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

The full list of changes done in this release can be found in our bug tracker

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!

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

The full list of changes done in this release can be found in our bug tracker

This is the latest major UGENE release, that introduces a lot of new features, brings stability, performance and usability improvements into UGENE

Short list of features and improvements:

• New tools: MrBayes, BWA (all platforms), update of Bowtie and BLAST tools
• Short reads assembly viewer: performance and reads coloring improvements
• Work with large data sets: open, view and annotate huge DNA files on a usual desktop
• Workflow designer: new data filtering elements
• Sequence viewer: new DNA flexibility and GC Frame Plot graphs
• All in one package: download UGENE, documentation and external tools in a single file!

The full list of changes done in this release can be found in our bug tracker

This is a patch release, that does not introduce any new features, but brings stability, performance and usability improvements into UGENE.

Short list of fixes:

• Fixed a crash during short reads export from the Assembly Browser
• Fixed a crash when using PsiPred package with some special data sets
• The ORF Marker now correctly processes boundaries of circular sequences
• Support of the BAM and GFF formats was improved
• Chinese translations were improved

The full list of changes done in this release can be found in our bug tracker. September 20, 2011: UGENE 1.9.7 is released

The new release fixes several critical bugs and a number of minor issues. You can find the detailed list of fixed issues here.

The new release is targeted on the improvement of stability and reliability of UGENE. It fixes several critical bugs and doesn't introduce any new features.

The following issues are fixed:

• Association between annotations and sequences in project files is restored
• Assembly Browser doesn't hang anymore on loading results from alignment algorithm
• Reverse-complementary sequences from results of CAP3 algorithm are visualized correctly
• MultiFASTA files can be opened as merged sequences

You can find the full change-list here.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


July 27, 2011: UGENE project at the BOSC-2011

UGENE project was presented at the 12th Annual Bioinformatics Open Source Conference on July 15. Thanks to Open Bioinformatics Foundation every year BOSC brings together scientists and developers from all over the world to discuss new and existing software projects. This year BOSC was held as a SIG at ISMB/ECCB 2011 meeting in Vienna, Austria.

Our team member Konstantin Okonechnikov gave a talk about UGENE during the Genome Content Management section. You can see him on the picture below with people from other open-source bioinformatics projects.


From left to right: James B.Procter(JalView), Peter Cock(Biopython), Konstantin Okonechnikov(UGENE) and Peter Troshin (JABAWS).

BOSC proceddings including UGENE project abstract can be downloaded from here.


July 25, 2011: UGENE 1.9.5 and changes in the release cycle

UGENE team is glad to announce a major change in the release cycle which will allow to improve stability and reliablity of the bioinformatics toolkit.

From now on we are going to ship hot-fix releases every time a major bug is discovered. Such releases can be distinguished by the third digit in the version nuber. You can read more about the new versioning system in the following forum thread.

The brand new version 1.9.5 fixes a number of critical bugs and can be downloaded from here.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter! July 12, 2011: UGENE 1.9.4 is released

Meet the brand new release of UGENE toolkit! It includes new powerful capabilities and several critical bugfixes.

Here are some of the most important new features:

• A framework for easy integration of external tools into the Workflow Designer
• Long-awaited support for contig assembly with CAP3
• Intelligent document format detection: opening suitable view for unambiguous data
• Assembly Browser: better and faster coverage calculation for BAM files viewing, integration with embedded aligners
• Export of NGS data: BAM to SAM format
• New plugin: DNA flexibility calculation
• and other improvements...

You can find full change-list here.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


July 6, 2011: UGENE on the Illumina iDEA 2011 Conference

As we mentioned earlier, UGENE project participated in the Illumina iDEA Challenge 2011. The contest was devoted to analysis and visualization of the data generated by Illumina technologies in the context of cancer genome research. For this challenge we presented the UGENE Assembly Browser, a neat BAM viewer.

The final of Illumina iDEA 2011 challenge took place in San Diego, CA, USA on the 14-15th June 2011. During the Illumina iDEA 2011 conference the finalists and guest scientists gave their talks about future of Next Generation Sequencing.

Our team member Mikhail Fursov was representing UGENE on this event.


June 3, 2011: Workshop on UGENE was held in Novosibirsk State University

A training workshop on UGENE organized by Unipro and Novosibirsk State University was held between the 30th May and 2nd June. A group of young biologists from several Siberian universities and research labs gathered together to study on how to work with UGENE and use the toolkit in their everyday research.

