Applications
Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list.
Instructions shown only to logged-in-to-wordpress users
The tables of apps for each category are now auto-generated. You should add two custom fields to each software app page:
RI_Summary giving the summary description of the app, and RI_Cat which can be a comma-separated list of one or more of: bioinf, chemistry, cfd, fea, gpu, maths, physics, ml, prog, viz. Categories tool, compiler, library can also be used but these will be displayed in tables on the appropriate page (see menu on left), not here. To add these custom fields you will need to click on ‘Screen Options’ (top-right when in the page editor) and tick ‘Custom Fields’ and then the boxes you need to fill in appear at the bottom of the page editor.
Available application categories: Bio-inf Chemistry CFD FEA Mathematics Physics Machine-learning Programming GPU-capable Visualization Python-packages
Bioinformatics
Please note: More bioinf apps are available than listed here by first running:module load apps/bioinf(then use module avail to list all modules)
|
| PACKAGE | NOTES |
|---|---|
| Affymetrix Power Tools (APT) | Algorithms for analyzing and working with GeneChip™ arrays |
| Alphafold | application for predicting models of protein structures |
| AMICO | Diffusion magnetic resonance data processing in python |
| Aspera | ascp fast downloader |
| 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 |
| 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. |
| Cell2Location | Python based transcriptomics for cells |
| CheckM | Quality assessment of genomes recovered from isolates, single cells, or metagenomes. |
| Compucell3d | Virtual Tissue in silico simulation modelling environment. |
| 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. |
| Diamond | Sequence aligner for protein and translated DNA searches |
| eggNOG mapper | Fast functional annotation of novel sequences. |
| 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. |
| FeGenie | Identify potential homologs and operons that may be linked to the microbial iron cycle |
| Freesurfer | Processing and visualisation of structural and functional brain imaging data |
| GTDB-tk | Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. |
| Guppy | GPU enabled basecaller |
| HMMRATAC | HMMRATAC peak caller for ATAC-seq data |
| HOMER | Software for motif discovery and next generation sequencing analysis |
| InterProScan | Scan sequences against InterPro's member database signatures |
| JAGS | Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. |
| Kaiju | Taxonomic classification of high-throughput sequencing reads. |
| KAS-Analyzer | a new comprehensive computational framework for exploring KAS-seq data |
| LoFreq | Fast and sensitive variant calling from next-gen sequencing data |
| MACS | Model-based Analysis of ChIP-Seq (MACS) |
| MAFFT | Multiple alignment program for amino acid or nucleotide sequences |
| MaxBin | Binning assembled metagenomic sequences |
| MaxQuant | proteomics software package |
| 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 |
| Modeltest-NG | Selection of best-fit model of evolution for DNA and protein alignments |
| Mothur | Tool for processing data generated from several DNA sequencing methods |
| MrBayes | Bayesian Inference of Phylogeny |
| MRIcron | NIfTI format image viewer |
| PBMPI | Bayesian phylogenetic reconstruction |
| Prodigal | Protein-coding gene prediction. |
| Prokka | Annotate bacterial, archaeal and viral genomes |
| 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 |
| Salmon | Transcript quantification from RNA-seq data |
| ScLimbic | Automatic brain image segment |
| SNPTest | Program for the analysis of single SNP association in genome-wide studies. |
| SPAdes | Genome assembler toolkit |
| STAR | Spliced Transcripts Alignment to a Reference |
| Structure | Software package for using multi-locus genotype data to investigate population structure. |
| subread | a tool kit for processing next-gen sequencing data |
| TEtranscripts | Including transposable elements in differential enrichment analysis of sequencing datasets. |
