hangs on removing document
  • SAFE_POINT triggers on reloading file with annotaitons
  • SAFE_POINT in Chromotogram view
  • Default file name in "Export Image" dialog can contain illegal characters
  • "Rename item" action has different behavior on linux and windows
  • Crash on short reads alignment
  • GFF files without a header
  • Document can not be unloaded in some cases
  • Annotations removing can hang GUI for some time
  • Bowtie2 test fails
  • Unexpected text in the MSA clipboard
  • Incorrect selection frame style in MSA Editor
  • UGENE opens only one sequence from .fa.gz
  • MSA Editor pattern search works wrong
  • HMM3 throws an unexpected error notification
  • Widgets do not fit in Options Panel
  • Some PDB files can not be recongized
  • UGENE crashes on opening short reads in sequence view
  • Failed to open BAM file
  • Warn a user when an assembly file is removed from file system
  • A big scheme with groupers/multiplexers crashes
  • The sequence view scroll bar is broken
  • New/improved new features:
  • Create "Intersect annotations" WD element
  • Downloading big UGENE packages
  • "Check primer pairs" workflow element
  • Export alignment to the clipboard in selected format
  • Recalculate regions in qualifiers when sequence is modified
  • Improved:
  • Add another version of CMV immediate early promoter to the plasmid features
  • Remove an alignment region shifting on a click within the region
  • Warning notifications with reports
  • Pairwise alignment default result file name is incorrect
  • Rename distances column in the Alignment Editor if "counts" profile mode is set
  • Failed to export an image of the "Chikungunya E1" alignment
  • Notification about empty sequences in FASTA
  • Add "unique" marker to "Intersect annotations" workflow
  • Optimize visualization of a big number of annotations
  • Rename "OK" to "Import" in the "Import Primers" dialog
  • Opening files of some non-supported formats from a dashboard
  • Add "Trim both ends" to NGS raw data processing wizards
  • Improve annotation search performance
  • Add options "collapse", "swap" and "reroot" to instrumental menu of tree viewer
  • In Silico PCR workflow
  • Align sequences to an existing alignment in the Alignment Editor
  • Clear pattern lineEdit in Project View
  • Bootstrap values are not displayed when PhyML is used
  • In silico PCR: no mismatches at 3' end
  • Update raw NGS samples
  • Describe wizards in the documentation
  • Make annotations creating dialog more convinient
  • Workflow sample for overlapped annotations
  • Find pattern widget: replace result count label with a progress animation
  • Fetching several sequences from a BLAST database
  • Sort by name function in MSA Editor is case sensitive
  • Allow resizing of Options Panel
  • Strange Behavior With Fasta File
  • Improve naming of "fragment"'s qualifers
  • Graphs should be calculated in separate tasks

New in Portable UGENE 1.16.2 (Jul 9, 2015)

  • Fixed:
  • PhyML tree building hangs for large alignments
  • PCR In Silico workflow trims result sequence
  • Fix several bugs in align sequences to an existing alignment
  • Order of elements reflects execution of a workflow with a CMD tool
  • Auto-annotations cannot be removed
  • UGENE can't process very long qualifiers
  • Missed scrollbar in the Circular View
  • Objects shown in AB aren't highlighted in Project view
  • BWA index algorithm setter works wrong
  • Read-write annotations in WD
  • Wrong position of restriction site arrows
  • Problems with opening specific .fa file
  • Assert on workflow run
  • Errors in log when running SnpEff
  • Bad performance for opening bed files
  • Annotation comments are displayed incorrectly
  • Find Pattern Widget: wrong annotation names
  • UGENE crashes on closing when "Import SAM" task is active
  • Optimize UGENE for opening GenBank files with ~1 million annotations
  • UGENE crashes in Query Designer
  • Wrong scroll for sequence zoom view
  • BWA: UGENE does not check external tool availability
  • Wrong names highlighting when tree view is shown with msa
  • Incorrect focus policy in consensus area
  • Export primers: raw sequence format error
  • Import primers: not ACGT sequence
  • Import primers dialog errors
  • Error during importing assembly to a shared DB
  • Correct misprint in the format name
  • Sequence view isn't updated after number of strands has changed
  • MSA Editor doesn't allow to select sequences that are not visible
  • "Add object to selected document" action copies the object in the main thread
  • No space for upper labels on the Circular View
  • Correct labels on the "Annotations Highlighting" tab
  • Documents without objects can cause crashes
  • Broken dashboard
  • UGENE crashes on insertion sequence into "Create document" dialog
  • Can't see name column of input data in the WD
  • Default file name in "Export Image" dialog can contain illegal characters
  • Crash on short reads alignment
  • Incorrect selection frame style in MSA Editor
  • UGENE crashes on opening short reads in sequence view
  • The sequence view scroll bar is broken
  • New:
  • Create "Intersect annotations" WD element
  • Downloading big UGENE packages
  • "Check primer pairs" workflow element
  • Recalculate regions in qualifiers when sequence is modified
  • Improved:
  • Notification about empty sequences in FASTA
  • Add "unique" marker to "Intersect annotations" workflow
  • Optimize visualization of a big number of annotations
  • Rename "OK" to "Import" in the "Import Primers" dialog
  • Opening files of some non-supported formats from a dashboard
  • Add "Trim both ends" to NGS raw data processing wizards
  • Improve annotation search performance
  • Add options "collapse", "swap" and "reroot" to instrumental menu of tree viewer
  • In Silico PCR workflow
  • Align sequences to an existing alignment in the Alignment Editor
  • Bootstrap values are not displayed when PhyML is used
  • In silico PCR: no mismatches at 3' end
  • Update raw NGS samples
  • Make annotations creating dialog more convinient
  • Workflow sample for overlapped annotations
  • Fetching several sequences from a BLAST database
  • Sort by name function in MSA Editor is case sensitive
  • Improve naming of "fragment"'s qualifers
  • Graphs should be calculated in separate tasks

New in Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable 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 Portable UGENE 1.12.3 (Dec 12, 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 Portable UGENE 1.12.2 (Dec 12, 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 Portable 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 Portable 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 Portable 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