{"id":243,"date":"2013-04-24T09:56:03","date_gmt":"2013-04-24T09:56:03","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=243"},"modified":"2018-08-30T08:51:27","modified_gmt":"2018-08-30T08:51:27","slug":"a-z","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/a-z\/","title":{"rendered":"A-Z List of Software"},"content":{"rendered":"

Not all software is accessible to all users. Where restrictions apply, typically licensing, this is detailed in the documentation.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
ABAQUS <\/a><\/td>\nFinite Element Analysis<\/td>\n<\/tr>\n
ACE<\/a><\/td>\nComputational Fluid Dynamics<\/td>\n<\/tr>\n
ADF<\/a><\/td>\nAmsterdam Density Functional computational chemistry<\/td>\n<\/tr>\n
Amber<\/a><\/td>\nA general purpose molecular mechanics\/dynamics suite<\/td>\n<\/tr>\n
Anaconda Python<\/a><\/td>\nA scientific python distribution<\/td>\n<\/tr>\n
ANSWERS<\/a><\/td>\nA suite of monte-carlo nuclear simulation tools<\/td>\n<\/tr>\n
ARWpost<\/a><\/td>\nWRF data post processing<\/td>\n<\/tr>\n
Augustus<\/a><\/td>\nGene prediction tools<\/td>\n<\/tr>\n
Autodock<\/a><\/td>\nAutodock4 and Vina – Molecular docking tools<\/td>\n<\/tr>\n
autoconf<\/a><\/td>\nA tool for producing configure scripts<\/td>\n<\/tr>\n
automake<\/a><\/td>\nA tool for producing portable makefiles<\/td>\n<\/tr>\n
BART<\/a><\/td>\n(Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors.<\/td>\n<\/tr>\n
BayesTraits<\/a><\/td>\nPhylogeny analysis of trait evolution.<\/td>\n<\/tr>\n
BCFtools<\/a><\/td>\nVariant Call Format file manipulation tools<\/td>\n<\/tr>\n
bcl2fastq<\/a><\/td>\nperforms BCL conversion and demultiplexing in a single step<\/td>\n<\/tr>\n
Bedops<\/a><\/td>\nA fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n
Bedtools<\/a><\/td>\nA fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n
BGEN (bgenix)<\/a><\/td>\nTools to process genome data in BGEN format<\/td>\n<\/tr>\n
Bioawk<\/a><\/td>\nAn extension to awk which adds the support of several common biological data formats.<\/td>\n<\/tr>\n
Bioconductor (in R)<\/a><\/td>\nTools for analysis and comprehension of high-throughput genomic data<\/td>\n<\/tr>\n
BioPerl<\/a><\/td>\nTools for analysis and comprehension of high-throughput genomic data<\/td>\n<\/tr>\n
BLAST<\/a><\/td>\nNucleotide or protein sequence matching statistics<\/td>\n<\/tr>\n
Block<\/a><\/td>\nDMRG computational chemistry code<\/td>\n<\/tr>\n
BLAT<\/a><\/td>\nProtein alignment tool<\/td>\n<\/tr>\n
Boost<\/a><\/td>\nC++ library<\/td>\n<\/tr>\n
Bowtie<\/a><\/td>\nSequence alignment tool<\/td>\n<\/tr>\n
Bowtie2<\/a><\/td>\nSequence alignment tool<\/td>\n<\/tr>\n
bwa<\/a><\/td>\nBurrows-Wheeler Aligner, genome sequence mapper<\/td>\n<\/tr>\n
Canu<\/a><\/td>\nSingle-molecule sequencing<\/td>\n<\/tr>\n
CASTEP<\/a><\/td>\nComputational chemistry<\/td>\n<\/tr>\n
CASTEPconv<\/a><\/td>\nScript to automate convergence calculations<\/td>\n<\/tr>\n
CFX<\/a><\/td>\nComputational Fluid Dynamics<\/td>\n<\/tr>\n
Chainer<\/a><\/td>\nNeural netowrks in python<\/td>\n<\/tr>\n
