Available Software

Introduction

Beside the original packages from the Linux distribution, we provide various other software packages.

The additional software is compiled for the following platforms:

  • Debian 5 (lenny)
  • Debian 6 (squeeze)
  • Debian 7 (wheezy)
  • Ubuntu 12.04 LTS / Linux Mint 13

Our environment modules software configuration and selected software packages  can also be used on:

  • Cygwin
  • Centos 6
  • Fedora 18+
  • OpenSuSE 12.2

Software Development

If you want to compile and test software on your own, you can use our development servers (ssh username@dev-linuxdistribution):

  • dev-debian5 - for the old cluster
  • dev-debian6
  • dev-debian7 - for the new cluster
  • dev-ubuntu12 - for e.g. desktop computers
  • dev-centos6

Software List

The list below is the current state of ported software for the usage on the current and new cluster.

You can use this software with the environment modules command:

module load package/version 

The list does not contain software which comes as Perl, Python or Ruby packages, even if they are already available.

For installed Python packages call:

  • module load python
  • yolk -l

For installed Ruby packages call:

  • module load ruby
  • gem list

Available Software Modules

  • adda/0.1.0 : decomposes protein sequences based on all-vs-all pairwise BLAST alignments
  • adda/2010-05-10 : decomposes protein sequences based on all-vs-all pairwise BLAST alignments
  • adxv/1.9.8 : a program to display X-Ray diffraction images
  • al2co/2011-08-15 : calculates positional conservation for a multiple sequence alignment
  • alignace/1.1 : a program which finds sequence elements conserved in a set of DNA sequences
  • alignlib/0.4.5 : is a C++ library for computing and manipulating sequence alignments of protein sequences
  • alscript/2.07 : format multiple sequence alignments in PostScript for publication and to assist in analysis
  • annie-tools/1.0 : Eisenhaber.GRP tools for the Annotator
  • apache-ant/1.8.3 : a Java library and command-line tool that helps building software
  • apbs/1.4 : software for evaluating the electrostatic properties of nanoscale biomolecular systems
  • aqua/3.2 : calculates restraint violations from a PDB or BIOSYM file
  • arp-warp/7.3 : builds proteins, RNA/DNA, secondary structure, side chains, loops, solvent and ligands
  • artemis/14.0.0 : a DNA sequence viewer and annotation tool
  • bam2fastq/1.1.0 : extract sequences from a BAM file
  • bamtools/2.1.1 : a C++ API & toolkit for reading/writing/manipulating BAM files
  • bedtools/2.16.2 : Utilities to address common genomics tasks such as finding feature overlaps and computing coverage
  • bedtools/2.17.0 : Utilities to address common genomics tasks such as finding feature overlaps and computing coverage
  • best/3.4.4 : a program for optimal planning of X-ray data collection from protein crystals
  • bioawk/2011-08-10 : fasta, fastq, SAM, BED, GFF aware awk programming
  • biomotif/4.1b : motif search program
  • bioprospector/2004 : discovers conserved transcription factor binding sites among upstream sequences from co-regulated genes
  • blat/34.13 : an alignment tool like BLAST
  • bnp/1.02 : the Buffalo 'n' Pittsburgh interface for complete protein phasing
  • boost/1.51.0 : provides free peer-reviewed portable C++ source libraries
  • bowtie/0.12.5 : short read aligner for short DNA sequences (reads) from next-gen sequencers
  • bowtie/0.12.9 : short read aligner for short DNA sequences (reads) from next-gen sequencers
  • bowtie2/2.0.0 : short read aligner for short DNA sequences (reads) from next-gen sequencers
  • bwa/0.6.2 : read mapping tool based on Burrows-Wheeler transformation
  • cap3/2007-12-21 : a DNA sequence assembly program
  • cast/1.0 : a novel algorithm for low-complexity region detection and selective masking
  • ccp4/6.3.0 : integrated suite of programs to determine macromolecular structures by X-ray crystallography
  • cd-hit/4.5.4 : Cluster Database at High Identity with Tolerance
  • cims/1.0.0 : a computational method to analyze HITS-CLIP data
  • cloudburst/1.1.0 : Highly Sensitive Short Read Mapping with MapReduce
  • clustalwx/2.1 : Clustal W and Clustal X multiple sequence alignment programs
  • clusterit/2.5 : a collection of clustering tools
  • cmake/2.8.8 : a cross-platform, open-source build system
  • cns-solve/1.3 : a flexible multi-level approach the most commonly used algorithms in macromolecular structure determination
  • coot/0.6.2 : is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
  • crest/1.0 : a algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data
  • ctf/3.5 : programs for finding CTFs of electron micrographs
  • cufflinks/1.3.0 : Transcript assembly, differential expression, and differential regulation for RNA-Seq
  • cufflinks/2.0.2 : Transcript assembly, differential expression, and differential regulation for RNA-Seq
  • delly/0.0.9 : an integrated structural variant prediction method
  • disopred/2.43 : intrinsic protein disorder prediction
