UGENE is a free cross-platform genome analysis suite.
It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install.
Main features:
Integrated tools
-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.
User interface
-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 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;
-Support for cloud computing: running computational tasks on Amazon EC2 cloud;
-Support for supercomputers and distributed computing.
Cooperation
-Can be used for education purposes 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.
