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Applications
Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list.
Bioinformatics
| PACKAGE | NOTES |
|---|---|
| Augustus | Gene prediction tools | BART | (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors. |
| BayesTraits | Phylogeny analysis of trait evolution. |
| PBMPI | Bayesian phylogenetic reconstruction |
| BCFtools | Variant Call Format file manipulation tools |
| 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 |
| 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 |
| BLAT | Protein alignment tool |
| Block | DMRG computational chemistry code |
| Bowtie | Sequence alignment |
| Bowtie2 | Sequence alignment |
| BWA | Burrows-Wheeler Aligner, genome sequence mapper |
| corHMM | Evaluate models of binary character evolution |
| Cufflinks | Sequence assembly |
| EMIRGE | Ribosomal gene reconstruction python scripts |
| Ensembl Tools | Varient Effect Predictor script in perl |
| EVM | Gene processing |
| Fast-LMM | GWAS python tools for large datasets |
| FASTA Number | FAST processing scripts |
| FastQC | Sequence data quality control tool |
| fastStructure | Large SNP genotype data population inference |
| FSL | Library of analysis tools for FMRI, MRI and DTI brain imaging data |
| GATK | Genome Analysis Toolkit |
| GeneMark-ES | Gene prediction |
| Geneland | Statistical analysis of population genetics data in R |
| HiCUP | Genome mapping |
| HOMER | Software for motif discovery and next generation sequencing analysis |
| IDBA and IDBA-UD | Graph assemblers for second-generation sequencing reads |
| LDSC | Heritability and genetic correlation estimates |
| MACS | Model-based Analysis for ChIP-Seq |
| MACS2 | Model-based Analysis for ChIP-Seq |
| Marge | Model-based Analysis of Regulation of Gene Expression |
| MaxBin | Binning assembled metagenomic sequences |
| MEGAHIT | Fast metagenomics assembly tool |
| metaVelvet | De novo metagenome assembly from short sequence reads |
| mmtsb toolset | Multiscale Modeling Tools for Structural Biology |
| MosaicFinder | Gene fusion identification tool |
| MrBayes | Bayesian Inference of Phylogeny |
| Picard | Tools for manipulating high-throughput sequence data |
| Primer3 | Design PCR primers for genetics and molecular biology |
| Prodigal | Protein-coding gene prediction. |
| PySnpTools | SNP genome data python file processing |
| Quast and MetaQuast | Evaluation of genome assemblies. |
| QIIME | Comparison and analysis of microbial communities |
| RapMap | testing ground for ideas in lightweight / quasi / pseudo transcriptome alignment |
| RAxML | Maximum Likelihood based inference of large phylogenetic trees |
| Salmon | Fast transcript quantification from RNA-seq data |
| SAMtools | Sequence alignment and mapping tools |
| SCENIC | R workflow to process single-cell RNA-seq data. |
| Shellfish | Analysis of genome-wide SNP data |
| STACKS | Short-read sequence processing |
| Structure | Genetics software for investigating population structure |
| tabix | Generic indexer for TAB-delimited genome position files |
| TopHat | Splice junction mapper |
| Relion | Statistical Cryo-EM reconstruction |
| USEARCH | Sequence analysis |
| vcftools | Package for working with VCFfiles |
| Velvet | Genomic assembler |
| vsearch | Sequence analysis |
| Xaim | Graphical Molecule tool |
| X! Tandem | Mass spectra and peptide matching tool |
Computational Chemistry, Molecular Dynamics
| PACKAGE | NOTES |
|---|---|
| ADF | Amsterdam Density Functional computational chemistry |
| Amber | A general purpose molecular mechanics/dynamics suite |
| Autodock | Autodock4 and Vina – Molecular docking tools |
| CASTEP | Computational chemistry |
| CASTEPconv | Script to automate convergence calculations |
| CHARMM | A many-particle molecular simulation program |
| Chem Shell | Interactive shell for computational chemistry calculations |
| CRYSTAL | A general-purpose program for the ab-initio study of crystalline solids |
| 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 |
| DynamO | Particle simulation and molecular dynamics |
| ELK | All-electron full-potential linearised augmented-plane wave code |
| Exciting | A full-potential linearised augmented-plane wave code |
| Gaussian | Performs semi-empirical and ab-initio molecular orbital calculations |
| GoodVibes | Quasi-harmonic thermochemical calculation from Gaussian files |
| Gold Suite | Protein Docking |
| GROMACS | GROMACS is a package for computing molecular dynamics of biochemical and non-biological systems |
| LAMMPS | Classical molecular dynamics code |
| Maestro | Molecular modeling tool |
| MDAnalysis | Molecular Dynamics trajectory analysis |
| MGLTools | Graphical molecular visualization tools. |
