Modules

Applications

This is a list of all applications installed on Viper. If you are looking for an application that requires a special license visit: Applications requiring special licenses

Click on the links below for support on the individual applications:

Package	Description
ABySS	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
Albacore	Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms
Anaconda	Anaconda is the leading open data science platform powered by Python. (See also Miniconda).
Autotools	Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 .
BayesTraits	BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
Bison	Bison, is a parser generator that is part of the GNU Project. Bison reads a specification of a context-free language, warns about any parsing ambiguities, and generates a parser (either in C, C++, or Java) which reads sequences of tokens and decides whether the sequence conforms to the syntax specified by the grammar.
Blender	Blender is the free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
Bowtie1	The aligner is typically used with short reads and a large reference genome, or for whole-genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences.
Bowtie2	Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method.
Bridger	Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
Centrifuge	Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem.
CMake	CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
Crop	CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
CP2K	CP2K is a quantum chemistry and solid-state physics software package that can perform atomistic simulations of solid-state, liquid, molecular, periodic, material, crystal, and biological systems.
CUDA	CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes.
Cufflinks	Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Delft3D	Delft3D is a world-leading 3D modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
FDS-SMV	Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.
ffmpeg	ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
Flex	Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognize lexical patterns in text.
Fiji	Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community.
gcc	gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
GNUplot	Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
Grace	Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
Guppy	Local accelerated basecalling for Nanopore data.
HyPhy	HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
Intel Parallel Studio	Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing.
IQtree	stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
Java	Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented.
Julia	Julia is a high-level general-purpose dynamic programming language that was originally designed to address the needs of high-performance numerical analysis and computational science
Likwid	Likwid is a simple to install and use tool suite of command-line applications for performance-oriented programmers.
Mafft	MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
Maker	MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
Mathematica	Symbolic mathematical computation program.
Matlab	Numerical Computing Environment.
Mercurial	Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap.
Mpich	MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Miniconda	Miniconda is a lite version of anaconda used for creating virtual environments.
Minimap2	Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
Mono	.NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
MrBayes	MrBayes: Bayesian Inference of Phylogeny
Mvapich2	MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.
Ncbi blast	It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Netcdf-c	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Nwchem	NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
Obitools	The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information.
Openfoam	OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
OpenMPI	Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
Orca	ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
Packmol	PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
Paraview	ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
Perl	Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large number of libraries.
PGI	PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi-core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
Prinseq-lite	PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
Python	Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
Qiime2	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community developed.
Quantum Package Shell	Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2).
R	R is an open source programming language and software environment for statistical computing and graphics.
RaXML	RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
Readline	GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash.
RStudio	RStudio provides popular open source and enterprise-ready professional software for the R statistical computing environment.
Samtools	Tools (written in C using htslib) for manipulating next-generation sequencing data
Savu	Python package to assist with the processing and reconstruction of parallel-beam tomography data.
Scalapack	The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
Siesta	SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
STAR	Ultrafast universal RNA-seq aligner.
Tophat	It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons.
Transabyss	Software pipeline for analysing ABySS-assembled transcriptome contigs
Transrate	Transrate is software for de-novo transcriptome assembly quality analysis
Trinityrnaseq	Trinity assembles transcript sequences from Illumina RNA-Seq data.
Utilities	General utilities module including zip, wget and git utilities.
Voxfe	VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised easily.
Yt	yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography.

Libraries

Library software listed here refer to those list in the libs section of typing module avail.

Library	Description
Boost	C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
Expat	Expat XML parser library in C
Fftw3	FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT).
Gsl	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
Hdf5	HDF5 is a data model, library, and file format for storing and managing data.
Hypre	A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
Libbeagle	BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
Libgd	The module LibGD is an open-source code library for the dynamic creation of images.
Libjpeg-turbo	The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression
Libpng	The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files.
Ncurses	ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.
Openblas	OpenBLAS is an optimized BLAS library (based on GotoBLAS2 1.13 BSD version).
Parmetis	ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
Qt	Qt is a cross-platform framework, that is usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
Zlib	zlib is a software library used for data compression.

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