A-Z List of Software
Not all software is accessible to all users. Where restrictions apply, typically licensing, this is detailed in the documentation.
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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 |
| Alphafold 3 | A program developed by Google DeepMind and Isomorphic Labs to efficiently predict 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 Fluent | A computational fluid dynamics package |
| 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. |
| BEAST 2 | Bayesian phylogenetic analysis of molecular sequences |
| 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. |
| CARLA | Autonomous driving systems using the Unreal Engine. |
| 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. |
| COLMAP | general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline |
| Compucell3d | Virtual Tissue in silico simulation modelling environment. |
| COMSOL | Multiphysics solver |
| ContigExtender (contig-extender) | Extend contigs, complementing de novo assembly. |
| CoverM | Fast DNA read coverage and relative abundance calculator focused on metagenomics applications. |
| CP2K | Atomistic and molecular simulations |
| Critic2 | Analysis of quantum mechanical calculation results in molecules and periodic solids. |
| 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 |
| Curl and libcurl | Downloader and development library |
| 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. |
| Deleting or Modifying Jobs (Slurm) | Deleting or Modifying Jobs |
| dfnWorks | Parallelized three-dimensional discrete fracture networks (DFN) creation and simulation of flow and transport. |
| 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 |
| DualSPhysics | DualSPhysics - for free-surface flow phenomena where Eulerian methods can be difficult to apply. |
| 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 |
| 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. |
| GATK | Variant discovery and genotyping tools |
| Gaussian 09 | Performs semi-empirical and ab-initio molecular orbital calculations |
| Gaussian 16 | Performs semi-empirical and ab-initio molecular orbital calculations |
| Gaussian16 Linda (multinode) | Multi-node version of Gaussian |
| 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 |
| gnina | A deep learning framework for molecular docking |
| GNU Compilers | gcc, g++ and gfortran |
| Gnuplot | A command-line driven graphing utility. |
| Gold suite | Protein Docking |
| gprMax | Electromagnetic wave propagation simulation |
| gpyro | Models the thermal response of solid materials exposed to radiative or convective heating |
| 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 (no longer recommended please use intel oneAPI) |
| Intel oneAPI | icx, icpx and ifx (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 (slurm) | Web-based python notebook |
| Kaiju | Taxonomic classification of high-throughput sequencing reads. |
| KAS-Analyzer | a new comprehensive computational framework for exploring KAS-seq data |
| 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 |
| LoFreq | Fast and sensitive variant calling from next-gen sequencing data |
| 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 |
| Multiwfn | electronic wavefunction analysis methods |
| 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. |
| OPAL | Parallel open source tool for charged-particle optics in linear accelerators |
| 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 |
| PyCharm | Python IDE |
| 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 |
| SAMTools | Tools for manipulating alignments in the SAM format |
| 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 / Apptainer | 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 | Weather Research and Forecasting (WRF) model coupled with Chemistry |
| xnedit - a simple text editor | A simple text editor, similar to Notepad |
| zstd | fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios |