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 |
| 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. |
| 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. |
| 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 |
| CoverM | CoverM calculates coverage of genomes/MAGs coverm genome or individual contigs coverm contig. Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats. |
| 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. |
| dfnWorks | dfnWorks is a parallelized computational suite to generate three-dimensional discrete fracture networks (DFN) and simulate flow and transport. Developed at Los Alamos National Laboratory, it has been used to study flow and transport in fractured media at scales ranging from millimeters to kilometers. |
| 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 |
| 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 |
| 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. |
| 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. |
| 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 |
| 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 | 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 |