The Computational Shared Facility 3

A-Z List of Software

Not all software is accessible to all users. Where restrictions apply, typically licensing, this is detailed in the documentation.

PACKAGENOTES
ABAQUSFinite Element Analysis package
acpypeGenerate topologies for chemical compounds
ADFAmsterdam Modeling Suite (DFT, semi-empirical, reactive force fields and fluid thermodynamics)
Affymetrix Power Tools (APT)Algorithms for analyzing and working with GeneChip™ arrays
AIMallSoftware for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems.
Alphafoldapplication for predicting models of protein structures
AMBERA general purpose molecular mechanics/dynamics suite
AMICODiffusion magnetic resonance data processing in python
Anaconda PythonA scientific python distribution
ANSWERSA suite of monte-carlo nuclear simulation tools
Ansys MechanicalAnsys finite element analysis application
Apache SparkCluster computing with Hadoop
Asperaascp fast downloader
Autodock4 and VinaAutodock4 and Vina – Molecular docking tools
BBToolsSuite of tools designed for analysis of DNA and RNA sequence data.
Bio-informatics Helper ModulefileModulefile to make more Bio-informatics apps available
BLASTsuite of tools for comparing primary biological sequence information
BoostC++ library.
Bowtie2tool for aligning sequencing reads to long reference sequences.
bwa-mem2Burrow-Wheeler Aligner
CanuHierarchical assembly pipeline for high-noise single-molecule sequencing.
CASTEPCASTEP is a leading code for calculating the properties of materials from first principles
CASTEPconvScript to automate CASTEP convergence calculations
CFXCFX is a general purpose fluid dynamics product from ANSYS
ChainerDeep-learning GPU-capable framework in python
CHARMMMacromolecular mechanics
CheckMQuality assessment of genomes recovered from isolates, single cells, or metagenomes.
ChemShellInteractive shell for computational chemistry calculations
ChimeraUCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures.
cmakeCross-platform, open-source build system
Code_Aster21.02.2019 - This application is being installed. Docs will be updated when it is available.
Code_Saturne21.02.2019 - This application is being installed. Docs will be updated when it is available.
Compucell3dVirtual Tissue in silico simulation modelling environment.
COMSOLMultiphysics solver
CP2KAtomistic and molecular simulations
CRYSTALAb initio simulations of periodic systems
Crystal Analysis Tool (draft)Code for analysing output of atomistic simulations
CSD-SystemThe Cambridge Structural Database
cuda-torchGPU enabled machine learning framework
CUDA, cuDNN, NCCL, TensorRT and HPC-SDKNvidia CUDA libraries and compiler
DakotaA Multilevel Parallel Object-Oriented Optimization Framework
DAMASKDAMASK is used for the simulation of crystal plasticity within a finite-strain continuum mechanical framework.
DeepLabCutTensorflow based markerless pose estimation of animals performing various tasks.
DiamondSequence aligner for protein and translated DNA searches
DL_MESOGeneral purpose mesoscale simulation package. LBE and DPD.
DL_MONTE2Monte Carlo simulation of condensed phases.
DL_POLYGeneral purpose classical molecular dynamics
eggNOG mapperFast functional annotation of novel sequences.
EMsoftComputation and visualization of scanning electron microscopy diffraction patterns.
Fasta_numberReplace 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.
FastANIFast alignment-free computation of whole-genome Average Nucleotide Identity
FastTreeInfer approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
FDSLarge-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.
FEAT-WMTFinite Element Weld Modelling Tool.
FeGenieIdentify potential homologs and operons that may be linked to the microbial iron cycle
FEPXPolycrystal Generation and Meshing
FFTWFFTW - Fast Fourier Transfrom library
fico-xpress21.02.2019 - This application is being installed. Docs will be updated when it is available.
FlameAgent-based modelling system
FluentA computational fluid dynamics package
FreesurferVisualisation of structural and functional brain imaging data
FSLLibrary of analysis tools for FMRI, MRI and DTI brain imaging data
GAMESS-USA general ab initio quantum chemistry package.
