UGENE is a free cross-platform genome analysis suite.
It works perfectly on Linux, Windows or Mac OS and requires only a few clicks to install.
Here are some key features of "UGENE":
Main features:
· Multiple sequence alignment using MUSCLE 3 and MUSCLE 4;
· HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
· PCR Primers design using Primer 3;
· Protein secondary structure prediction using GOR IV and PSIPRED;
· Search for restriction enzymes and integration with REBASE;
· Extremely fast repeat finder;
· Search for transcription factor binding sites using SITECON;
· ORF finder;
· Complete Smith-Waterman algorithm implementation.
User Interface:
· Visual and interactive genome browsing;
· Chromatograms visualization;
· 3D viewer for files in PDB and MMDB formats;
· Multiple sequence alignment editor;
· Easy to use workflow designer for custom computational workflows.
· High performance computing in UGENE
· Complete support of modern multicore processors and SSE instructions;
· Out of the box support of modern GPUs using NVIDIA CUDA and ATI Stream;
· Integrated solutions for Cell Broadband Engine;
· Private solutions for supercomputers and distributed computing.
Cooperation:
· Can be used for education in schools and universities;
· Features to be included into the next release are initiated by users;
· UGENE team is ready for collaboration in related projects, both free or commercial.
Requirements:
· Qt
What's New in This Release: [ read full changelog ]
New plugins:
· MUSCLE 4 - a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
· CUDA Support - an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms.
New features and bug fixes:
· CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
· The one of the most awaited features: sequence editing has been added;
· Exporting annotation tables to CSV has been provided;
· HMM2 models support has been added to HMM3;
· And many others. See the changelog for a full list of improvements.