CHARMM<\/a><\/td>\nA many-particle molecular simulation program<\/td>\n<\/tr>\n
chemshell<\/a><\/td>\nInteractive shell for computational chemistry calculations<\/td>\n<\/tr>\n
cmake<\/a><\/td>\nCross-platform, open-source build system<\/td>\n<\/tr>\n
Code Aster<\/a><\/td>\nFinite Element Analysis for structural and civil engineering<\/td>\n<\/tr>\n
Code Saturne<\/a><\/td>\nGeneral Purpose Computational Fluid Dynamics Software<\/td>\n<\/tr>\n
Compilers – AMD <\/a><\/td>\nopencc, openCC, openf90 and openf95<\/td>\n<\/tr>\n
Compilers – Intel <\/a><\/td>\nifort and icc<\/td>\n<\/tr>\n
Compilers – GNU <\/a><\/td>\ngcc, gfortran<\/td>\n<\/tr>\n
Compilers – PGI <\/a><\/td>\nPGI Compilers for C\/Fortran and Accelerator for NVIDIA CUDA<\/td>\n<\/tr>\n
corHMM<\/a><\/td>\nEvaluate models of binary character evolution<\/td>\n<\/tr>\n
CRYSTAL<\/a><\/td>\nA general-purpose program for the ab-initio study of crystalline solids<\/td>\n<\/tr>\n
CUDA<\/a><\/td>\nNvidia CUDA for GPU programming (see also OpenCL<\/a>)<\/td>\n<\/tr>\n
Cufflinks<\/a><\/td>\nSequence assembly<\/td>\n<\/tr>\n
DFTB+<\/a><\/td>\nDensity Functional Tight Binding<\/td>\n<\/tr>\n
DL_MESO<\/a><\/td>\nGeneral purpose mesoscale simulation package. LBE and DPD.<\/td>\n<\/tr>\n
DL_MONTE<\/a><\/td>\nMonte Carlo simulation of condensed phases.<\/td>\n<\/tr>\n
DL_POLY<\/a><\/td>\nDL_POLY_CLASSIC, a general purpose classic MD suite<\/td>\n<\/tr>\n
DL_POLY4<\/a><\/td>\nA general purpose classic MD suite<\/td>\n<\/tr>\n
Debugger – idb\/idbc<\/a><\/td>\nIntel Debugger<\/td>\n<\/tr>\n
Debugger – gdb<\/a><\/td>\nGNU Debugger<\/td>\n<\/tr>\n
DynamO<\/a><\/td>\nParticle simulation and molecular dynamics<\/td>\n<\/tr>\n
Editors<\/a><\/td>\nText file editors – gedit, nano, vi, emacs and advice for windows users<\/td>\n<\/tr>\n
ELK<\/a><\/td>\nAll-electron full-potential linearised augmented-plane wave code<\/td>\n<\/tr>\n
Elmer<\/a><\/td>\nmultiphysical simulation<\/td>\n<\/tr>\n
EMAN2<\/a><\/td>\nGreyscale scientific image processing<\/td>\n<\/tr>\n
EMIRGE<\/a><\/td>\nRibosomal gene reconstruction python scripts<\/td>\n<\/tr>\n
Ensembl Tools<\/a><\/td>\nVarient Effect Predictor script in perl<\/td>\n<\/tr>\n
Evince<\/a><\/td>\nA document viewer, particularly useful for accessing PDF documentation<\/td>\n<\/tr>\n
EVM<\/a><\/td>\nGene processing<\/td>\n<\/tr>\n
Exciting<\/a><\/td>\nA full-potential linearised augmented-plane wave code<\/td>\n<\/tr>\n
Fast-LMM<\/a><\/td>\nGWAS python tools for large datasets<\/td>\n<\/tr>\n
FASTA Number<\/a><\/td>\nFASTA processing scripts<\/td>\n<\/tr>\n
FastQC<\/a><\/td>\nSequence data quality control tool<\/td>\n<\/tr>\n
fastStructure<\/a><\/td>\nLarge SNP genotype data population inference<\/td>\n<\/tr>\n
FDS<\/a><\/td>\nFire Dynamics Simulator<\/td>\n<\/tr>\n
FE-SAFE<\/a><\/td>\n<\/td>\n<\/tr>\n
ffmpeg<\/a><\/td>\nImage processing<\/td>\n<\/tr>\n
FFTW<\/a><\/td>\nFourier Transform library<\/td>\n<\/tr>\n
FICO Xpress<\/a><\/td>\nOptimization and data analytics tools<\/td>\n<\/tr>\n
Fluent<\/a><\/td>\nA computational fluid dynamics package<\/td>\n<\/tr>\n
Freesurfer<\/a><\/td>\nVisualisation of structural and functional brain imaging data<\/td>\n<\/tr>\n
FSL<\/a><\/td>\nAnalysis of structural and functional brain imaging data<\/td>\n<\/tr>\n
GATK<\/a><\/td>\nGenome Analysis Toolkit<\/td>\n<\/tr>\n
Gaussian<\/a><\/td>\nPerforms semi-empirical and ab-initio molecular orbital calculations<\/td>\n<\/tr>\n
Geneland<\/a><\/td>\nStatistical analysis of population genetics data in R<\/td>\n<\/tr>\n
GeneMark-ES<\/a><\/td>\nGene prediction<\/td>\n<\/tr>\n
Gephi<\/a><\/td>\nGraph visualization and analysis<\/td>\n<\/tr>\n
Gerris2D \/ 3D<\/a><\/td>\nFluid flow solver<\/td>\n<\/tr>\n
Gold Suite<\/a><\/td>\nProtein Docking<\/td>\n<\/tr>\n
GoodVibes<\/a><\/td>\nQuasi-harmonic thermochemical calculation from Gaussian files<\/td>\n<\/tr>\n
gpyro<\/a><\/td>\nGeneralized Pyrolysis Model for Combustible Solids<\/td>\n<\/tr>\n
Gubbins<\/a><\/td>\nGenealogies Unbiased By recomBinations In Nucleotide Sequences<\/td>\n<\/tr>\n
HOMER<\/a><\/td>\nSoftware for motif discovery and next generation sequencing analysis<\/td>\n<\/tr>\n
grace\/xmgrace<\/a><\/td>\n2D plotting tool<\/td>\n<\/tr>\n
git<\/a><\/td>\nVersion Control<\/td>\n<\/tr>\n
gnuplot<\/a><\/td>\nCommand line driven plotting tool<\/td>\n<\/tr>\n
gprof<\/a><\/td>\nGNU Profiler<\/td>\n<\/tr>\n
GROMACS<\/a><\/td>\nGROMACS is a package for computing molecular dynamics of biochemical and non-biological systems<\/td>\n<\/tr>\n
GPUs<\/a><\/td>\nHow to get started with using software on the Nvidia GPUs (see also OpenCL<\/a>)<\/td>\n<\/tr>\n
HDF<\/a><\/td>\nA data format for large scientific data files<\/td>\n<\/tr>\n
HiCUP<\/a><\/td>\nGenome mapping<\/td>\n<\/tr>\n
IDBA and IDBA-UD<\/a><\/td>\nGraph assemblers for second-generation sequencing reads<\/td>\n<\/tr>\n
IDL<\/a><\/td>\nData visualization programming language<\/td>\n<\/tr>\n
Illumina CASAVA-1.8 FASTQ Filter<\/a><\/td>\nThis program can filter FASTQ files produced by CASAVA 1.8, and keep\/discard reads based on this filter flag.<\/td>\n<\/tr>\n
java<\/a><\/td>\nJava application launcher<\/td>\n<\/tr>\n
Javac<\/a><\/td>\nJava Compiler 1.6.0<\/td>\n<\/tr>\n
Jupyter Notebook<\/a><\/td>\nJupyter Notebook interactive web-base python server<\/td>\n<\/tr>\n
Keras<\/a><\/td>\nNeural Network python API using Tensorflow<\/td>\n<\/tr>\n
LAMMPS<\/a><\/td>\nClassical molecular dynamics code<\/td>\n<\/tr>\n
LDSC<\/a><\/td>\nHeritability and genetic correlation estimates<\/td>\n<\/tr>\n
LENS<\/a><\/td>\nNeural Network Simulator<\/td>\n<\/tr>\n
LFTP<\/a><\/td>\nCommand-line File Transfer Program (FTP)<\/td>\n<\/tr>\n
LS-DYNA<\/a><\/td>\nA general purpose explicit solver<\/td>\n<\/tr>\n
MACS<\/a><\/td>\nModel-based Analysis for ChIP-Seq<\/td>\n<\/tr>\n
MACS2<\/a><\/td>\nModel-based Analysis for ChIP-Seq<\/td>\n<\/tr>\n
Maestro<\/a><\/td>\nMolecular modeling tool<\/td>\n<\/tr>\n
Marge<\/a><\/td>\nModel-based Analysis of Regulation of Gene Expression<\/td>\n<\/tr>\n
MaxBin<\/a><\/td>\nBinning assembled metagenomic sequences<\/td>\n<\/tr>\n
Materials Studio<\/a><\/td>\nMaterials modeling and simulation<\/td>\n<\/tr>\n
Mathematica<\/a><\/td>\nNumeric and symbolic computing and programming<\/td>\n<\/tr>\n
MATLAB<\/a><\/td>\nNumerical computation, visualization and programming.<\/td>\n<\/tr>\n
MDAnalysis<\/a><\/td>\nMolecular Dynamics trajectory analysis<\/td>\n<\/tr>\n
MEGAHIT<\/a><\/td>\nFast metagenomics assembly tool<\/td>\n<\/tr>\n
metaVelvet<\/a><\/td>\nDe novo metagenome assembly from short sequence reads<\/td>\n<\/tr>\n
MGLTools<\/a><\/td>\nGraphical molecular visualization tools.<\/td>\n<\/tr>\n
MKL<\/a><\/td>\nIntel’s Maths Kernel Library – Optimised BLAS, LAPACK, ScaLAPACK1, sparse solvers, fast Fourier transforms, vector math etc<\/td>\n<\/tr>\n
mmtsb toolset<\/a><\/td>\nMultiscale Modeling Tools for Structural Biology<\/td>\n<\/tr>\n
Modules<\/a><\/td>\nUser environment modules<\/td>\n<\/tr>\n
MOE<\/a><\/td>\nMolecular Operating Environment<\/td>\n<\/tr>\n
MOLCAS<\/a><\/td>\nAb initio quantum chemistry software<\/td>\n<\/tr>\n
MOLPRO<\/a><\/td>\nAb initio quantum chemistry software<\/td>\n<\/tr>\n
MOLDEN<\/a><\/td>\nMolecular Graphics Visualisation Tool<\/td>\n<\/tr>\n
MosaicFinder<\/a><\/td>\nGene fusion identification tool<\/td>\n<\/tr>\n
MrBayes<\/a><\/td>\nBayesian Inference of Phylogeny<\/td>\n<\/tr>\n
MUMPS<\/a><\/td>\nMUltifrontal Massively Parallel sparse direct Solver on AMD Bulldozer compute nodes<\/td>\n<\/tr>\n
MPI<\/a><\/td>\nMessage Passing Interface<\/td>\n<\/tr>\n
MPI on Bulldozer <\/a><\/td>\nMPI on AMD Bulldozer compute nodes<\/td>\n<\/tr>\n
NAG Libraries<\/a><\/td>\nUser callable routines for mathematical and statistical computation<\/td>\n<\/tr>\n
NAMD<\/a><\/td>\nMolecular Dynamics code<\/td>\n<\/tr>\n
Nanopolish<\/a><\/td>\nSignal-level analysis of Oxford Nanopore sequencing data<\/td>\n<\/tr>\n
NetCDF Libraries<\/a><\/td>\nLibraries and tools for array-oriented scientific data<\/td>\n<\/tr>\n
ncl<\/a><\/td>\nNCAR Command Language for post-processing and visualization<\/td>\n<\/tr>\n
ngmlr<\/a><\/td>\nlong-read mapper to align PacBilo or Oxford Nanopore to reference genomes<\/td>\n<\/tr>\n
Octave (GNU)<\/a><\/td>\nFree MATLAB-like application for numerical calculations<\/td>\n<\/tr>\n
openbabel<\/a><\/td>\nMolecular data processing<\/td>\n<\/tr>\n
OpenCL<\/a><\/td>\nNvidia OpenCL for GPU programming<\/td>\n<\/tr>\n
openeye<\/a><\/td>\nA portfolio of molecular modeling applications for pharmaceutical research<\/td>\n<\/tr>\n
OpenFOAM<\/a><\/td>\nFluid dynamics platform<\/td>\n<\/tr>\n
OpenMP<\/a><\/td>\nThe standard method for Shared Memory parallel programming<\/td>\n<\/tr>\n
ORCA<\/a><\/td>\nAb initio, DFT and semiempirical SCF-MO package for quantum chemistry<\/td>\n<\/tr>\n
Ovito<\/a><\/td>\nScientific visualization and analysis of atomistic simulation data<\/td>\n<\/tr>\n
Packmol<\/a><\/td>\nInitial configurations for Molecular Dynamics Simulations by packing optimization<\/td>\n<\/tr>\n
pandaseq<\/a><\/td>\nAssembles paired-end Illumina reads into sequences<\/td>\n<\/tr>\n
ParaView<\/a><\/td>\nScientific Visualization application based on VTK<\/td>\n<\/tr>\n