Gaussian 09Performs semi-empirical and ab-initio molecular orbital calculations
Gaussian 16Performs semi-empirical and ab-initio molecular orbital calculations
GDALTranslator library for raster and vector geospatial data formats
Geant 4Geant4 is a toolkit for the simulation of the passage of particles through matter.
gedit - a simple text editorA simple text editor, similar to notepad
GenXRefine x-ray, neutron reflectivity data and surface x-ray diffraction data
GeoChemFoamAn open source pore-scale numerical simulator based on OpenFOAM
GEOSC++ port of the Java Topology Suite (JTS)
git & git-lfsVersion Control
GNU Compilersgcc, g++ and gfortran
GnuplotA command-line driven graphing utility.
Gold suiteProtein Docking
gprMaxElectromagnetic wave propagation simulation
gpyroOpen 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 / xmgrace2D interactive plotting tool
GROMACSMolecular Dynamics simulation package.
GTDB-tkToolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy.
GuppyGPU enabled basecaller
HDF5Library and tools to process hierarchical data format files for large scientific data files.
HMMRATACHMMRATAC peak caller for ATAC-seq data
HOMERSoftware for motif discovery and next generation sequencing analysis
HOOMD-blueHard-particle Monte Carlo simulations toolkit
HYPREHigh performance preconditioners and solvers featuring multigrid methods
Intel Compilersicc, icpc and ifort (recommended when compiling your own software on the CSF)
InterProScanScan sequences against InterPro's member database signatures
ispcIntel ispc experimental SPMD compiler
JAGSProgram for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
Java CompilersJava compiler
JuliaPower mathematical programming and scripting language with native parallel capability
Jupyter NotebookWeb-based python notebook
KaijuTaxonomic classification of high-throughput sequencing reads.
KerasNeural Network python API using Tensorflow
LAMMPSClassical 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-DYNAA general purpose explicit solver from ANSYS
MACSModel-based Analysis of ChIP-Seq (MACS)
MAFFTMultiple alignment program for amino acid or nucleotide sequences
Materials StudioMaterials modelling and simulation application (chemical, materials, pharmaceutical)
MathematicaNumeric and symbolic computing and programming
MATLABNumerical computation, visualization and programming
MaxBinBinning assembled metagenomic sequences
MDAnalysisPython library to analyze trajectories from molecular dynamics (MD) simulations.
MedakaCreate a consensus sequence from nanopore sequencing data
MEGAHITFast metagenomics assembly tool
MemeSuiteMotif-based sequence analysis tools
Microsoft R Open (MRO)Statistical computing and graphics. Includes bioconductor.
Minimap2Sequence alignment
miRDeep2Discovers active known or novel miRNAs from deep sequencing data
MKLIntel Math Kernel Library of optimized maths routines
MOEMolecular Operating Environment
MOLCAS@UUAb initio quantum chemistry software
MOLDENMolecular Graphics Visualisation Tool
MolproAb initio quantum chemistry software
MonaiFramework for deep learning in healthcare imaging
mopacSemiempirical quantum chemistry software package
MothurTool for processing data generated from several DNA sequencing methods
MPI (OpenMPI)Message Passing Interface library
MrBayesBayesian Inference of Phylogeny
MRIcronNIfTI format image viewer
mumaxGPU-accelerated micromagnetic simulation
NAG LibrariesUser callable routines for mathematical and statistical computation
NAMD21.02.2019 - This application is being installed. Docs will be updated when it is available.
NBONatural Bond Orbital program (Electron analysis)
NeperPolycrystal Generation and Meshing
ninjaSoftware build system
NWChemab initio quantum chemistry
ONETEPLinear-scaling code for quantum-mechanical calculations based on density-functional theory.
OpenbabelOpen Babel is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas.
OpeneyeA portfolio of molecular modeling applications for pharmaceutical research.
