What is UGENE?

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 the 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 of data formats, and a 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.
  • A fully featured command-line version for remote desktops.
  • Automatic detection and optimization for multicore hardware, GPGPU, and special instruction sets available on the user’s PC.
  • Setting up the UGENE package automatically gets dozens of tools installed and configured for immediate use.

Tools provided with UGENE installation

  • BLAST - a popular tool for searching similarities between biological sequences.
  • HMMER2/HMMER3 - sequence analysis using profile hidden Markov models, constructed from multiple sequence alignments.
  • ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee multiple sequence alignment algorithms.
  • Repeat finding and sequence comparison algorithms with convenient dot-plot-based results visualization.
  • Open reading frames visualization and export.
  • Restriction sites visualization tool with the integrated REBASE database.
  • Transcription factor binding sites analysis with SITECON, weight-matrix-based algorithms, and included versions of the JASPAR database.
  • Short read aligners: BWA, BWA-MEM, Bowtie, Bowtie2, TopHat, etc.
  • GC-content, AT-content graphs.
  • MrBayes, Phylip, and PhyML tools for phylogenetic tree construction.
  • … and dozens of other popular and highly cited tools.

Commercial support

The commercial support includes bug-fixing on a priority basis, implementation of new features, and more. To learn more, please contact us.

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