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A-Z List of Software
Not all software is accessible to all users. Where restrictions apply, typically licensing, this is detailed in the documentation.
| PACKAGE | NOTES |
|---|---|
| ABAQUS | Finite Element Analysis |
| ACE | Computational Fluid Dynamics |
| ADF | Amsterdam Density Functional computational chemistry |
| Amber | A general purpose molecular mechanics/dynamics suite |
| Anaconda Python | A scientific python distribution |
| ANSWERS | A suite of monte-carlo nuclear simulation tools |
| ARWpost | WRF data post processing |
| Augustus | Gene prediction tools |
| Autodock | Autodock4 and Vina – Molecular docking tools |
| autoconf | A tool for producing configure scripts |
| automake | A tool for producing portable makefiles |
| BART | (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors. |
| BayesTraits | Phylogeny analysis of trait evolution. |
| BCFtools | Variant Call Format file manipulation tools |
| bcl2fastq | performs BCL conversion and demultiplexing in a single step |
| Bedops | A fast, flexible toolset for genome arithmetic. |
| Bedtools | A fast, flexible toolset for genome arithmetic. |
| BGEN (bgenix) | Tools to process genome data in BGEN format |
| Bioawk | An extension to awk which adds the support of several common biological data formats. |
| Bioconductor (in R) | Tools for analysis and comprehension of high-throughput genomic data |
| BioPerl | Tools for analysis and comprehension of high-throughput genomic data |
| BLAST | Nucleotide or protein sequence matching statistics |
| Block | DMRG computational chemistry code |
| BLAT | Protein alignment tool |
| Boost | C++ library |
| Bowtie | Sequence alignment tool |
| Bowtie2 | Sequence alignment tool |
| bwa | Burrows-Wheeler Aligner, genome sequence mapper |
| Canu | Single-molecule sequencing |
| CASTEP | Computational chemistry |
| CASTEPconv | Script to automate convergence calculations |
| CFX | Computational Fluid Dynamics |
| Chainer | Neural netowrks in python |
| CHARMM | A many-particle molecular simulation program |
| chemshell | Interactive shell for computational chemistry calculations |
| cmake | Cross-platform, open-source build system |
| Code Aster | Finite Element Analysis for structural and civil engineering |
| Code Saturne | General Purpose Computational Fluid Dynamics Software |
| Compilers – AMD | opencc, openCC, openf90 and openf95 |
| Compilers – Intel | ifort and icc |
| Compilers – GNU | gcc, gfortran |
| Compilers – PGI | PGI Compilers for C/Fortran and Accelerator for NVIDIA CUDA |
| corHMM | Evaluate models of binary character evolution |
| CRYSTAL | A general-purpose program for the ab-initio study of crystalline solids |
| CUDA | Nvidia CUDA for GPU programming (see also OpenCL) |
| Cufflinks | Sequence assembly |
| DFTB+ | Density Functional Tight Binding |
| DL_MESO | General purpose mesoscale simulation package. LBE and DPD. |
| DL_MONTE | Monte Carlo simulation of condensed phases. |
| DL_POLY | DL_POLY_CLASSIC, a general purpose classic MD suite |
| DL_POLY4 | A general purpose classic MD suite |
| Debugger – idb/idbc | Intel Debugger |
| Debugger – gdb | GNU Debugger |
| DynamO | Particle simulation and molecular dynamics |
| Editors | Text file editors – gedit, nano, vi, emacs and advice for windows users |
| ELK | All-electron full-potential linearised augmented-plane wave code |
| Elmer | multiphysical simulation |
| EMAN2 | Greyscale scientific image processing |
| EMIRGE | Ribosomal gene reconstruction python scripts |
| Ensembl Tools | Varient Effect Predictor script in perl |
| Evince | A document viewer, particularly useful for accessing PDF documentation |
| EVM | Gene processing |
| Exciting | A full-potential linearised augmented-plane wave code |
| Fast-LMM | GWAS python tools for large datasets |
| FASTA Number | FASTA processing scripts |
| FastQC | Sequence data quality control tool |
| fastStructure | Large SNP genotype data population inference |
| FDS | Fire Dynamics Simulator |
| FE-SAFE | |
| ffmpeg | Image processing |
| FFTW | Fourier Transform library |
| FICO Xpress | Optimization and data analytics tools |