| Trimmomatic | Program to perform a variety of useful trimming tasks for Illumina paired-end and single ended data. |
| UKBioBank Helper Modulefile | Environment variables to help access UK BioBank full-release datasets. |
| USEARCH | Sequence analysis tool |
| VSEARCH | Sequence analysis tool |
Computational Chemistry and Molecular Dynamics
| PACKAGE | NOTES |
|---|---|
| acpype | Generate topologies for chemical compounds |
| ADF/AMS | Amsterdam Modeling Suite (DFT, semi-empirical, reactive force fields and fluid thermodynamics) |
| AIMall | Software for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems. |
| AMBER | A general purpose molecular mechanics/dynamics suite |
| Autodock4 and Vina | Autodock4 and Vina – Molecular docking tools |
| CASTEP | CASTEP is a leading code for calculating the properties of materials from first principles |
| CASTEPconv | Script to automate CASTEP convergence calculations |
| CHARMM | Macromolecular mechanics |
| ChemShell | Interactive shell for computational chemistry calculations |
| Chimera | UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures. |
| 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 |
| 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 |
| 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 |
| Geant 4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. |
| Gold suite | Protein Docking |
| 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. |
| GROMACS | Molecular Dynamics simulation package. |
| HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
| LAMMPS | Classical molecular dynamics code. |
| Materials Studio | Materials modelling and simulation application (chemical, materials, pharmaceutical) |
| MOLCAS@UU | Ab initio quantum chemistry software |
| MOLDEN | Molecular Graphics Visualisation Tool |
| Molpro | Ab initio quantum chemistry software |
| Multiwfn | electronic wavefunction analysis methods |
| NAMD | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
| NBO | Natural Bond Orbital program (Electron analysis) |
| 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. |
| OpenMolcas | Quantum chemistry software package using a multiconfigurational approach to the electronic structure. |
| ORCA | Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry |
| Packmol | Initial configurations for Molecular Dynamics Simulations by packing optimization |
| Phenix and Rosetta Commons | Python-based Hierarchical ENvironment for Integrated Xtallography |
| PSA | Chemistry related app |
| PubChemPy | PubChem interaction in Python |
| Quantum Espresso | Ab initio simulations of periodic systems |
| Rosetta Commons | Algorithms for computational modeling and analysis of protein structures |
| Towhee | Towhee is a Monte Carlo molecular simulation code. |
| TURBOMOLE | Quantum chemistry – electronic structure calculations |
| UMMAP | UMMAP is a trajectory analysis package for molecular dynamics type simulations. |
| VASP | The Vienna Ab initio Simulation Package |
| Visual Colloids | Visual Colloids is used to produce images of colloidal systems. |
| Votca | VOTCA is a software package which focuses on the analysis of molecular dynamics data. |
| 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. |
Computational Fluid Dynamics
| PACKAGE | NOTES |
|---|---|
| CFX | CFX is a general purpose fluid dynamics product from ANSYS |
| Code_Saturne | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
| FDS | Large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. |
| Fluent | A computational fluid dynamics package |
| GeoChemFoam | An open source pore-scale numerical simulator based on OpenFOAM |
| LS-DYNA | A general purpose explicit solver from ANSYS |
| OpenFOAM | Fluid dynamics platform |
| StarCCM+ | A computation continuum mechanics application |
| Telemac | Free-surface flow solvers. |
Finite Element Analysis
| PACKAGE | NOTES |
|---|---|
| ABAQUS | Finite Element Analysis package |
| Ansys Mechanical | Ansys finite element analysis application |
| Code_Aster | 21.02.2019 - This application is being installed. Docs will be updated when it is available. |
| DAMASK | DAMASK is used for the simulation of crystal plasticity within a finite-strain continuum mechanical framework. |
