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
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User Interface
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Cooperation
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- Powerful viewers and editors for nucleic and protein sequences
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- multiple sequence alignments
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- Visual and interactive DNA, RNA and protein sequence navigation
- Circular plasmid visualization
- Dotplots
- Multiple sequence alignment editor with integrated tree viewer
- Chromatograms editor
- 3D viewer for files in PDB and MMDB formats
- Phylogenetic tree viewer
- Assembly browser
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- , 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 philogenetic trees construction.
- ... and dozens of other popular and highly cited tools.
Hardware requirements
- UGENE runs smoothly on almost all hardware available: single core Pentium III or higher computer with 200Mb of free disk size and 64Mb memory is enough.
- Use UGENE on Mac, Windows or Linux operating systems. Both 32 and 64 bit versions are available.
- No 3rd-party software is needed to be installed to use UGENE!
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!