| MOE | Molecular Operating Environment |
| MOLCAS | Ab initio quantum chemistry software |
| MOLPRO | Ab initio quantum chemistry software |
| MOLDEN | Molecular Graphics Visualisation Tool |
| NAMD | Molecular Dynamics code |
| openbabel | Molecular data processing |
| openeye | A portfolio of molecular modeling applications for pharmaceutical research |
| Ovito | Scientific visualization and analysis of atomistic simulation data |
| ORCA | Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry |
| Packmol | Initial configurations for Molecular Dynamics Simulations by packing optimization |
| pcazip | Trajectory compression tools |
| Phenix and Rosetta | Python-based Hierarchical ENvironment for Integrated Xtallography |
| Plumed | Free energy calculations in molecular systems |
| POLYRATE | Chemical reaction rates for polyatomics |
| PyCoCo | Process conformations within an ensemble of molecular structures using Python |
| pymol | Molecular visualization |
| PyPcaZip | Trajectory compression tools using Python |
| Quantum Espresso | Nanoscale materials modelling and electronic-structure calculations. |
| Towhee | Monte Carlo molecular simulation code |
| TURBOMOLE | Quantum chemistry – electronic structure calculations |
| VASP | VASP |
| Visual Colloids | Molecular visualization tool |
| VOTCA | Molecular Dynamics |
| VMD | Molecular Graphics Visualisation Tool |
Computational Fluid Dynamics
| PACKAGE | NOTES |
|---|---|
| ABAQUS | Finite Element Analysis |
| ACE | Computational Fluid Dynamics |
| CFX | Computational Fluid Dynamics |
| Code Aster | Finite Element Analysis for structural and civil engineering |
| Code Saturne | General Purpose Computational Fluid Dynamics Software |
| DynamO | Particle simulation and molecular dynamics |
| FDS | Fire Dynamics Simulator |
| Fluent | A computational fluid dynamics package |
| Gerris2D / 3D | Fluid flow solver |
| gpyro | Generalized Pyrolysis Model for Combustible Solids |
| OpenFOAM | Fluid dynamics platform |
| PowerFLOW | Fluid flow simulation |
| StarCCM+ | A computation continuum mechanics application |
| Star-CD | Computational fluid dynamics simulation |
| Telemac | Free-surface flow solvers |
Finite Element Modelling
| PACKAGE | NOTES |
|---|---|
| ABAQUS | Finite Element Analysis |
| LS-DYNA | A general purpose explicit solver |
| Materials Studio | Materials modeling and simulation |
| MUMPS | MUltifrontal Massively Parallel sparse direct Solver on AMD Bulldozer compute nodes |
| Yade | C++/Python DEM framework |
Mathematics
| PACKAGE | NOTES |
|---|---|
| FICO Xpress | Optimization and data analytics tools |
| Mathematica | Numeric and symbolic computing and programming |
| MATLAB | Numerical computation, visualization and programming. |
| Octave (GNU) | Free MATLAB-like application for numerical calculations |
| PyGMO | Parallel optimization framework in python |
| R | Statistical computing and graphics. Includes bioconductor. |
| RStudio | GUI-based development environment for R |
| Stata | Data analysis and statistical software |
Multiphysics and Solvers
| PACKAGE | NOTES |
|---|---|
| ANSWERS | A suite of monte-carlo nuclear simulation tools |
| LS-DYNA | A general purpose explicit solver |
| Elmer | multiphysical simulation |
| Materials Studio | Materials modeling and simulation |
| PyGMO | Parallel optimization framework in python |
| Serpent | Monte-carlo Nuclear reactor physics |
| StarCCM+ | A computation continuum mechanics application |
| WRF (and WPS) | WRF weather research and forecasting model |
| WRF-Chem | Weather Research and Forecasting (WRF) model coupled with Chemistry |
| Yade | C++/Python DEM framework |
Neural Networks and Machine Learning
| PACKAGE | NOTES |
|---|---|
| Chainer | Neural netowrks in python |
| Keras | Neural Network python API using Tensorflow |
| LENS | Neural Network Simulator |
| TensorFlow | Data flow graph processing |
| Theano | Multi-dimensional array processing |
Visualization
| PACKAGE | NOTES |
|---|---|
| EMAN2 | Greyscale scientific image processing |
| ffmpeg | Image processing |
| Freesurfer | Visualisation of structural and functional brain imaging data |
| FSL | Analysis of structural and functional brain imaging data |
| Gephi | Graph visualization and analysis |
| IDL | Data visualization programming language |
| MGLTools | Graphical molecular visualization tools. |
| Ovito | Scientific visualization and analysis of atomistic simulation data |
| Povray | Raytracer for rendering 3D models |
| ParaView | Scientific Visualization application based on VTK |
| Visual Colloids | Molecular visualization tool |
| VMD | Molecular Graphics Visualisation Tool |
| XCrySDen | Molecular visualisation tool |