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Unipro UGENE is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools for visualization, analysis, annotation of genetic sequences. Unipro UGENE is a powerful piece of software that provides you with advanced tools for creating, editing and annotating nucleic acid and protein sequences. In addition, the application also helps you view and edit chromatograms. In terms of features, let us just say that the application does not suffer any kind of shortages. It comes with support for multiple biological data formats and it provides visualization modules for objects ranging from next-generation sequencing data all the way up to phylogenetic trees and other complex 3D structures. aking all of the above into careful consideration, Unipro UGENE is a complex computational tool that provides bioinformatics researchers with a new way to process NGS data.

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 short reads to reference alignment using Bowtie;
De novo assembly with CAP3;
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.

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