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.
Website: ugene.net
Support: Manual
Developer: Unipro
License: GNU General Public License v2.0
UGENE is written in C++. Learn C++ with our recommended free books and free tutorials.
Return to Bioinformatics Tools | Return to Desktop Genome Browsers
| Popular series | |
|---|---|
 | The largest compilation of the best free and open source software in the universe. Each article is supplied with a legendary ratings chart helping you to make informed decisions. |
 | Hundreds of in-depth reviews offering our unbiased and expert opinion on software. We offer helpful and impartial information. |
 | The Big List of Active Linux Distros is a large compilation of actively developed Linux distributions. |
 | Replace proprietary software with open source alternatives: Google, Microsoft, Apple, Adobe, IBM, Autodesk, Oracle, Atlassian, Corel, Cisco, Intuit, and SAS. |
 | Awesome Free Linux Games Tools showcases a series of tools that making gaming on Linux a more pleasurable experience. This is a new series. |
 | Machine Learning explores practical applications of machine learning and deep learning from a Linux perspective. We've written reviews of more than 40 self-hosted apps. All are free and open source. |
 | New to Linux? Read our Linux for Starters series. We start right at the basics and teach you everything you need to know to get started with Linux. |
 | Alternatives to popular CLI tools showcases essential tools that are modern replacements for core Linux utilities. |
 | Essential Linux system tools focuses on small, indispensable utilities, useful for system administrators as well as regular users. |
 | Linux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine. |
 | Surveys popular streaming services from a Linux perspective: Amazon Music Unlimited, Myuzi, Spotify, Deezer, Tidal. |
 | Saving Money with Linux looks at how you can reduce your energy bills running Linux. |
 | Home computers became commonplace in the 1980s. Emulate home computers including the Commodore 64, Amiga, Atari ST, ZX81, Amstrad CPC, and ZX Spectrum. |
 | Now and Then examines how promising open source software fared over the years. It can be a bumpy ride. |
 | Linux 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 Candy reveals the lighter side of Linux. Have some fun and escape from the daily drudgery. |
 | Getting Started with Docker helps you master Docker, a set of platform as a service products that delivers software in packages called containers. |
 | Best Free Android Apps. We showcase free Android apps that are definitely worth downloading. There's a strict eligibility criteria for inclusion in this series. |
 | These best free books accelerate your learning of every programming language. Learn a new language today! |
 | These free tutorials offer the perfect tonic to our free programming books series. |
 | Linux Around The World showcases usergroups that are relevant to Linux enthusiasts. Great ways to meet up with fellow enthusiasts. |
 | Stars and Stripes is an occasional series looking at the impact of Linux in the USA. |