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Release Notes

Version 1.30
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:

Check the issues tracker for technical details.

Version 1.29
This version includes:

  • 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.
  • A new mode for amino acid translations visualization in the Sequence View.
  • Handy resizing of a selected region in the Sequence View and the Alignment Editor
  • 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.

See also the following documentation chapters:

Check the issues tracker for technical details.

Version 1.28.1
This version includes:

  • 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.

Check the issues tracker for details.

Version 1.28.0
This version includes:

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

Check the issues tracker for details.

Version 1.27.0
This version includes:

  • Sanger Reads Editor – a brand new framework for analysis of Sanger sequencing results. The main features are:

    • Reads mapping to a reference sequence.
    • Browsing of the result alignment with trace chromatograms.
    • Reads editing.
    • Exporting of the results.

    See this introductory video for the quick start.

  • Bug fixes and minor improvements.

Check the issues tracker for details.

Version 1.26.3
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Version 1.26.2
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Version 1.26.1
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Version 1.26.0
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Version 1.25.0
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Version 1.24.0
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Version 1.23.0
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Version 1.22.0
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Version 1.21.0
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Version 1.20.0
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Version 1.19.0
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Version 1.18.0
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Version 1.17.0
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Version 1.16.2
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Version 1.16.1
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Version 1.16.0
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Version 1.15.1
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Version 1.15.0
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Version 1.14.2
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Version 1.14.1
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Version 1.14.0
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Version 1.13.3
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Version 1.13.2
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Version 1.13.1
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Version 1.13.0
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Version 1.12.3
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Version 1.12.2
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Version 1.12.1
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Version 1.12.0
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Version 1.11.5
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Version 1.11.4
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Version 1.11.3
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Version 1.11.2
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Version 1.11.1
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Version 1.11.0
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Version 1.10.4
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Version 1.10.3
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Version 1.10.2
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Version 1.10.1
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Version 1.10
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Version 1.9.8
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Version 1.9.7
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Version 1.9.6
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Version 1.9.5
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Version 1.9.4

New features, improvements, bug fixes

  • Fixed reported crashes with ORF auto-annotations
  • Assembly Browser: better & faster coverage
  • Integrated new tool: CAP3
  • New plugin: DNA flexibility
  • Check the issues tracker for details.
Version 1.9.3

New features, improvements, bug fixes

  • New plugin: Assembly Browser
  • Sequence View: added functionality to manage number of visible rows in Zoom View
  • Circular View: added map of restriction sites
  • Phylip plugin: added tree bootstrap support
  • Biostruct3D viewer: introduced structural alignment visualization
  • Automatic annotation highlighting is provided for ORFs
  • Check the issues tracker for details.
Version 1.9.2

New features, improvements, bug fixes

  • Added auto-annotation high-lighting capabilities
  • Added support of export annottions in GFF format
  • Added support of lauching workflows in separte processes
  • Added multiple optimizations to Genome Aligner
  • Fixed problem with project export
  • Fixed bug with remote requests to NCBI CDD
  • Workflow Designer: added support of FASTA files as queries for Smith-Waterman search
  • Workflow Designer: added export/merge annotations workers
  • Workflow Designer: fixed bug with iterations (append and rename)
  • Added version string and estimated size to uninstall info in Windows “Add/Remove programs”
  • and more minor bugfixes… Check the issues tracker for details.
Version 1.9.1

New features, improvements, bug fixes

  • Circular view: zooming added
  • Export of rev-comple annotations fixed
  • MSA dialogs: GUI fixes
  • Enzymes: fixed search in range option
  • Workflow Designer: fixed workers promts
  • Workflow Designer: openning schema with no meta info fixed
  • Worfklow Designer: added ordering to element options
  • Workflow Designer: added element “Retrive data from remote DB”
  • Query Designer: added strand direction parameter to queries
  • Supported pDRAW document format
  • Added option to export group of annotations or annotation table to CSV
  • KAlign crash fixed on amino MSA
  • Cloning in silico: added option to edit fragments
  • Cloning in silico: added option to annotate new fragments
  • Cloning in silico: fixed incorrect ligation
  • and more minor bugfixes…
Version 1.9.0

New features, improvements, bug fixes

  • 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…
Version 1.8.0

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
  • Disabling of 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
  • and much more…
Version 1.7.2

