| style="width:25%; background: #cccccc;" | <Strong>Package</Strong>

| style="width:75%; background: #cccccc;" | <Strong>Description</Strong>

| Anaconda is the leading open data science platform powered by Python. (See also [[Applications/Miniconda|Miniconda]]).

|  Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.

| 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.

| 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.  

| 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.

| Delft3D is a world-leading 3D modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.

| [[Applications/ffmpeg|ffmpeg]]

| FFmpeg is a very fast video and audio converter that can also grab from a live audio/video source.

| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognize lexical patterns in text.

| [[applications/Gcc|gcc]]

| Gnuplot is a portable command-line-driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.

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| [[applications/guppy|Guppy]]

| Local accelerated basecalling for Nanopore data.

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| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.

| HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers as well as the freely available implementation of the High-Performance Computing Linpack Benchmark.

|  Likwid is a simple to install and use tool suite of command-line applications for performance-oriented programmers.

|  General-purpose finite element program capable of simulating complex real-world problems.

|  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 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 create genome databases.

| Mathematica

|  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 is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.

| MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.

| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.

| ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.

| 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 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 is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.

| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.

| 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 is an open-source programming language and software environment for statistical computing and graphics.

| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.

| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.

|  Integrated software libraries, databases, and system utilities which provide common programming and data analysis environment for Solar Physics

| Software pipeline for analysing ABySS-assembled transcriptome contigs

| 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 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.