PBMPI<\/a><\/td>\nBayesian phylogenetic reconstruction<\/td>\n<\/tr>\n
pcazip<\/a><\/td>\nTrajectory compression tools<\/td>\n<\/tr>\n
Perl<\/a><\/td>\nPerl and Bioperl<\/td>\n<\/tr>\n
Phenix and Rosetta<\/a><\/td>\nPython-based Hierarchical ENvironment for Integrated Xtallography<\/td>\n<\/tr>\n
Picard<\/a><\/td>\nTools for manipulating high-throughput sequence data<\/td>\n<\/tr>\n
Pigz<\/a><\/td>\nParallel gzip file compress\/decompression<\/td>\n<\/tr>\n
Plumed<\/a><\/td>\nFree energy calculations in molecular systems<\/td>\n<\/tr>\n
POLYRATE<\/a><\/td>\nChemical reaction rates for polyatomics<\/td>\n<\/tr>\n
Povray<\/a><\/td>\nRaytracer for rendering 3D models<\/td>\n<\/tr>\n
PowerFLOW<\/a><\/td>\nFluid flow simulation<\/td>\n<\/tr>\n
Primer3<\/a><\/td>\nDesign PCR primers for genetics and molecular biology<\/td>\n<\/tr>\n
Prodigal<\/a><\/td>\nProtein-coding gene prediction.<\/td>\n<\/tr>\n
Profiler – gprof<\/a><\/td>\nGNU Profiler<\/td>\n<\/tr>\n
Profiler – tau<\/a><\/td>\nTuning and Analysis Utilities<\/td>\n<\/tr>\n
PyCoCo<\/a><\/td>\nProcess conformations within an ensemble of molecular structures<\/td>\n<\/tr>\n
PyGMO<\/a><\/td>\nParallel optimization framework in python<\/td>\n<\/tr>\n
pymol<\/a><\/td>\nMolecular visualization<\/td>\n<\/tr>\n
PyPcaZip<\/a><\/td>\nTrajectory compression tools using Python<\/td>\n<\/tr>\n
PySnpTools<\/a><\/td>\nSNP genome data python file processing<\/td>\n<\/tr>\n
Python<\/a><\/td>\nAn interpreted, general-purpose high-level programming language<\/td>\n<\/tr>\n
Quast and MetaQuast<\/a><\/td>\nEvaluation of genome assemblies.<\/td>\n<\/tr>\n
Questaal<\/a><\/td>\nModelling arbitrary materials.<\/td>\n<\/tr>\n
Quantum Espresso<\/a><\/td>\nNanoscale materials modelling and electronic-structure calculations.<\/td>\n<\/tr>\n
QIIME<\/a><\/td>\nComparison and analysis of microbial communities<\/td>\n<\/tr>\n
R<\/a><\/td>\nStatistical computing and graphics. Includes bioconductor.<\/td>\n<\/tr>\n
RapMap<\/a><\/td>\ntesting ground for ideas in lightweight \/ quasi \/ pseudo transcriptome alignment<\/td>\n<\/tr>\n
RAxML<\/a><\/td>\nMaximum Likelihood based inference of large phylogenetic trees<\/td>\n<\/tr>\n
Relion<\/a><\/td>\nStatistical Cryo-EM reconstruction<\/td>\n<\/tr>\n
RepeatMasker<\/a><\/td>\nprogram that screens DNA sequences for interspersed repeats and low complexity DNA sequences<\/td>\n<\/tr>\n
RStudio<\/a><\/td>\nGUI-based development environment for R<\/td>\n<\/tr>\n
Salmon<\/a><\/td>\nSequence alignment and mapping tools<\/td>\n<\/tr>\n
SAMtools<\/a><\/td>\nFast transcript quantification from RNA-seq data<\/td>\n<\/tr>\n
SCENIC<\/a><\/td>\nR workflow to process single-cell RNA-seq data.<\/td>\n<\/tr>\n
Sickle<\/a><\/td>\nA windowed adaptive trimming tool for FASTQ files using quality<\/td>\n<\/tr>\n
Serpent<\/a><\/td>\nMonte-carlo Nuclear reactor physics<\/td>\n<\/tr>\n
Shellfish<\/a><\/td>\nAnalysis of genome-wide SNP data<\/td>\n<\/tr>\n
SPAdes<\/a><\/td>\nGenome assembler<\/td>\n<\/tr>\n
STACKS<\/a><\/td>\nShort-read sequence processing<\/td>\n<\/tr>\n
