A-Z List of Software
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PACKAGE | NOTES |
---|---|
ABAQUS | Finite Element Analysis package |
acpype | Generate topologies for chemical compounds |
ADF/AMS | Amsterdam Modeling Suite (DFT, semi-empirical, reactive force fields and fluid thermodynamics) |
Affymetrix Power Tools (APT) | Algorithms for analyzing and working with GeneChip™ arrays |
AIMall | Software for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems. |
Alphafold | application for predicting models of protein structures |
AMBER | A general purpose molecular mechanics/dynamics suite |
AMICO | Diffusion magnetic resonance data processing in python |
Anaconda Python | A scientific python distribution |
ANSWERS | A suite of monte-carlo nuclear simulation tools |
Ansys Mechanical | Ansys finite element analysis application |
Apache Spark | Cluster computing with Hadoop |
Aspera | ascp fast downloader |
Autodock4 and Vina | Autodock4 and Vina – Molecular docking tools |
BBTools | Suite of tools designed for analysis of DNA and RNA sequence data. |
Bio-informatics Helper Modulefile | Modulefile to make more Bio-informatics apps available |
BLAST | suite of tools for comparing primary biological sequence information |
Boost | C++ library. |
Bowtie2 | tool for aligning sequencing reads to long reference sequences. |
Breseq | Short-read DNA re-sequencing data processing |
bwa-mem2 | Burrow-Wheeler Aligner |
Canu | Hierarchical assembly pipeline for high-noise single-molecule sequencing. |
CASTEP | CASTEP is a leading code for calculating the properties of materials from first principles |
CASTEPconv | Script to automate CASTEP convergence calculations |
Cell2Location | Python based transcriptomics for cells |
CFX | CFX is a general purpose fluid dynamics product from ANSYS |
Chainer | Deep-learning GPU-capable framework in python |
CHARMM | Macromolecular mechanics |
CheckM | Quality assessment of genomes recovered from isolates, single cells, or metagenomes. |
ChemShell | Interactive shell for computational chemistry calculations |
Chimera | UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures. |
cmake | Cross-platform, open-source build system |
Code_Aster | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
Code_Saturne | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
Compucell3d | Virtual Tissue in silico simulation modelling environment. |
COMSOL | Multiphysics solver |
CP2K | Atomistic and molecular simulations |
CRYSTAL | Ab initio simulations of periodic systems |
Crystal Analysis Tool (draft) | Code for analysing output of atomistic simulations |
CSD-System | The Cambridge Structural Database |
cuda-torch | GPU enabled machine learning framework |
CUDA, cuDNN, NCCL, TensorRT and HPC-SDK | Nvidia CUDA libraries and compiler |
Dakota | A Multilevel Parallel Object-Oriented Optimization Framework |
DAMASK | DAMASK is used for the simulation of crystal plasticity within a finite-strain continuum mechanical framework. |
dcm2niix | DICOM to the NIfTI file converter |
DeepLabCut | Tensorflow based markerless pose estimation of animals performing various tasks. |
Diamond | Sequence aligner for protein and translated DNA searches |
DL_MESO | General purpose mesoscale simulation package. LBE and DPD. |
DL_MONTE2 | Monte Carlo simulation of condensed phases. |
DL_POLY | General purpose classical molecular dynamics |
eggNOG mapper | Fast functional annotation of novel sequences. |
EMsoft | Computation and visualization of scanning electron microscopy diffraction patterns. |
Fasta_number | Replace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commend-line argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc. |
FastANI | Fast alignment-free computation of whole-genome Average Nucleotide Identity |
FastTree | Infer approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. |
FDS | Large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. |
FEAT-WMT | Finite Element Weld Modelling Tool. |
FeGenie | Identify potential homologs and operons that may be linked to the microbial iron cycle |
FEPX | Polycrystal Generation and Meshing |
FFTW | FFTW - Fast Fourier Transfrom library |
fico-xpress | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
Flame | Agent-based modelling system |
Fluent | A computational fluid dynamics package |
Freesurfer | Processing and visualisation of structural and functional brain imaging data |
FSL | Library of analysis tools for FMRI, MRI and DTI brain imaging data |
GAMESS-US | A general ab initio quantum chemistry package. |
