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.
- 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.
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