StarCCM+<\/a><\/td>\nA computation continuum mechanics application<\/td>\n<\/tr>\n
Star-CD<\/a><\/td>\nComputational fluid dynamics simulation<\/td>\n<\/tr>\n
Stata<\/a><\/td>\nData Analysis and Statistical software<\/td>\n<\/tr>\n
Structure<\/a><\/td>\nGenetics software for investigating population structure<\/td>\n<\/tr>\n
Subversion\/svn<\/a><\/td>\nVersion Control<\/td>\n<\/tr>\n
tabix<\/a><\/td>\nGeneric indexer for TAB-delimited genome position files<\/td>\n<\/tr>\n
TAU<\/a><\/td>\nTuning and Analysis Utilities<\/td>\n<\/tr>\n
Telemac<\/a><\/td>\nFree-surface flow solvers<\/td>\n<\/tr>\n
TensorFlow<\/a><\/td>\nData flow graph processing<\/td>\n<\/tr>\n
Theano<\/a><\/td>\nMulti-dimensional array processing<\/td>\n<\/tr>\n
TopHat<\/a><\/td>\nSplice junction mapper<\/td>\n<\/tr>\n
Towhee<\/a><\/td>\nMonte Carlo molecular simulation code<\/td>\n<\/tr>\n
trimmomatic<\/a><\/td>\nA flexible read trimming tool for Illumina NGS data<\/td>\n<\/tr>\n
TURBOMOLE<\/a><\/td>\nQuantum chemistry – electronic structure calculations<\/td>\n<\/tr>\n
UKBioBank Env Vars<\/a><\/td>\nEnvironment variables to help access UK BioBank full-release datasets.<\/td>\n<\/tr>\n
unrar<\/a><\/td>\nRAR archive decompressor<\/td>\n<\/tr>\n
USEARCH<\/a><\/td>\nSequence analysis<\/td>\n<\/tr>\n
VASP<\/a><\/td>\nVienna Ab initio Simulation Package<\/td>\n<\/tr>\n
VCFtools<\/a><\/td>\nPackage for working with VCFfiles<\/td>\n<\/tr>\n
Velvet<\/a><\/td>\nGenomic assembler<\/td>\n<\/tr>\n
Visual Colloids<\/a><\/td>\nMolecular visualization tool<\/td>\n<\/tr>\n
VOTCA<\/a><\/td>\nMolecular Dynamics<\/td>\n<\/tr>\n
VMD<\/a><\/td>\nMolecular Graphics Visualisation Tool<\/td>\n<\/tr>\n
vsearch<\/a><\/td>\nSequence analysis<\/td>\n<\/tr>\n
wget<\/a><\/td>\nDownloader tool<\/td>\n<\/tr>\n
WRF (and WPS)<\/a><\/td>\nWRF weather research and forecasting model<\/td>\n<\/tr>\n
WRF-Chem<\/a><\/td>\nWeather Research and Forecasting (WRF) model coupled with Chemistry<\/td>\n<\/tr>\n
Xaim<\/a><\/td>\nGraphical Molecule tool<\/td>\n<\/tr>\n
XCrySDen<\/a><\/td>\nMolecular visualization tool<\/td>\n<\/tr>\n
Xmgr<\/a><\/td>\n2D interactive plotting tool<\/td>\n<\/tr>\n
xmgrace<\/a><\/td>\n2D plotting tool<\/td>\n<\/tr>\n
xmlstarlet<\/a><\/td>\nCommand line XML toolkit<\/td>\n<\/tr>\n
X! Tandem<\/a><\/td>\nMass spectra and peptide matching tool<\/td>\n<\/tr>\n
Yade<\/a><\/td>\nC++\/Python DEM framework<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

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.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":8,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-243","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/243","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=243"}],"version-history":[{"count":25,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/243\/revisions"}],"predecessor-version":[{"id":4844,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/243\/revisions\/4844"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/8"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=243"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}