| PRISMS-PF | Parallel finite element code for microstructural evolution |
Mathematics
| PACKAGE | NOTES |
|---|---|
| Dakota | A Multilevel Parallel Object-Oriented Optimization Framework |
| Julia | Power mathematical programming and scripting language with native parallel capability |
| Jupyter Notebook | Web-based python notebook |
| Keras | Neural Network python API using Tensorflow |
| Mathematica | Numeric and symbolic computing and programming |
| MATLAB | Numerical computation, visualization and programming |
| Microsoft R Open (MRO) | Statistical computing and graphics. Includes bioconductor. |
| MKL | Intel Math Kernel Library of optimized maths routines |
| NAG Libraries | User callable routines for mathematical and statistical computation |
| PRISMS-PF | Parallel finite element code for microstructural evolution |
| PyTorch | Deep learning framework in python |
| R & bioconductor | Statistical computing and graphics. Includes bioconductor. |
| RStudio | GUI-based development environment for R |
Multi-physics and solvers
| PACKAGE | NOTES |
|---|---|
| ANSWERS | A suite of monte-carlo nuclear simulation tools |
| COMSOL | Multiphysics solver |
| Dakota | A Multilevel Parallel Object-Oriented Optimization Framework |
| 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. |
| EMsoft | Computation and visualization of scanning electron microscopy diffraction patterns. |
| Geant 4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. |
| gprMax | Electromagnetic wave propagation simulation |
| HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
| mumax | GPU-accelerated micromagnetic simulation |
| PartMC | Monte Carlo code for atmospheric aerosol simulation |
| PRISMS-PF | Parallel finite element code for microstructural evolution |
| Serpent | Monte-carlo Nuclear reactor physics |
Neural Networks and Machine Learning
| PACKAGE | NOTES |
|---|---|
| Chainer | Deep-learning GPU-capable framework in python |
| cuda-torch | GPU enabled machine learning framework |
| DeepLabCut | Tensorflow based markerless pose estimation of animals performing various tasks. |
| Keras | Neural Network python API using Tensorflow |
| 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 |
| Monai | Framework for deep learning in healthcare imaging |
| PyTorch | Deep learning framework in python |
| Tensorflow | Data flow graph processing on GPUs and CPUs |
Programming and Development
| PACKAGE | NOTES |
|---|---|
| Anaconda Python | A scientific python distribution |
| Apache Spark | Cluster computing with Hadoop |
| Boost | C++ library. |
| Chainer | Deep-learning GPU-capable framework in python |
| cmake | Cross-platform, open-source build system |
| Flame | Agent-based modelling system |
| git & git-lfs | Version Control |
| GNU Compilers | gcc, g++ and gfortran |
| HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
| Java Compilers | Java compiler |
| Julia | Power mathematical programming and scripting language with native parallel capability |
| Jupyter Notebook | Web-based python notebook |
| Keras | Neural Network python API using Tensorflow |
| MATLAB | Numerical computation, visualization and programming |
| Microsoft R Open (MRO) | Statistical computing and graphics. Includes bioconductor. |
| MKL | Intel Math Kernel Library of optimized maths routines |
| MPI (OpenMPI) | Message Passing Interface library |
| NAG Libraries | User callable routines for mathematical and statistical computation |
| OpenMP | Open Multi-Processing library |
| PRISMS-PF | Parallel finite element code for microstructural evolution |
| PyTorch | Deep learning framework in python |
| R & bioconductor | Statistical computing and graphics. Includes bioconductor. |
| RStudio | GUI-based development environment for R |
| Singularity | Container execution |
| SLiM | Evolutionary simulation framework |
| SQLite browser (DB4S) | Graphical browser for sqlite files |
| Subversion (svn) | Version Control |
| TBB | Intel Thread Building Blocks for parallel software development. |
| Tensorflow | Data flow graph processing on GPUs and CPUs |
GPU capable
| PACKAGE | NOTES |
|---|---|
| ABAQUS | Finite Element Analysis package |
| AMBER | A general purpose molecular mechanics/dynamics suite |