  • emboss/6.5.7 : a software analysis package specially developed for the needs of the molecular biology
  • far/2.13 : removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q format
  • fastqc/0.10.1 : a quality control application for high throughput sequence data
  • fastx-toolkit/0.0.13 : a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
  • ffmpeg/0.11.1 : a complete, cross-platform solution to record, convert and stream audio and video
  • ffmpeg/1.0 : a complete, cross-platform solution to record, convert and stream audio and video
  • fragrep/2.0 : an efficient algorithm for detecting nucleotide pattern fragments in genomes that occur in a given order
  • gimmemotifs/0.65 : a systematic de novo motif prediction pipeline
  • gmap/2012-07-20 : a genomic mapping and alignment program for mRNA and EST sequences
  • gnu-parallel/2012-08-22: a shell tool for executing jobs in parallel using one or more computers
  • gridengine/2011.11 : a free and open-source batch-queuing system for distributed resource management
  • gridengine-client/2011.11: client binaries for a free and open-source batch-queuing system for distributed resource management
  • gromacs/4.5.1m : is a versatile package to perform molecular dynamics (MIT modified version)
  • gromacs/4.5.5 : is a versatile package to perform molecular dynamics
  • hadoop/1.0.4 : a framework for running applications on large cluster built of commodity hardware
  • handbrake/0.9.8 : a commandline and GUI-based video transcoder
  • hdf5/1.8.9 : HDF5 is a data model, library, and file format for storing and managing data
  • hh-suite/2.0.15 : a software package for sensitive protein sequence searching
  • hkl-2000/098.703g : a package of programs intended for the analysis of X-ray diffraction data collected from single crystals
  • hkl-2000/098.704k : a package of programs intended for the analysis of X-ray diffraction data collected from single crystals
  • hmmer/2.3.2 : Biosequence analysis using profile hidden Markov models
  • hmmer/3.0 : Biosequence analysis using profile hidden Markov models
  • homer/4.1 : a suite of tools for Motif Discovery and ChIP-Seq analysis
  • hyphy/2.1.2 : is an package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning
  • illumina2bam/0.03 : a collection of tools to generate or process BAM/SAM files using Picard Java API
  • illumina2bam/1.10 : a collection of tools to generate or process BAM/SAM files using Picard Java API
  • imagemagick/6.7.7 : ImageMagick is a software suite to create, edit, compose, or convert bitmap images
  • imagic/2012-10-22 : a high end environment for the analysis of images, spectra and other multi-dimensional data-sets
  • inca/2.5 : detects Grid infrastructure problems by executing periodic, automated, user-level testing of Grid software and services
  • irods-tools/3.2 : commandline tools for a data grid software system
  • jad/1.5.8 : Java Decompiler
  • jpredictor/1.23 : a tool for the prediction of cis-regulatory elements
  • kalign2/2.04 : a fast and accurate multiple sequence alignment algorithm
  • kent-ucsc/2.79 : UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs
  • libgtk/1.2 : glib1.2 and libgtk+1.2
  • littler/0.1.1 : a command-line program that provides the R statistical language interpreter without the environment
  • macs/1.3.6.1 : Model-based Analysis for ChIP-Seq
  • macs/1.4.2 : Model-based Analysis for ChIP-Seq
  • macs/2.0.10 : Model-based Analysis for ChIP-Seq
  • mafft/6.910 : multiple alignment program for amino acid or nucleotide sequences
  • maq/0.7.1 : a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way
  • matlab-runtime/717 : matlab compiler runtime
  • meme/4.8.1 : Motif-based sequence analysis tools
  • meme/4.9.0.2rc5 : Motif-based sequence analysis tools
  • motif-suite/3.2.1 : a platform for de novo regulatory motif detection
  • mpich/3.0.2 : a high performance message passing library
  • mummer/3.23 : a modular system for the rapid whole genome alignment of finished or draft sequence
  • muscle/3.8.31 : multiple sequence alignment
  • ncbi-blast/2.2.26 : The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences
  • ncbi-blast+/2.2.26 : The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences
  • ncbi-blast+/2.2.27 : The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences
  • netcdf/4.2.1 : a set of software libraries for sharing array-oriented scientific data
  • node/0.8.1 : is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications
  • novocraft/2.08.03 : an aligner for single-ended and paired-end reads from the Illumina Genome Analyser
  • O/13.0 : is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
  • O/14.0 : a crystallographic toolset
  • oases/0.2.08 : De novo transcriptome assembler for very short reads
  • oligoarray/2.1.3 : compute gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
  • opencv/2.4.1 : a library of programming functions for real time computer vision
  • openmpi/1.6 : a high performance message passing library