| Fluent | A computational fluid dynamics package |
| Freesurfer | Visualisation of structural and functional brain imaging data |
| FSL | Analysis of structural and functional brain imaging data |
| GATK | Genome Analysis Toolkit |
| Gaussian | Performs semi-empirical and ab-initio molecular orbital calculations |
| Geneland | Statistical analysis of population genetics data in R |
| GeneMark-ES | Gene prediction |
| Gephi | Graph visualization and analysis |
| Gerris2D / 3D | Fluid flow solver |
| Gold Suite | Protein Docking |
| GoodVibes | Quasi-harmonic thermochemical calculation from Gaussian files |
| gpyro | Generalized Pyrolysis Model for Combustible Solids |
| Gubbins | Genealogies Unbiased By recomBinations In Nucleotide Sequences |
| HOMER | Software for motif discovery and next generation sequencing analysis |
| grace/xmgrace | 2D plotting tool |
| git | Version Control |
| gnuplot | Command line driven plotting tool |
| gprof | GNU Profiler |
| GROMACS | GROMACS is a package for computing molecular dynamics of biochemical and non-biological systems |
| GPUs | How to get started with using software on the Nvidia GPUs (see also OpenCL) |
| HDF | A data format for large scientific data files |
| HiCUP | Genome mapping |
| IDBA and IDBA-UD | Graph assemblers for second-generation sequencing reads |
| IDL | Data visualization programming language |
| Illumina CASAVA-1.8 FASTQ Filter | This program can filter FASTQ files produced by CASAVA 1.8, and keep/discard reads based on this filter flag. |
| java | Java application launcher |
| Javac | Java Compiler 1.6.0 |
| Jupyter Notebook | Jupyter Notebook interactive web-base python server |
| Keras | Neural Network python API using Tensorflow |
| LAMMPS | Classical molecular dynamics code |
| LDSC | Heritability and genetic correlation estimates |
| LENS | Neural Network Simulator |
| LFTP | Command-line File Transfer Program (FTP) |
| LS-DYNA | A general purpose explicit solver |
| MACS | Model-based Analysis for ChIP-Seq |
| MACS2 | Model-based Analysis for ChIP-Seq |
| Maestro | Molecular modeling tool |
| Marge | Model-based Analysis of Regulation of Gene Expression |
| MaxBin | Binning assembled metagenomic sequences |
| Materials Studio | Materials modeling and simulation |
| Mathematica | Numeric and symbolic computing and programming |
| MATLAB | Numerical computation, visualization and programming. |
| MDAnalysis | Molecular Dynamics trajectory analysis |
| MEGAHIT | Fast metagenomics assembly tool |
| metaVelvet | De novo metagenome assembly from short sequence reads |
| MGLTools | Graphical molecular visualization tools. |
| MKL | Intel’s Maths Kernel Library – Optimised BLAS, LAPACK, ScaLAPACK1, sparse solvers, fast Fourier transforms, vector math etc |
| mmtsb toolset | Multiscale Modeling Tools for Structural Biology |
| Modules | User environment modules |
| MOE | Molecular Operating Environment |
| MOLCAS | Ab initio quantum chemistry software |
| MOLPRO | Ab initio quantum chemistry software |
| MOLDEN | Molecular Graphics Visualisation Tool |
| MosaicFinder | Gene fusion identification tool |
| MrBayes | Bayesian Inference of Phylogeny |
| MUMPS | MUltifrontal Massively Parallel sparse direct Solver on AMD Bulldozer compute nodes |
| MPI | Message Passing Interface |
| MPI on Bulldozer | MPI on AMD Bulldozer compute nodes |
| NAG Libraries | User callable routines for mathematical and statistical computation |
| NAMD | Molecular Dynamics code |
| Nanopolish | Signal-level analysis of Oxford Nanopore sequencing data |
| NetCDF Libraries | Libraries and tools for array-oriented scientific data |
| ncl | NCAR Command Language for post-processing and visualization |
| ngmlr | long-read mapper to align PacBilo or Oxford Nanopore to reference genomes |
| Octave (GNU) | Free MATLAB-like application for numerical calculations |
| openbabel | Molecular data processing |
| OpenCL | Nvidia OpenCL for GPU programming |
| openeye | A portfolio of molecular modeling applications for pharmaceutical research |
| OpenFOAM | Fluid dynamics platform |
| OpenMP | The standard method for Shared Memory parallel programming |
| ORCA | Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry |
| Ovito | Scientific visualization and analysis of atomistic simulation data |
| Packmol | Initial configurations for Molecular Dynamics Simulations by packing optimization |
| pandaseq | Assembles paired-end Illumina reads into sequences |
| ParaView | Scientific Visualization application based on VTK |
| PBMPI | Bayesian phylogenetic reconstruction |
| pcazip | Trajectory compression tools |
| Perl | Perl and Bioperl |
| Phenix and Rosetta | Python-based Hierarchical ENvironment for Integrated Xtallography |
| Picard | Tools for manipulating high-throughput sequence data |
| Pigz | Parallel gzip file compress/decompression |
| Plumed | Free energy calculations in molecular systems |
| POLYRATE | Chemical reaction rates for polyatomics |
| Povray | Raytracer for rendering 3D models |
| PowerFLOW | Fluid flow simulation |
| Primer3 | Design PCR primers for genetics and molecular biology |
| Prodigal | Protein-coding gene prediction. |
| Profiler – gprof | GNU Profiler |
| Profiler – tau | Tuning and Analysis Utilities |
| PyCoCo | Process conformations within an ensemble of molecular structures |
| PyGMO | Parallel optimization framework in python |
| pymol | Molecular visualization |
| PyPcaZip | Trajectory compression tools using Python |
| PySnpTools | SNP genome data python file processing |
| Python | An interpreted, general-purpose high-level programming language |
| Quast and MetaQuast | Evaluation of genome assemblies. |
| Questaal | Modelling arbitrary materials. |
| Quantum Espresso | Nanoscale materials modelling and electronic-structure calculations. |
| QIIME | Comparison and analysis of microbial communities |
| R | Statistical computing and graphics. Includes bioconductor. |
| RapMap | testing ground for ideas in lightweight / quasi / pseudo transcriptome alignment |
| RAxML | Maximum Likelihood based inference of large phylogenetic trees |
| Relion | Statistical Cryo-EM reconstruction |
| RepeatMasker | program that screens DNA sequences for interspersed repeats and low complexity DNA sequences |
| RStudio | GUI-based development environment for R |
| Salmon | Sequence alignment and mapping tools |
| SAMtools | Fast transcript quantification from RNA-seq data |
| SCENIC | R workflow to process single-cell RNA-seq data. |
| Sickle | A windowed adaptive trimming tool for FASTQ files using quality |
| Serpent | Monte-carlo Nuclear reactor physics |
| Shellfish | Analysis of genome-wide SNP data |
| SPAdes | Genome assembler |
| STACKS | Short-read sequence processing |
| StarCCM+ | A computation continuum mechanics application |
| Star-CD | Computational fluid dynamics simulation |
| Stata | Data Analysis and Statistical software |
| Structure | Genetics software for investigating population structure |
| Subversion/svn | Version Control |
| tabix | Generic indexer for TAB-delimited genome position files |
| TAU | Tuning and Analysis Utilities |
| Telemac | Free-surface flow solvers |
| TensorFlow | Data flow graph processing |
| Theano | Multi-dimensional array processing |
| TopHat | Splice junction mapper |
| Towhee | Monte Carlo molecular simulation code |
| trimmomatic | A flexible read trimming tool for Illumina NGS data |
| TURBOMOLE | Quantum chemistry – electronic structure calculations |
| UKBioBank Env Vars | Environment variables to help access UK BioBank full-release datasets. |
| unrar | RAR archive decompressor |
| USEARCH | Sequence analysis |
| VASP | Vienna Ab initio Simulation Package |
| VCFtools | Package for working with VCFfiles |
| Velvet | Genomic assembler |
| Visual Colloids | Molecular visualization tool |
| VOTCA | Molecular Dynamics |
| VMD | Molecular Graphics Visualisation Tool |
| vsearch | Sequence analysis |
| wget | Downloader tool |
| WRF (and WPS) | WRF weather research and forecasting model |
| WRF-Chem | Weather Research and Forecasting (WRF) model coupled with Chemistry |
| Xaim | Graphical Molecule tool |
| XCrySDen | Molecular visualization tool |
| Xmgr | 2D interactive plotting tool |
| xmgrace | 2D plotting tool |
| xmlstarlet | Command line XML toolkit |
| X! Tandem | Mass spectra and peptide matching tool |
| Yade | C++/Python DEM framework |