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.
Version 1.7.1

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 analysis improvements;
  • New Workflow Designer samples and built-in command line schemas;
  • Circular view: support for annotations with virtual gap.
Version 1.7.0

New features & plugins:

  • 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.
Version 1.6.2

New features & plugins:

  • New plugin: Circular view;
  • Export plugin: back translation feature added;
  • Importing annotation tables from CSV has been implemented;
  • MSA Editor: consensus mode added, usability improvements;
  • Phylogenetic tree view improvements;
  • Workflow designer: added support for launching tasks remotely;
  • Enzymes plugin: added support for creating custom enzyme databases in BAIROCH format;
  • Binary Linux distribution is available for download;
Version 1.6.1

New features & plugins:

  • KAlign: new plugin for multiple alignment based on popular tool;
  • New format support: GFF;
  • Phylogenetic tree viewer improvements: support for Newick format;
  • Phylip plugin: distance matrix models added;
  • Proxy authentification added.

Bug fixes:

  • Smith-Waterman algorithm runs now properly from GUI;
  • Fixed memory managment in Muscle plugin;
  • Document deletion from Project View issue solved;
  • Document format detection improved;
  • MacOS version is distributed now as DMG image.
Version 1.6.0

New plugins:

  • Phylip plugin for building phylogenetic trees. Based on original Phylip 3.6 package.
    • Neighbor Joining algorithm;
    • Phylogenetic trees visualization;
    • Integration with Multiple Alignment Editor.
  • Distributed computing in UGENE
    • Support for launching HMMER 3, Smith-Waterman, MUSCLE tasks on remote machines.
    • Remote tasks support;

New features and bug fixes:

  • Search for tandem repeats added introduced in Repeat Finder plugin;
  • Project files transferability support;
  • “Export project” feature;
  • Remote databases interaction: NCBI, PDB, Swiss Prot;
  • BioStruct3D plugin: anaglyph stereo mode;
  • Sequence editor: several minor improvements and bugfixes;
  • Lots of minor stability and usability fixes.
Version 1.5.2

New plugins:

  • MUSCLE 4 – a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
  • CUDA Support – an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms (Windows only).

New features and bug fixes:

  • CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
  • The one of the most awaited features: sequence editing has been added;
  • Primer 3 integration has been finished – a complete set of preferences is available now;
  • Exporting annotation tables to CSV has been provided;
  • New workers have been added to Workflow Designer: Sequence splitter and Remote request;
  • Collecting statistical reports feature has been added. See the dialog on the first launch of v1.5.2;
  • HMM2 models support has been added to HMM3;
  • Filtering by hits number has been added to enzymes search;
  • Now UGENE drops ‘fantom’ documents on project closing;
  • Bug with incorrect handling of sequence range selectors has been fixed in SSP dialog;
  • SSP algorithms, Primer3 and PDB parser now work correctly when launched in parallel;
  • A serious bug affecting Fedora users has been fixed in PSIPRED.
Version 1.5.1

New plugins:

  • BALL – adds new types of molecular surfaces to UGENE 3D viewer

New features and bug fixes:

  • New feature: sequence line view and MSA editor now support saving fancy screenshots
  • Congene crash on windows has been fixed
  • HMM3 crash with malformed models has been fixed
  • Crash with simultaneous primer3 tasks has been fixed
  • Remote request is now stable when launched on Linux systems
  • Missing Smith-Waterman search is restored
  • Primer3 tasks now support cancelling
  • Choosing selection color has been added to 3D viewer
  • Sequence selection in Detailed View has been fixed a bit
Version 1.5.0

New plugins:

  • HMM3 – modern set of tools for HMM profiles build and search, based on HMMER 3.0b2
  • Primer3 – integration of the primer3 tool for PCR primers design
  • GOR IV and PSIPRED – protein secondary structure prediction tools
  • congene – command-line version of UGENE which allows user to launch workflows from the command-line

New features and bug fixes:

  • BioStruct3D viewer: molecular surface visualization
  • Loading remote documents from PDB, Uniprot, Swissprot
  • ‘Create document from text’ feature
  • Annotations editing significantly improved
  • Some critical bugs in Qt 4.5.0 are workarounded
  • Stability fixes for parallel MUSCLE: deadlock prevention
Version 1.4.2

Improvements and bugfixes:

  • Introduced Undo/Redo support for MSA Editor
  • Search in MSA Editor now works more accurate with different case of pattern
  • Extra filters for SITECON search procedure added
  • Now UGENE is capable of reading CLUSTAL X files
  • Smith-Waterman plugin became more accurate
  • Some concurrent-related bugs in MUSCLE fixed
  • Some Qt 4.5 compatibility issues fixed
  • Lots of minor stability fixes
Version 1.4.1

Improvements and bugfixes:

  • Color schemes support in Alignment editor
  • A camera lock option for multiple 3D protein models
  • Sequence viewer optimized to be used with large amount of annotations (up to 1 million)
  • Sequence viewer can show qualifier values instead of annotation names now
  • Chromatogram viewer: quality values are now shown by default for ABIF files
  • Several stability and compatibility issues fixed in BLAST, MUSCLE and HMMER modules
  • A number of minor stability fixes
Version 1.4.0

New features:

  • New plugin: Smith-Waterman. A complete implementation of Smith-Waterman algorithm
  • New plugin: Restriction Enzymes. Marks restriction enzymes in a sequence. Supports ‘bairoch’ file format provided by REBASE database
  • New plugin: Repeats Finder. Searches direct and invert repeats in DNA sequences. Optimized for huge sequences
  • New plugin: DNA Statistics. Exportable statistical reports
  • Workflow Designer: runtime state visualization of executed schema
  • Workflow Designer: integrated support of workflow samples
  • Workflow Designer: resizable items + snap to grid, customizable colors and fonts.
  • MSA Editor: show non-gapped offsets for each sequence in alignment
  • MSA Editor: a tool to search patterns in alignment
  • Sequence view: support scale locks and synchronization for different sequences
  • Sequence view: support for arbitrary number of rulers created by user
  • BioStruct3D viewer: export of 3D PDB and MMDB models into 2D vector format (SVG)
  • BioStruct3D viewer: a fast and extensible way to link active 3D model to Web resources
  • Project view: supports 3 different view mode: grouping data objects by type, by document and flat view
  • Project view: list of data objects for unloaded documents is shown
  • Performance: UGENE now allows to specify ideal count of CPUs, threads and memory to be used
  • DNA Export plugin: export of arbitrary multiple sequence alignments to FASTA format
  • New file formats supported: FASTQ, MMDB (plain text ASN)
  • Support for large (> 10Gb) files indexing for a fast data access
  • Custom application GUI themes supported. Windows version of UGENE uses Office GUI theme by default.

Improvements & bugfixes:

  • MUSCLE plugin: part of the original algorithm was optimized to utilize multicore CPUs.
  • HMMER plugin: SSE2 implementation of the algorithm was added;
  • HMMER plugin: hmmsearch now works in parallel mode for a single sequence by default (gives >30x boost for quad-core CPU when used with SSE2)
  • SITECON plugin: >50 new prokaryotic profiles to recognize transcription factor binding sites added
  • Most the views and dialogs got performance and usability improvements
  • Workflow Designer: now preserves additional info of processed data (like accessions, source etc) throughout overall computation.
  • Workflow Designer: write tasks now provide controls to override existing target file (either overwrite, append or rename).
  • Project view: supports relocation and copying of documents.
  • Annotation creation: new annotations now can be added to an unloaded annotation table object. The object is automatically loaded in this case.
  • MSA Editor: allows to change fonts, initial and limited support for zooming operations
  • BioStruct3D viewer: support for single structure with multiple 3d models
Version 1.3.3

Improvements and bugfixes:

  • A QT4.4 bug that prevents correct rendering of OpenGL widgets on some Linux platforms is work-arounded.
  • Group naming erorrs when nested groups used is fixed.
  • A new and more complete implementations for ABIF and SCF formats added.
  • Fixed bug that prevented ‘z’ char to be used in annotation names.
  • Annotations tree widget performance improved.
  • Sitecon plugin now processes custom regions correctly.
  • Workflow Designer crash when multiple iterations are used is fixed
  • For very short DNA sequences without ‘U’ and ‘T’ letters DNA genetic code is used now by default instead of RNA.
  • ‘Tab’ characters in FASTA and Genbank plain text formats do not produce error messages anymore.
  • Ubuntu package of UGENE was split into 2 packages (data and gui) to satisfy Ubuntu packaging rules.
Version 1.3.2

Improvements and bugfixes:

