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":
· 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.
· 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.
· 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.
What's New in This Release: [ read full changelog ]
The new release includes the long awaited DNA assembly functionality. Since now short read alignment can be performed with UGENE. Two methods are available:
· Genome aligner plugin, based on unique algorithm;
· Port of popular open-source tool Bowtie.
· A lot of improvements were made to console version of UGENE. It has become much more flexible and powerful. Since now it is possible to use command line version of UGENE in complex scripts and shell scenarios. There are useful prebuilt scenarios available: align, convert, find repeats etc. Check documenation for more details.
Other cool features available:
· New advanced sequence analysis algorithm based on weight matrices;
· Circular view improvements: zoooming, rotating and more;
· Support for advanced search options of NCBI BLAST in redesigned Remote Request plugin.
· Alignment logo feature;
· New fancy widget: global sequence overview;
· Tree viewer is re-worked: stand-alone interface, new visualization modes.
· GFF format now supports writing;
· Scripting framework is introduced;
· and a lot more...