Unipro UGENE is a multiplatform open-source software with the main
goal of assisting molecular biologists without much expertise in
bioinformatics to manage, analyze and visualize their data.

UGENE integrates widely used bioinformatics tools within a common user
interface. The toolkit supports multiple biological data formats and
allows the retrieval of data from remote data sources. It provides
visualization modules for biological objects such as:

- annotated genome sequences
- Next Generation Sequencing (NGS) assembly data
- multiple sequence alignments
- phylogenetic trees
- 3D structures

Most of the integrated algorithms are tuned for maximum performance by
the usage of multithreading and special processor instructions. UGENE
includes a visual environment for creating reusable workflows that can
be launched on local resources or in a High Performance Computing
(HPC) environment. UGENE is written in C++ using the Qt framework. The
built-in plugin system and structured UGENE API make it possible to
extend the toolkit with new functionality.

CITING:
Unipro UGENE: a unified bioinformatics toolkit
Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
Bioinformatics 2012 28: 1166-1167

EXTERNAL TOOLS
UGENE can use and drive a number of external tools, providing a nice
and unified GUI. These are not needed at build time, but are highly
recommended for the complete (and extended) functionality of the
program. All of them are available at SlackBuilds.org:

- bedGraphToBigWig (Convert bedGraph to bigWig file)
- bedtools (A powerful toolset for genome arithmetic)
- bowtie (A short read aligner of DNA sequences)
- bowtie2 (A tool for aligning sequencing reads)
- bwa (Burrows-Wheeler Aligner)
- cap3 (CAP3: A DNA sequence assembly program)
- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
- cistrome-conductGO (Find the top-n highest expressed TFs)
- cistrome-extra (Cistrome Applications Harvard extra apps)
- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
- clustalo (Clustal Omega)
- clustalw (Multiple Sequence Alignment)
- cufflinks (A reference-guided assembler for RNA-Seq experiments)
- cutadapt (Trim adapters from high-throughput sequencing reads)
- fastqc (A quality control tool for high throughput sequence data)
- HMMER (Biosequence analysis using profile hidden Markov models)
- ncbi-blast (BLAST: Basic Local Alignment Search Tool)
- ncbi-blast-plus (BLAST+ Command Line Applications)
- PhyML (Phylogenetic estimation using Maximum Likelihood)
- samtools (Sequence Alignment/Map Tools)
- snpEff (Genetic variant annotation and effect prediction toolbox)
- spades (SPAdes Genome Assembler)
- spidey (mRNA-to-genomic alignment)
- t_coffee (A multiple sequence alignment program)
- tabix (Generic indexer for TAB-delimited genome position files )
- tophat (Splice junction mapper for RNA-Seq reads)
- vcftools (A program package designed for working with VCF files)

Alternatively, check the program's website if you want to get them
precompiled: http://ugene.net/external.html