Gaussian 09 | Performs semi-empirical and ab-initio molecular orbital calculations |
Gaussian 16 | Performs semi-empirical and ab-initio molecular orbital calculations |
GDAL | Translator library for raster and vector geospatial data formats |
Geant 4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. |
gedit - a simple text editor | A simple text editor, similar to notepad |
GenX | Refine x-ray, neutron reflectivity data and surface x-ray diffraction data |
GeoChemFoam | An open source pore-scale numerical simulator based on OpenFOAM |
GEOS | C++ port of the Java Topology Suite (JTS) |
git & git-lfs | Version Control |
GNU Compilers | gcc, g++ and gfortran |
Gnuplot | A command-line driven graphing utility. |
Gold suite | Protein Docking |
gprMax | Electromagnetic wave propagation simulation |
gpyro | Open source computer model that describes the thermal response of solid materials exposed to radiative or convective heating, including thermo-oxidative pyrolysis of the condensed phase. |
Grace / xmgrace | 2D interactive plotting tool |
GROMACS | Molecular Dynamics simulation package. |
GTDB-tk | Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. |
Guppy | GPU enabled basecaller |
HDF5 | Library and tools to process hierarchical data format files for large scientific data files. |
HMMRATAC | HMMRATAC peak caller for ATAC-seq data |
HOMER | Software for motif discovery and next generation sequencing analysis |
HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
HYPRE | High performance preconditioners and solvers featuring multigrid methods |
Intel Compilers | icc, icpc and ifort (recommended when compiling your own software on the CSF) |
InterProScan | Scan sequences against InterPro's member database signatures |
ispc | Intel ispc experimental SPMD compiler |
JAGS | Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. |
Java Compilers | Java compiler |
JPEG | Independent JPEG Group's JPEG library and tools |
Julia | Power mathematical programming and scripting language with native parallel capability |
Jupyter Notebook | Web-based python notebook |
Kaiju | Taxonomic classification of high-throughput sequencing reads. |
Keras | Neural Network python API using Tensorflow |
LAMMPS | Classical molecular dynamics code. |
lens (Light Efficient Network Simulator) | Lens is an efficient, yet flexible, neural network simulator that runs on a variety of platforms, is able to handle large, complex simulations |
LS-DYNA | A general purpose explicit solver from ANSYS |
MACS | Model-based Analysis of ChIP-Seq (MACS) |
MAFFT | Multiple alignment program for amino acid or nucleotide sequences |
Materials Studio | Materials modelling and simulation application (chemical, materials, pharmaceutical) |
Mathematica | Numeric and symbolic computing and programming |
MATLAB | Numerical computation, visualization and programming |
MaxBin | Binning assembled metagenomic sequences |
MaxQuant | proteomics software package |
MDAnalysis | Python library to analyze trajectories from molecular dynamics (MD) simulations. |
Medaka | Create a consensus sequence from nanopore sequencing data |
MEGAHIT | Fast metagenomics assembly tool |
MemeSuite | Motif-based sequence analysis tools |
Microsoft R Open (MRO) | Statistical computing and graphics. Includes bioconductor. |
Minimap2 | Sequence alignment |
miRDeep2 | Discovers active known or novel miRNAs from deep sequencing data |
MKL | Intel Math Kernel Library of optimized maths routines |
Modeltest-NG | Selection of best-fit model of evolution for DNA and protein alignments |
MOE | Molecular Operating Environment |
MOLCAS@UU | Ab initio quantum chemistry software |
MOLDEN | Molecular Graphics Visualisation Tool |
Molpro | Ab initio quantum chemistry software |
Monai | Framework for deep learning in healthcare imaging |
mopac | Semiempirical quantum chemistry software package |
Mothur | Tool for processing data generated from several DNA sequencing methods |
MPI (OpenMPI) | Message Passing Interface library |
MrBayes | Bayesian Inference of Phylogeny |
MRIcron | NIfTI format image viewer |
mumax | GPU-accelerated micromagnetic simulation |
NAG Libraries | User callable routines for mathematical and statistical computation |
NAMD | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
NBO | Natural Bond Orbital program (Electron analysis) |
Neper | Polycrystal Generation and Meshing |
ninja | Software build system |
NWChem | ab initio quantum chemistry |
ONETEP | Linear-scaling code for quantum-mechanical calculations based on density-functional theory. |
Openbabel | Open Babel is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas. |