The workshop covered various topics in bioinformatics: homology searching in databases, performing multiple alignment, working with NGS data and much more. An important goal of the workshop was to familiarize scientists with the usage of high-performance computing. The participants also learned the innovative concepts of Workflow Desinger and Query Designer. The lectures and tutorial sessions were conducted by UGENE team members and experienced scientists from NSU and local research institutions.

The workshop was supported by a grant from Russian Federal Targeted Program �R&D in Priority Fields of the S&T Complex of Russia�.


May 23, 2011: UGENE 1.9.3 is released

Starting from this version UGENE provides advanced support for NGS data analysis. The most notable feature of current release is the Assembly Browser, a powerful GUI tool to visualize BAM files. It was tested against data from 1000 Genomes project, Illumina iDEA Challenge and data from other sources. Find out more about Assembly Browser in UGENE user manual.

The new version also includes multiple improvements and bugfixes. Here are some of them:

• 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

You can find full change-list in our bug-tracker .

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


April 7, 2011: UGENE wins award in a contest devoted to GPU computations

We are pleased to announce that Unipro UGENE project won award in the contest "Efficient Use of GPU-Accelerators to Solve Large Problems". The contest is held by T-Platforms company - a leading provider of high-performance computing systems in Russia and Europe.

The contest consists of several parts. In the first part each participant presented a detailed description of a scientific project in the area of GPU computing. The winners of the first part will now start working on the implementation of the project. As part of this contest a new feature will be included into UGENE: fast assembly of NGS data using modern GPUs.


March 24, 2011: UGENE 1.9.2 is released

New version includes several critical bug fixes and some new features:

• UGENE Genome Aligner is optimized towards better performance. Now it can use modern GPUs to boost the computations
• Workflow Designer improvements:
  • Added new workflow elements: merge and write annotations
  • Added support of FASTA files as queries for Smith-Waterman search
• Query Designer improvements:
  • Added HMM query element
  • Search query can be customized for specific strand
• Automatic annotation highlighting for Restriction Enzymes plugin is introduced. Once configured, restriction sites search is performed for newly opened sequences automatically — no need to launch search every time for new molecule.
• Fixed bug with remote access to NCBI CDD
• Fixed bug with project export

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


March 15, 2011: UGENE bug-tracker is open for public

UGENE makes a big step towards openness - from now on UGENE project developement process will be visible for our users. Feel free to check out bug-tracker.

Anyone can register and submit their ideas and suggestions as tickets for UGENE developers team. The tracker also allows to follow interesting issues and vote for project road map.

We are using Atlassian JIRA as a bug tracking system for UGENE, you can find out more about it here.


February 7, 2011: UGENE 1.9.1 is released

This release is primarily a bug fix release with an emphasis on stability and reliability improvements. However, the release also contains a number of new features:

• Workflow Designer: scripting GUI improvements
• Query Designer: supported strand direction for queries
• DNA Circular view: added zooming capabilities
• Cloning "in silico": added option to edit fragment terms, annotation of newly created fragments
• New document format is supported: pDRAW
• External tools usability improvements

From now on UGENE users don't need to search and manually install supported external tools. Follow this link to download "all-in-one" external-tools pack.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


December 25, 2010: Development snapshots are available

Great news for those who are impatient to check new features of UGENE before official release! From now on the latest unstable snapshots are available from our web-site.

The development snapshots include MS Windows, Linux and source packages. Please note that Windows binary snapshot is represented as portable zip archive: just unpack it to any directory and launch ugeneui.exe.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


December 21, 2010: UGENE wins the Best Open Source Project contest

We are happy to announce that Unipro UGENE project was honored as Best Open-Source Project in Russian Federation. The annual contest is held by Linux Format magazine with the support of Intel, PingWin Software, IBM developerWorks and GNU/Linuxcenter companies. About 100 participants took part in the contest this year.

UGENE team is proud to win the award and we want to thank all our users for help and support! Without your useful suggestions and feedback UGENE wouldn't get this far.

We are planning to make our project 200% better and win more awards next year :)


December 17, 2010: What's new in UGENE 1.9 podcast

A special episode of our podcast series is available on Unipro UGENE YouTube channel!

