UGENE – bioinformatics software

UGENE is free open-source cross-platform set of integrated 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.

Features include:

  • Graphical User interface offering:
    • Visual and interactive genome browsing including circular plasmid view.
    • Multiple alignment editor.
    • Chromatograms visualization.
    • 3D viewer for files in PDB and MMDB formats with anaglyph stereo mode support.
    • Phylogenetic tree viewer.
    • Dot plot visualization.
    • Query designer enables search for complex annotation patterns.
    • Easy to use workflow designer for custom computational workflow.
  • Multiple sequence alignment using MUSCLE 3, KAlign, Clustal.
  • HMM profiles build and search, based on the source of HMMER 2 and HMMER 3.
  • PCR Primers design using Primer 3.
  • Cloning in silico capabilities.
  • Queries to NCBI BLAST and CDD databases.
  • Protein secondary structure prediction using GOR IV and PSIPRED.
  • Phylogenetic analysis with Phylip.
  • Search for restriction enzymes and integration with REBASE.
  • Extremely fast repeat finder.
  • DNA reference assembly using Bowtie.
  • Search for transcription factor binding sites using SITECON.
  • Protein back translation.
  • ORF finder.
  • Complete Smith-Waterman algorithm implementation.
  • Support for external tools: BLAST+, MAFFT, T-Coffee.
  • Assembly Browser — a shiny BAM viewer.
  • Biostruct3D viewer.
  • Complete support of modern multicore processors and SSE instructions.
  • Out of the box support of modern GPUs using NVIDIA CUDA and ATI Stream.
  • Support for cloud computing: running computational tasks on Amazon EC2 cloud.
  • Support for supercomputers and distributed computing.

Support: Manual
Developer: Unipro
License: GNU GPL v2


UGENE is written in C++. Learn C++ with our recommended free books and free tutorials.

Return to Bioinformatics Tools Home Page | Return to Desktop Genome Browsers Home Page

Popular series
Linux for StartersNew to Linux? Read our Linux for Starters series.
Free and Open Source SoftwareThe largest compilation of the best free and open source software in the universe. Supplied with our legendary ratings charts.
Linux ReviewsHundreds of in-depth reviews offering our unbiased and expert opinion on software.
Alternatives to GoogleAlternatives to Google's Products and Services examines your options to migrate from the Google ecosystem with open source Linux alternatives.
MicrosoftAlternatives to Microsoft's Products and Services recommends open source Linux software.
AdobeAlternatives to Adobe Cloud is a new series looking at free and open source alternatives to products available from Adobe Cloud's subscription service.
Linux System ToolsEssential Linux system tools looks at small, indispensable utilities, useful for system administrators as well as regular users.
Linux ProductivityLinux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine.
Home Computer EmulatorsHome computers became commonplace in the 1980s. Emulate home computers including the Commodore 64, Amiga, Atari ST, ZX81, Amstrad CPC, and ZX Spectrum.
Now and ThenNow and Then examines how promising open source software fared over the years.
Linux at HomeLinux at Home looks at a range of home activities where Linux can play its part, making the most of our time at home, keeping active and engaged.
Linux CandyLinux Candy opens up to the lighter side of Linux. Have some fun!
Best Free Android AppsBest Free Android Apps. There's a strict eligibility criteria for inclusion in this series
Programming BooksThese best free books accelerate your learning of every programming language
Programming TutorialsThese free tutorials offer the perfect tonic to the free programming books series
Stars and StripesStars and Stripes is an occasional series looking at the impact of Linux in the USA
Share this article

Share your Thoughts

This site uses Akismet to reduce spam. Learn how your comment data is processed.