Openeye | A portfolio of molecular modeling applications for pharmaceutical research. |
OpenFOAM | Fluid dynamics platform |
OpenMolcas | Quantum chemistry software package using a multiconfigurational approach to the electronic structure. |
OpenMP | Open Multi-Processing library |
ORCA | Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry |
ovito | Scientific visualization and analysis of atomistic simulation data |
p7zip | 7z archive compression and decompression |
Packmol | Initial configurations for Molecular Dynamics Simulations by packing optimization |
ParaView | Scientific data visualization using parallel software rendering. |
PartMC | Monte Carlo code for atmospheric aerosol simulation |
PBMPI | Bayesian phylogenetic reconstruction |
PGI Compilers | PGI c/c++/fortran/openacc compilers |
Phenix and Rosetta Commons | Python-based Hierarchical ENvironment for Integrated Xtallography |
pigz and unpigz | Parallel gzip file compression/decompression |
PRISMS-PF | Parallel finite element code for microstructural evolution |
Prodigal | Protein-coding gene prediction. |
PROJ | Geospatial coordinates coordinate reference system transformations |
Prokka | Annotate bacterial, archaeal and viral genomes |
Proxy (for web downloads) | Envronment setup to give name of proxy server |
PSA | Chemistry related app |
PubChemPy | PubChem interaction in Python |
Pymol | Pymol is a molecular visualisation tool. |
pyro-ppl | Universal probabilistic programming language (PPL) written in Python and supported by PyTorch on the backend |
PyTorch | Deep learning framework in python |
Quantum Espresso | Ab initio simulations of periodic systems |
R & bioconductor | Statistical computing and graphics. Includes bioconductor. |
RAxML | Maximum Likelihood based inference of large phylogenetic trees |
Relion | Statistical Cryo-EM reconstruction |
RepeatMasker | screens DNA sequences for interspersed repeats and low complexity DNA sequences |
Rosetta Commons | Algorithms for computational modeling and analysis of protein structures |
RSEM | Software package for estimating gene and isoform expression levels from RNA-Seq data |
RStudio | GUI-based development environment for R |
Salmon | Transcript quantification from RNA-seq data |
scikit-cuda | Python interfaces to many of the functions in the CUDA device/runtime libraries. |
ScLimbic | Automatic brain image segment |
SCons | Software configuration tool |
Serpent | Monte-carlo Nuclear reactor physics |
Singularity | Container execution |
SLiM | Evolutionary simulation framework |
SNPTest | Program for the analysis of single SNP association in genome-wide studies. |
SPAdes | Genome assembler toolkit |
SQLite browser (DB4S) | Graphical browser for sqlite files |
STAR | Spliced Transcripts Alignment to a Reference |
StarCCM+ | A computation continuum mechanics application |
Structure | Software package for using multi-locus genotype data to investigate population structure. |
subread | a tool kit for processing next-gen sequencing data |
Subversion (svn) | Version Control |
TBB | Intel Thread Building Blocks for parallel software development. |
Telemac | Free-surface flow solvers. |
Tensorflow | Data flow graph processing on GPUs and CPUs |
TEtranscripts | Including transposable elements in differential enrichment analysis of sequencing datasets. |
theano | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
Towhee | Towhee is a Monte Carlo molecular simulation code. |
Trimmomatic | Program to perform a variety of useful trimming tasks for Illumina paired-end and single ended data. |
TURBOMOLE | Quantum chemistry – electronic structure calculations |
UDUNITS | C library and tool for units of physical quantities |
UKBioBank Helper Modulefile | Environment variables to help access UK BioBank full-release datasets. |
UMMAP | UMMAP is a trajectory analysis package for molecular dynamics type simulations. |
unzip | Extract files from zip archives |
USEARCH | Sequence analysis tool |
VASP | The Vienna Ab initio Simulation Package |
Visual Colloids | Visual Colloids is used to produce images of colloidal systems. |
VMD | Molecular Graphics Visualisation Tool |
Votca | VOTCA is a software package which focuses on the analysis of molecular dynamics data. |
VSCode | A popular source-code editor by Microsoft. |
VSEARCH | Sequence analysis tool |
WPS | Weather Research and Forecasting Preprocessors |
WRF | Weather Research and Forecasting |
WRF-Chem | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
zstd | fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios |