UGENE
UGENE is free open-source cross-platform set of integrated
bioinformatics software.
It integrates dozens of well-known biological tools and
algorithms, mproviding 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
Return
to Bioinformatics Tools Home Page
Last Updated Saturday, April 13 2013 @ 04:22 PM EDT
| 