| Chainer | Deep-learning GPU-capable framework in python |
| COLMAP | general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline |
| CP2K | Atomistic and molecular simulations |
| cuda-torch | GPU enabled machine learning framework |
| DeepLabCut | Tensorflow based markerless pose estimation of animals performing various tasks. |
| EMsoft | Computation and visualization of scanning electron microscopy diffraction patterns. |
| FSL | Library of analysis tools for FMRI, MRI and DTI brain imaging data |
| gprMax | Electromagnetic wave propagation simulation |
| GROMACS | Molecular Dynamics simulation package. |
| Guppy | GPU enabled basecaller |
| HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
| Keras | Neural Network python API using Tensorflow |
| LAMMPS | Classical molecular dynamics code. |
| Medaka | Create a consensus sequence from nanopore sequencing data |
| MEGAHIT | Fast metagenomics assembly tool |
| mumax | GPU-accelerated micromagnetic simulation |
| PyTorch | Deep learning framework in python |
| Relion | Statistical Cryo-EM reconstruction |
| Tensorflow | Data flow graph processing on GPUs and CPUs |
Visualization
| PACKAGE | NOTES |
|---|---|
| ANSWERS | A suite of monte-carlo nuclear simulation tools |
| Compucell3d | Virtual Tissue in silico simulation modelling environment. |
| Dakota | A Multilevel Parallel Object-Oriented Optimization Framework |
| FEPX | Polycrystal Generation and Meshing |
| Freesurfer | Processing and visualisation of structural and functional brain imaging data |
| FSL | Library of analysis tools for FMRI, MRI and DTI brain imaging data |
| Gold suite | Protein Docking |
| Grace / xmgrace | 2D interactive plotting tool |
| Jupyter Notebook | Web-based python notebook |
| Mathematica | Numeric and symbolic computing and programming |
| MATLAB | Numerical computation, visualization and programming |
| Microsoft R Open (MRO) | Statistical computing and graphics. Includes bioconductor. |
| MOLDEN | Molecular Graphics Visualisation Tool |
| MRIcron | NIfTI format image viewer |
| mumax | GPU-accelerated micromagnetic simulation |
| Neper | Polycrystal Generation and Meshing |
| ovito | Scientific visualization and analysis of atomistic simulation data |
| ParaView | Scientific data visualization using parallel software rendering. |
| Pymol | Pymol is a molecular visualisation tool. |
| R & bioconductor | Statistical computing and graphics. Includes bioconductor. |
| RStudio | GUI-based development environment for R |
| ScLimbic | Automatic brain image segment |
| Visual Colloids | Visual Colloids is used to produce images of colloidal systems. |
| VMD | Molecular Graphics Visualisation Tool |
Python Packages
| PACKAGE | NOTES |
|---|---|
| acpype | Generate topologies for chemical compounds |
| AMICO | Diffusion magnetic resonance data processing in python |
| Cell2Location | Python based transcriptomics for cells |
| DeepLabCut | Tensorflow based markerless pose estimation of animals performing various tasks. |
| eggNOG mapper | Fast functional annotation of novel sequences. |
| 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. |
| FeGenie | Identify potential homologs and operons that may be linked to the microbial iron cycle |
| GenX | Refine x-ray, neutron reflectivity data and surface x-ray diffraction data |
| gprMax | Electromagnetic wave propagation simulation |
| GTDB-tk | Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. |
| HOOMD-blue | Hard-particle Monte Carlo simulations toolkit |
| MACS | Model-based Analysis of ChIP-Seq (MACS) |
| Medaka | Create a consensus sequence from nanopore sequencing data |
| Monai | Framework for deep learning in healthcare imaging |
| PubChemPy | PubChem interaction in Python |
| pyro-ppl | Universal probabilistic programming language (PPL) written in Python and supported by PyTorch on the backend |
| PyTorch | Deep learning framework in python |
| scikit-cuda | Python interfaces to many of the functions in the CUDA device/runtime libraries. |
| Tensorflow | Data flow graph processing on GPUs and CPUs |
| TEtranscripts | Including transposable elements in differential enrichment analysis of sequencing datasets. |