The episode starts a new season of UGENE podcast series devoted to the brand new UGENE release. In this video you will find an overview of the multiple new UGENE features including such significant ones as

• Cloning "in silico" support capabilities,
• Query Designer complex sequence analysis tool,
• A new human-readable schema format and language
• and more.

To see this video, please follow this YouTube link.

In the next episodes all the new features will be covered in detail, so feel free to subscribe to our YouTube Channel.

Click here to subscribe via the RSS, or go to Unipro UGENE YouTube channel's page and subscribe from your YouTube account.

Click here to download the latest version of Unipro UGENE.

We hope you will enjoy UGENE 1.9 and the video tutorials.


December 15, 2010: UGENE 1.9.0 is released

Meet the hot new UGENE release! Originally we planned to roll out version 1.8.1, but the new version includes so many new features that we decided to name it 1.9.0.

The release includes:

• Support for "cloning in silico". From now on it is possible to automatically digest sequences into fragments and construct new molecules from defined fragments. This functionality is the first step to fully support cloning feature, which is one of the top requests from UGENE users. For detailed overview of new functionality check out this tutorial available from UGENE User Manual.
• Brand new feature: Query Designer. This tool allows to analyze complex signals in the DNA sequence using simple rules to set constraints for algorithms. Check more details in the corresponding documentation section.
• HPC and GPGPU support: Smith-Waterman algorithm now works using OpenCL on both AMD and NVIDIA cards
• Workflow Designer: new human-readable schema format and language
• GUI improvements: balloon notification system
• External tool support: BLAST+ and T-Coffee tools are integrated
• Multiple Alignment Editor: alignment sequences can be translated to amino alphabet
• Remote database interaction: fetching sequences by registered qualifier of annotation

The release also includes multiple minor improvements and bugfixes. The full changelist is available here. Thanks to your feedback UGENE is becoming better and better — most of the current bugfixes are initiated by our users.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


December 6, 2010: UGENE Team needs community help

Dear Users!

In the beginning of 2011 our project will participate in the All-Russian grant competition for
innovative projects (here is the link for russian-speaking users). We plan to spend the grant on
the development of UGENE in the most prioritized directions: genome assembly, web service, cloud computing.

We believe that the best foundation of our bid is the satisfaction of our users which
is more important than anything in determining the value of our project.

So we ask you kindly to about your experience with UGENE, i.e. a recommendation letter.
Below we suggest some points good to emphasize:

• How long do you use UGENE;
• Which problems do you solve using it;
• Reasons of using UGENE;
• Any testimonials;
• Contacts: your name, e-mail, position, laboratory or department, institution, city and country.

Thank you for your attention,
UGENE Team.


November 3, 2010: UGENE wins award at contest held by Intel and Rusnano

This year Unipro UGENE project participated in the High Performance Computing contest held by Rusnano and Intel corporations. The main goal of the HPC-2010 contest was to determine best academic projects in Russia in the area of scientific computing.

About 100 projects took part in the contest. Most of them were strong and promising. In result UGENE won the Bronze Third Place award.

UGENE team-member Konstantin Okonechnikov recieved the prize at the Rusnano HPC-2010 awards ceremony during Rusnanotech forum in Moscow.


October 21, 2010: UGENE 1.8.0 is released

Meet the brand new release of the unified bioinformatics toolkit! It includes several long-awaited features and enhancements, mostly initiated by our users.

In version 1.8.0 UGENE team concentrated efforts on the stability and reliability of the project, which resulted in over than 100 bugfixes implemented.

New features:

• 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 and bugfixes:

• Command line interface improvements: comprehensive help-system and verbose error diagnostics.
• Fixed crash when calculating surface for large proteins;
• Workflow designer fixes in GUI and usability;
• Crash handler is improved: now you can send us report is something unexpected happend.
• ... and many more. Check full list in version history.

In version 1.8.0 we decided to give up old Remote Task protocol model. From now on all remote tasks are exectued only via UGENE remote service based on Amazon EC2. The UGENE remote service is ready for testing.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


August 20, 2010: UGENE 1.7.2 is released

UGENE team is glad to announce UGENE 1.7.2. The new version includes several awesome new features and numerous enhancements.

