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UGENE is a free cross-platform bioinformatics software package.

Working with genomic data in UGENE 1.9.0
Developer Unipro
Latest release 1.9.0 / 15 December 2010
Operating system N/A
Programming language N/A
Language English, Russian, Czech
Genre Bioinformatics toolkit
License GPL

UGENE is free open-source cross-platform bioinformatics software.

It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces. Using UGENE Workflow Designer one can arrange the required tools and algorithms into a workflow schema.

In order to provide maximum possible performance UGENE utilizes multicore CPUs and GPUs to optimize some of its computational routines. Another way to speed up computations is to use Amazon EC2 cloud resources.


Key features

The software supports the following features:

User interface

The software has three main views to display biological data on the user’s screen.

1. The Sequence view is used to visualize, analyze and modify nucleic acid or protein sequences. Depending on the sequence type and the options selected the followings views can be presented inside the Sequence view window:

2. The Alignment editor is used to visualize, analyze and modify a nucleic acid or protein multiple sequence alignment.

3. The Phylogenetic tree viewer.

UGENE Workflow Designer

UGENE Workflow Designer allows creating and running complex computational workflow schemas.

The elements that a schema consists of correspond to the bulk of algorithms integrated into UGENE. Using the Workflow Designer one can also create custom workflow elements.

The workflow schemas can be run both locally and remotely, either using the graphical interface or launched from the command line.

UGENE Query Designer

UGENE Query Designer allows a user to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.

A schema of the algorithms and constraints is either created from the GUI or edited as a plain text.

The results are saved as a set of annotations to a specified file in the GenBank format.

Supported biological data formats

Release cycle

UGENE is primarily developed by Unipro LLC. Each iteration lasts about 6 weeks. By the end of iteration a release comes out. One can also download a development snapshot of the software.

The features to be included into the next release are mostly initiated by users.


UGENE was awarded "The best FOSS project in Russia – 2010" in the category "Group project" at the Linux Format magazine contest.

See also

Related software


External links

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