  • oracle-jdk/1.6.0 : JDK - Java Platform, Standard Edition Development Kit
  • oracle-jdk/1.7.0 : JDK - Java Platform, Standard Edition Development Kit
  • pagit/1.64 : PAGIT - Post Assembly Genome Improvement Toolkit
  • paml/4.6 : a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood
  • passion/1.2.1 : a pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data
  • pdb2pqr/1.8 : an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
  • phenix/1.8 : a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods
  • phenix/1.8.1 : a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods
  • picard-tools/1.82 : comprises Java-based command-line utilities that manipulate SAM files
  • pindel/0.2.4s : detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data
  • piranha/1.1.1 : a peak-caller for CLIP- and RIP-Seq data
  • postgresql/8.4.16 : PostgreSQL database tools
  • primer3/2.3.5 : a widely used program for designing PCR primers
  • probcons/1.12 : an probabilistic consistency-based multiple alignment of amino acid sequences
  • procheck/3.5.4 : checks the stereochemical quality of a protein structure
  • psipred/3.3 : a highly accurate method for protein secondary structure prediction
  • pymol/1.5.0.1 : a comprehensive software package for rendering and animating 3D structures
  • python/2.7.3 : Python programming language
  • python/3.2.3 : Python programming language
  • python/3.3.0 : Python programming language
  • qualimap/0.6 : facilitate the quality control of alignment sequencing data
  • quest/2.4 : analysis of massively parallel sequencing data from chromatin immunoprecipitations
  • R/2.15.3 : The R Project for Statistical Computing
  • R/3.0.0 : The R Project for Statistical Computing
  • radar/1.1.5 : identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats
  • rnahybrid/2.1.1 : a tool for finding the minimum free energy hybridisation of a long and a short RNA
  • robinhood/2.4.0 : a multi-purpose tool for managing content of large filesystems
  • ruby/1.9.3 : Ruby programming language
  • samtools/0.1.18 : SAM tools provide efficient utilities on manipulating alignments in the SAM format
  • sap/1.1.3 : pairwise protein structure alignment
  • segemehl/0.0.9.4 : a software to map short sequencer reads to reference genomes
  • segemehl/0.1.4 : a software to map short sequencer reads to reference genomes
  • shelx/2013.2 : a set of programs for crystal structure determination from single-crystal diffraction data
  • shogun/2.0.0 : a large scale machine learning toolbox
  • sissrs/1.4 : Genome-Wide Identification of in Vivo Protein-DNA Binding Sites From ChIP-Seq Data
  • situs/2.7.2 : a program for the modeling of atomic resolution structures into low-resolution density maps
  • smalt/0.6.2 : SMALT efficiently aligns DNA sequencing reads with a reference genome
  • snb/2.3 : a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data
  • soapsplice/1.9 : a tool for genome-wide ab initio detection of splice junction sites from RNA-Seq
  • solve/2.13 : automated crystallographic structure solution for MIR, SAD, and MAD
  • spidermonkey/17 : is Mozilla's JavaScript engine written in C/C++
  • sra-toolkit/2.3.2-4 : tools for easy reading (dumping) of sequencing files from SRA database and writing (loading) to the SRA database
  • stamp/1.1 : Alignment, Similarity, & Database Matching for DNA Motifs
  • stampy/1.0.20 : a package for the mapping of short reads from illumina sequencing machines onto a reference genome
  • star/2.1.1d : aligns RNA-seq reads to a reference genome
  • t-coffee/9.03.r1318 : a collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
  • timat/3.4.4 : Tiling Microarray Analysis Tools
  • tophat/1.4.1 : maps short sequences from spliced transcripts to whole genomes
  • tophat/2.0.6 : maps short sequences from spliced transcripts to whole genomes
  • usf/2008-11-28 : Uppsala Software Factory tools
  • vcftools/0.1.9 : a program package designed for working with VCF files
  • velvet/1.2.07 : Sequence assembler for very short reads
  • vienna-rna/2.0.7 : several stand-alone programs for the prediction and comparison of RNA secondary structures
  • vigra/1.8.0 : a computer vision library that puts its main emphasis on customizable algorithms and data structures
  • vmatch/2.1.7 : a versatile software tool for efficiently solving large scale sequence matching tasks
  • vmd/1.9.1 : a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
  • weblogo/2.8.2 : tool for a graphical representation of an amino acid or nucleic acid multiple sequence alignment
  • weeder/1.4.2 : motif discovery in sequences from coregulated genes of a single species
  • wise2/2.4.1 : a program for aligning proteins or protein HMMs to DNA
  • xds/2013 : a program package for the reduction of 2-dimensional data images obtained from crystals irradiated with monochromatic X-rays
  • xmipp/3.0 : a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy
  • xz/5.0.4 : a data compression software with high compression ratio
  • yasm/1.2.0 : Yasm modular assembler