New features:

• Launch your computational tasks on Amazon EC2 with UGENE! The release includes experimental support for cloud computing. Check the details in the corresponding documentation section.
• Support for external tools: now Clustal and Mafft alignment available in UGENE.
• Customize computational workflows using scripting capabilities.
• New format is supported: Nexus
• UGENE documentation is being reworked and improved. From now on UGENE user manual is available as printable PDF.

Improvements and bugfixes:

• Multiple Alignment Editor: delete columns with relative number of gaps;
• DotPlot: search inverted repeats, zooming, synchromisation with sequence view;
• DNA & protein sequence renaming, export sequences with annotations;
• ... and many more. Check full list in version history.

Watch new UGENE podcast episode devoted solely to the new version: part1 and part2 .

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


July 9, 2010: UGENE 1.7.1 is released

The new release includes several important updates and one new plugin:

• 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.

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


June 2, 2010: What's new in UGENE 1.7.0 podcast

A special episode of our podcast series is available on Unipro UGENE YouTube channel!
It is devoted to the new UGENE version 1.7.0 and its features.

The episode consists of 2 parts: first and second.
The following topics are covered:

• New features of sequence circluar view;
• Scripting framework;
• DNA to reference assembly;
• New algorithms for auto-annotation.

Moreover, UGENE documentation has been significantly updated!
New chapters about UGENE multiple alignment editor have been added:

• Editor overview;
• Editing the alignment;
• Advanced functions.

To download the latest version of Unipro UGENE click here.
Follow us on Twitter!


May 19, 2010: UGENE 1.7.0 is released

The new release includes the long awaited DNA assembly functionality. Since now short read alignment can be performed with UGENE. Two methods are available:

• Genome aligner plugin, based on unique algorithm;
• Port of popular open-source tool Bowtie.

A lot of improvements were made to console version of UGENE. It has become much more flexible and powerful. Since now it is possible to use command line version of UGENE in complex scripts and shell scenarios. There are useful prebuilt scenarios available: align, convert, find repeats etc. Check documenation for more details.

Other cool features available:

• New advanced sequence analysis algorithm based on weight matrices;
• Circular view improvements: zoooming, rotating and more;
• Support for advanced search options of NCBI BLAST in redesigned Remote Request plugin.
• Alignment logo feature;
• New fancy widget: global sequence overview;
• Tree viewer is re-worked: stand-alone interface, new visualization modes.
• GFF format now supports writing;
• Scripting framework is introduced;
• and a lot more...

Click here to download the latest version of Unipro UGENE.

Feel free to check out Unipro UGENE YouTube channel, and follow us on Twitter!


April 2, 2010: What's new in UGENE 1.6.2 podcast

A special episode of our podcast series is available on Unipro UGENE YouTube channel!

It is devoted solely to the new UGENE version 1.6.2 and its features.

The following topics are covered:

• Sequence circluar view;
• New capabilities of Multiple Alignment Editor: selections and consensus mode;
• Protein back translation;
• Running remote workflows;
• Restriction enzymes plugin improvements;
• New scoring matrices;
• Importing annotations from CSV.

To download the latest version of Unipro UGENE click here.


April 2, 2010: UGENE on Twitter

Follow Unipro UGENE project on Twitter!

The hottest news about the project, development process status, new podcast announcements and advices for our users.

Available via weekly updates!


March 29, 2010: UGENE 1.6.2 is released

UGENE team gladly presents our next regularly scheduled release.

This release brings several really long-awaited features such as circular view and sequence reverse translation.

Note for our linux users: UGENE is now available as a universal binary package intended to be installed independently of package managers.

New features:

• 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;
• And many others!

To download the latest version of Unipro UGENE click here.

Feel free to check out Unipro UGENE YouTube channel .


February 25, 2010: UGENE video tutorials series have been started

Since now we start UGENE video podcast on YouTube. The podcast episodes will provide useful product tutorials and give answers to popular users questions of UGENE (for instance, from UGENE forum).

The series begin with 5 tutorial videos available at Unipro UGENE YouTube channel. The topics include working with sequences, annotations and qualifiers and making a multiple sequence alignment.

We appreciate any comments and suggestions. If you want to be new episodes first watcher, click here to subscribe to the RSS, or go to Unipro UGENE YouTube channel's page and subscribe from your YouTube account.

Also you could watch all the episodes at our web page.


February 16, 2010: UGENE 1.6.1 is released

UGENE v 1.6.1 is a bug fix release which is strongly recommended to install since it fixes several serious issues.

