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14.2 > Academic > ugene (35.0)

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.

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

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

- 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)
- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers)
- clustalo (Clustal Omega)
- clustalw (Multiple Sequence Alignment)
- cufflinks (A reference-guided assembler for RNA-Seq experiments)
- cutadapt (Trim adapters from high-throughput sequencing reads)
- diamond (A sequence aligner for protein and translated DNA)
- fastqc (A quality control tool for high throughput sequence data)
- HMMER (Biosequence analysis using profile hidden Markov models)
- kraken (Assign taxonomic labels to short DNA sequences)
- MetaPhlAn (Metagenomic Phylogenetic Analysis)
- ncbi-blast (BLAST: Basic Local Alignment Search Tool)
- ncbi-blast+ (BLAST+ Command Line Applications)
- PhyML (Phylogenetic estimation using Maximum Likelihood)
- samtools-legacy (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-legacy (Generic indexer for TAB-delimited genome position files )
- tophat (Splice junction mapper for RNA-Seq reads)
- trimmomatic (A flexible read trimming tool for Illumina NGS data)
- vcftools (A program package designed for working with VCF files)

Alternatively, check the program's website if you want to get them

This requires: qt5-webkit

Maintained by: Petar Petrov
Keywords: bioinformatics,alignment,sequence,biology
ChangeLog: ugene


Source Downloads:
ugene-35.0.tar.gz (c1cb1ee73140d09568706f1fc1b798dd)

Download SlackBuild:
ugene.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Individual Files:

Validated for Slackware 14.2

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