Unipro UGENE is a free cross-platform genome analysis suite. It is distributed under the terms of the GNU General Public License. To learn more about UGENE visit UGENE website. It works on Windows, Mac OS X or Linux and requires only a few clicks to install.
Key Features
- Powerful viewers and editors for DNA and protein sequences, multiple sequence alignments, chromatograms, 3D-structures, short read assemblies and phylogenetic trees.
- Support for dozens data formats, set of tools for importing and exporting data.
- Visual designer, runner and debugger for computational workflows from over 100 embedded algorithmic elements.
- Reusable computational workflows that can be shared, published and read as plain text by everyone.
- Full featured command line only version for remote desktops.
- Automatic detection and optimization for multi-core hardware, GPGPU, special instruction sets available on user's PC
- Setting up UGENE package user automatically gets dozens of tools installed and configured for immediate use
Tools provided with UGENE installation
- BLAST, Smith-Waterman - popular basic local sequence alignment tools.
- HMMER2/HMMER3 - sequence analysis using profile hidden Markov Models constructed from multiple sequence alignments.
- ClustalW, ClustalO, Muscle, K-Align, Mafft, T-Coffee multiple sequence alignment algorithms.
- Repeat finding and sequence comparison algorithms with a convenient dot-plot based results visualization.
- Open reading frames visualization and export.
- Restriction sites visualization tool with included version of REBASE database.
- Transcription factor binding sites analysis with SITECON, weight-matrix based algorithms and included version of JASPAR database.
- Short read aligners: BWA, Bowtie, Bowtie2, UGENE Aligner.
- GC-content, AT-content graphs.
- Mr bayes and Phylip tools for phylogenetic trees construction.
- ... and dozens of other popular and highly cited tools.
Hardware requirements
- The system requirements for UGENE are these:
- Operating system (32 or 64 bit):
- Windows XP, Windows Vista, Windows 7, Windows 8
Using a zip package it is possible to use UGENE without administrative rights on Windows - Mac OS X 10.5 or later
For older Mac OS X versions (PowerPC, 10.4) UGENE version 1.10.3 is avaialble. - Linux
- Ubuntu 12.04 or later
- Fedora 19 or later
- If you have another Linux system, you may use a universal binary package
- Windows XP, Windows Vista, Windows 7, Windows 8
- RAM:
512 Mb RAM required
2 Gb RAM recommended
- Disk space:
Minimum required disk space depends on the UGENE package- Standard package: 200-300 Mb
- Full package: 500-900 Mb
- NGS package: 21-24 Gb
- Display:
- It is recommended to set the screen resolution to a value greater than 1280x1024.
- It is recommended to set the screen resolution to a value greater than 1280x1024.
- Internet:
- Internet connection is required for some tasks like loading data from online databases.
- Internet connection is required for some tasks like loading data from online databases.
UGENE takes care to use capabilities of your system: the more RAM and cores you have, the more quickly you'll get results of your calculations.
Also, if you have an OpenCL-capable video card, you can use GPU-optimized versions of the following tools:
In most cases it is recommended to use UGENE full package, as it embeds additional external tools, such as local BLAST, Bowtie, etc. When the full package is used, the external tools can be run out of the box.
The list of the external tools and their availability for different operating systems can be seen on this page.
For details about UGENE packages, see this page.
- Operating system (32 or 64 bit):
Customization and cooperation
- UGENE is opensource software: it's easy to customize UGENE, add new features and tools!
- UGENE team welcomes all developers and researchers to participate in joined projects to improve UGENE or create customizations needed by user!