Please note, that before installing v1.6.1 it is needed to completely remove any previous installations of UGENE.

New features & plugins:

• KAlign: new plugin for multiple alignment based on popular tool; it is very fast (even faster then MUSCLE!) and accurate;
• New format support: GFF;
• Phylogenetic tree viewer improvements: support for Newick format;
• Phylip plugin: distance matrix models added;
• Proxy authentication 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;
• and many more...

To download the latest version of Unipro UGENE click here.


December 22, 2009: UGENE 1.6.0 is released

UGENE v 1.6.0 is finally released! New plugins are introduced, a lot of features and improvements are included!

Please note, that before installing v1.6.0 it is required to completely remove any previous installations of UGENE.

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;
• and a lot more...

Click here to download the latest version of Unipro UGENE.


October 06, 2009: Russian website introduced

Our team is glad to announce that UGENE users from Russia can use translated version of the website. You are welcome!


September 22, 2009: UGENE 1.5.2 released

V. 1.5.2 is a feature-oriented release which brings several really unique possibilities for UGENE users.

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.

• CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
• The one of the most awaited features: sequence editing has been added;
• Exporting annotation tables to CSV has been provided;
• HMM2 models support has been added to HMM3;
• And many others. See the changelog for a full list of improvements.

UGENE team is glad to announce that beginning from today, users of PowerPC-based Macs can use our software right out of the box. Feel free to check the downloads page for the new Mac universal package which is able to run on both x86 and ppc platforms.


July 17, 2009: UGENE 1.5.1 released

UGENE v 1.5.1 is a bug fix release which is strongly recommended to install since it fixes several serious issues.

Please note, that before installing v1.5.1 (or v1.5.0) it is required to completely remove any previous installations of UGENE.

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

To download the latest version of Unipro UGENE click here.

Ubuntu binaries as always will be available during the next couple of days


July 10, 2009: UGENE 1.5 released

Long-awaited version 1.5 adds 4 new plugins and brings countless improvements:

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 (feel free to check corresponding documentation )
• Introduced congene - command-line version of UGENE which allows user to launch workflows from the command-line

New features and bug fixes:

• Major update for Biostruct3D plugin: molecular surface visualization (please check plugin documentation)
• Loading remote documents from PDB, Uniprot, Swissprot
• 'Create document from text' feature
• Annotations editing significantly improved
• Some critical bugs in Qt 4.5 workarounded
• Added some stability fixes for parallel MUSCLE
• Lots of minor fixes and improvements

To download the latest version of Unipro UGENE click here.


May 21, 2009: UGENE 1.4.2 released

Improvements and bugfixes in Unipro UGENE v1.4.2:

• 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

To download the latest version of Unipro UGENE click here.

Linux binaries will be updated on Fedora and Ubuntu webservers a bit later.


May 13, 2009: UGENE at Biotech World'2009

UGENE has been presented at The Fifth Moscow International Congress "Biotechnology: State of the Art and Prospects of Development" and the VII International Specialized Exhibition "Biotech World' 2009"

Also UGENE has been presented at PaVT' 2009 ( official russian web site ) - an international conference devoted to parallel computing. It was held in Nizhny Novgorod, Russia.

The following materials were published:

Fursov, M. Y.; Oshchepkov, D. Y; Novikova, O. S. (2009). "UGENE: interactive computational schemes for genome analysis". Proceedings of the Fifth Moscow International Congress on Biotechnology 3: 14-15. ISBN 5-7237-0372-2.

Efremov, I. E.; Fursov, M. Y; Danilova, Yu. E. (2009). "UGENE: high performance genome analysis suite". Proceedings of the Fifth Moscow International Congress on Biotechnology 2: 405-406. ISBN 5-7237-0372-2.

Fifth Moscow International Congress on Biotechnology proceedings (link to PDF file)


May 7, 2009: UGENE becomes a part of Ubuntu Linux

UGENE is now a part of recently released Ubuntu Linux 9.04 (Jaunty Jackalope) distribution.

Ubuntu-compatible binary packages of UGENE for multiple hardware platforms are available to download from here. Bug reporting is also available through Ubuntu LaunchPad

You can install UGENE in Ubuntu using visual interface of package manager or running this command via shell:

     sudo apt-get install ugene

Current UGENE version included into Ubuntu is 1.3.3, but soon UGENE version 1.4.1 will be available from backports.