OpenFOAMFluid dynamics platform
OpenMolcasQuantum chemistry software package using a multiconfigurational approach to the electronic structure.
OpenMPOpen Multi-Processing library
ORCAAb initio, DFT and semiempirical SCF-MO package for quantum chemistry
ovitoScientific visualization and analysis of atomistic simulation data
p7zip7z archive compression and decompression
PackmolInitial configurations for Molecular Dynamics Simulations by packing optimization
ParaViewScientific data visualization using parallel software rendering.
PBMPIBayesian phylogenetic reconstruction
PGI CompilersPGI c/c++/fortran/openacc compilers
Phenix and Rosetta CommonsPython-based Hierarchical ENvironment for Integrated Xtallography
pigz and unpigzParallel gzip file compression/decompression
PRISMS-PFParallel finite element code for microstructural evolution
ProdigalProtein-coding gene prediction.
PROJGeospatial coordinates coordinate reference system transformations
ProkkaAnnotate bacterial, archaeal and viral genomes
Proxy (for web downloads)Envronment setup to give name of proxy server
PubChemPyPubChem interaction in Python
PymolPymol is a molecular visualisation tool.
pyro-pplUniversal probabilistic programming language (PPL) written in Python and supported by PyTorch on the backend
PyTorchDeep learning framework in python
Quantum EspressoAb initio simulations of periodic systems
R & bioconductorStatistical computing and graphics. Includes bioconductor.
RAxMLMaximum Likelihood based inference of large phylogenetic trees
RelionStatistical Cryo-EM reconstruction
RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences
Rosetta CommonsAlgorithms for computational modeling and analysis of protein structures
RSEMSoftware package for estimating gene and isoform expression levels from RNA-Seq data
RStudioGUI-based development environment for R
SalmonTranscript quantification from RNA-seq data
scikit-cudaPython interfaces to many of the functions in the CUDA device/runtime libraries.
SConsSoftware configuration tool
SerpentMonte-carlo Nuclear reactor physics
SingularityContainer execution
SNPTestProgram for the analysis of single SNP association in genome-wide studies.
SPAdesGenome assembler toolkit
SQLite browser (DB4S)Graphical browser for sqlite files
STARSpliced Transcripts Alignment to a Reference
StarCCM+A computation continuum mechanics application
StructureSoftware package for using multi-locus genotype data to investigate population structure.
subreada tool kit for processing next-gen sequencing data
Subversion (svn)Version Control
TBBIntel Thread Building Blocks for parallel software development.
TelemacFree-surface flow solvers.
TensorflowData flow graph processing on GPUs and CPUs
TEtranscriptsIncluding transposable elements in differential enrichment analysis of sequencing datasets.
theano21.02.2019 - This application is being installed. Docs will be updated when it is available.
TowheeTowhee is a Monte Carlo molecular simulation code.
TrimmomaticProgram to perform a variety of useful trimming tasks for Illumina paired-end and single ended data.
TURBOMOLEQuantum chemistry – electronic structure calculations
UDUNITSC library and tool for units of physical quantities
UKBioBank Helper ModulefileEnvironment variables to help access UK BioBank full-release datasets.
UMMAPUMMAP is a trajectory analysis package for molecular dynamics type simulations.
unzipExtract files from zip archives
USEARCHSequence analysis tool
VASPThe Vienna Ab initio Simulation Package
Visual ColloidsVisual Colloids is used to produce images of colloidal systems.
VMDMolecular Graphics Visualisation Tool
VotcaVOTCA is a software package which focuses on the analysis of molecular dynamics data.
VSCodeA popular source-code editor by Microsoft.
VSEARCHSequence analysis tool
WPSWeather Research and Forecasting Preprocessors
WRFWeather Research and Forecasting
WRF-Chem21.02.2019 - This application is being installed. Docs will be updated when it is available.
zstdfast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios

Last modified on September 28, 2018 at 2:51 pm by George Leaver