The 25th episode of our podcast series is out! It is available on YouTube.
The video is dedicated to UGENE version 1.7.1 release and shows the new UGENE features:

• Dotplot plugin,
• Advanced chromatogram analysis,
• New DNA Assembly Workflow Designer schemas and console commands,
• and more!

You can subscribe to our channel as YouTube user or via the RSS!

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

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.