March 25, 2009: UGENE version 1.4.1 - a bug fix release

Improvements and bugfixes in Unipro UGENE v1.4.1:

• 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 stabiliity and compatibility issues fixed in BLAST, MUSCLE and HMMER modules
• A number of minor stability fixes

To download the latest version of Unipro UGENE use this link.


March 24, 2009: UGENE discussion board is open

Now UGENE users can easily ask questions, post feature requests or send bug reports using forum

Feel free to register and give us any feedback you have.


March 10, 2009: UGENE v1.4 released

Version 1.4 adds 4 new plugins and brings numerous improvements and bug fixes.

New plugins: restriction enzymes support, complete Smith-Waterman algorithm, repeats analysis and exportable sequence and alignment statistics.

The major user interface improvements were made in Workflow Designer, Sequence and Project views.

Most of the computational algorithms (like MUSCLE) are now able to work in parallel mode. HMMER2 integration got SSE2 optimized version.

PDB and MMDB 3D structures viewer now is able to save 3D models in 2D vector format.
...

The complete list of changes can be found here


February 02, 2009: UGENE v1.3.3 - a bug fix release

Improvements and bugfixes in Unipro UGENE v1.3.3:

• A QT4.4 bug that prevents correct rendering of OpenGL widgets on some Linux platforms is work-arounded.
• Group naming when nested groups used if 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 errors anymore.
• Ubuntu Linux package of UGENE was split into 2 packages (data and gui) to satisfy Ubuntu packaging rules.

Improvements and bugfixes in Unipro UGENE v1.3.2:

• 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.

Unipro UGENE v1.3.1 fixes several minor issues found since the v1.3 release and adds the following improvements:

• Improved tasks management/description in Workflow Designer
• MUSCLE integration improvements: 3 presets for a single profile alignment, profile to profile alignment and very fast aligning of unaligned sequence to a profile
• Some compilation issues fixed for 64-bit platform
• Most of the user operations emit more details into log.
• 3D-structure viewer supports export of the active image to 'jpg', 'png' and 'tiff' formats.

Unipro UGENE v1.3 is the next minor release of the product.
It adds 3 new plugins: BioStruct 3D, SITECON, and Workflow Designer, source package for all supported platforms and a lot of performance and usability improvements for almost all of its components.

The complete list of changes can be found here.


November 25, 2008: UGENE v1.2.2 for Linux released

UGENE v1.2.2 is a first Linux release of UGENE Bioinformatics Suite.
We provide prebuilt packages for Fedora 9 for IBM Cell and Intel IA32 platforms.

Version changes:
Optimization for Cell processor was enabled in HMMER plugin.
Fixed crash when "Remote Request" plugin is used with active Tasks view.


October 31, 2008: UGENE v1.2.1 is released

UGENE v1.2.1 is a bug-fix only release. It includes set of stabilty and compatibility improvements.
Major fixes: multithreaded mode related fixes for HMMER2 package.


October 20, 2008: UGENE team participated in "Molecular Oncology" conference

Poster and computer presentation "New multitasking software system for real-time analysis of genomic sequences" devoted to UGENE project use cases and perspectives was held at "Molecular Oncology" conference.

The conference was organized at Novosibirsk by branch of Russian Academy of Medical sciences. link


September 19, 2008: UGENE v1.2.0 is released

Unipro UGENE v1.2 is the next minor release of the product.
It adds several new plugins, MacOS X platform support and dozens of performance, usability and compatibility improvements.

The complete list of changes can be found here.


August 19, 2008: UGENE v1.1.1 is available

UGENE v1.1.1 is bug fix only release. It includes set of performance, stabilty and compatibility improvements made since the release of version 1.1.0 in July 2008.


July 22, 2008: Unipro releases UGENE v1.1
This version adds HMMER package integration, support for compressed files and fixes several usability and performance issues.

The complete list of changes can be found here.


June 23, 2008: BGRS 2008 conference

Unipro UGENE team participated in "The Sixth International Conference on Bioinformatics of Genome Regulation and Structure" (BGRS'2008) with a computer demonstration in "High Performance Computing in Bioinformatics" section.


June 17, 2008: The first version of Unipro UGENE

We proud to announce the first version of Unipro uGENE project for Solaris and Windows operating systems.
Check download page to select the version you need.