  • Fixed issue that can disallow to open more that 1 view on some 64-bit systems.
  • Fixed crashes when several PDB models are opened side by side in a single 3D-viewer window.
  • Fixed crash when opening ABI file with a very short sample name.
  • Added “Check For Updates” menu.
  • Fixed crash in “Find pattern” dialog when complement strand is selected for amino sequences.
  • Fixed chromatogram objects association for ABIF and SCF files.
  • Fixed genetic code autodetection for PDB file format.
  • Improved docked labels appearance for Linux and Mac OS X platforms.
  • Improved ‘Add object to view’ menu logic.
Version 1.3

New features:

  • Linux support. Packages for Fedora and Ubuntu
  • New plugin! Workflow Designer: allows to design custom computational workflows
  • New plugin! SITECON: search for Transcription Factor Binding Sites (TFBS) in DNA sequences
  • New plugin! BioStruct3D: 3D molecular protein and DNA structure viewer for PDB format
  • Stockholm and PDB formats support
  • Browsing multiple sequences side by side in a single sequence view window
  • Sorting by annotation qualifier values
  • ‘db_xref’ qualifiers made interactive and are linked to corresponding web databases
  • Translation and complement strands can be hidden in sequence view
  • Support for localization. English and Russian translations are included into the default distribution
  • Tasks can generate detailed reports now

Improvements & bugfixes:

  • Task progress is now shown in status bar
  • Critical fix: Memory leaks and crashes fixed in code that integrates MUSCLE package into UGENE
  • Critical fix: Default parameters of HMMER-related dialogs are now the same as in original HMMER
  • Logs view now do not show traces by default
  • Drag&drop support for all file types supported by UGENE
  • >100 other minor fixes, usablity and performance improvements !
Version 1.2

New features:

  • MacOS v10.4 and v10.5 support.
  • Multiple sequence alignment editor. MUSCLE alignment algorithm integrated as a separate plugin.
  • New plugin! ORF Marker: Searches for ORFs in DNA-sequences.
  • New plugin! ChromaView: The plugin integrates chromatogram viewer into ‘Annotated DNA View’
  • New plugin! Remote request: Annotates selected DNA-sequence regions by sending requests to BLASTn, BLASTp and CDD servers. Can be extended to use other servers with scripts.
  • New plugin! UMUSCLE: Adds MUSCLE alignment algorithm to the system.
  • Files located on remote servers can be added to project by HTTP protocol
  • Scripting support for custom WEB-based BLAST/CDD-like queries. Binding for all GUI/Utility classes and ability to create any algorithms using script.
  • DNAGraphPack plugin supports 4 new graph types: GC & AT deviations, Karlin Signature Difference and Informational Entropy
  • All genetic translation tables of Genbank database are supported and can be selected by user.
  • SCF format support added.
  • Support for unloading documents without removal them from a project.

Improvements & bugfixes:

  • UGENE can be associated to open all file types it supports from command line. File binding comes by default with Windows installer.
  • Better integration of uHMMER plugin with Annotated DNA View and MSA Editor
  • DNAGraphPack plugin now shows interval based graphs for large zooms to keep min/max information precise.
  • Drag&Drop functionality between ‘Project View’ and ‘Annotated DNA View’
  • Dozens of GUI, performace and compatibility improvements and bug fixes.
Version 1.1

New features:

  • EMBL, ABI, CLUSTALW and raw sequence file formats supported.
  • Custom document format settings option added when adding documents to project. Use this option if you need to merge all DNA sequences found in document into a single sequence.
  • New plugin: uHMMER . This is a port for hmmbuild, hmmcalibrate and hmmsearch tools from HMMER2.3.2 package
  • New plugin: DNA Export. This plugin adds functionality to export various types of DNA sequence selection to FASTA file format.
  • Starting from this version UGENE works transparently with compressed documents in GZIP format. For example, compressed files can be added to project.
  • New plugin: DNA Annotator. This plugin adds annotation based searches to runtime. Current version allows to find regions that contain a predefined set of annotations.

Improvements & bugfixes:

  • Multi-selection support added for annotations tree used in ‘Annotated DNA View’.
  • Annotations’ colors, placement and visibility properties were made customizable.
  • “Find DNA sequence” algorithm was tuned. Several bugs fixed.
  • A lot of minor GUI and performance improvements.