\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n |
\n| Augustus<\/a><\/td>\n | Gene prediction tools<\/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 |
\n| BayesTraits<\/a><\/td>\n | Phylogeny analysis of trait evolution.<\/td>\n<\/tr>\n |
\n| PBMPI<\/a><\/td>\n | Bayesian phylogenetic reconstruction<\/td>\n<\/tr>\n |
\n| BCFtools<\/a><\/td>\n | Variant Call Format file manipulation tools<\/td>\n<\/tr>\n |
\n| Bedops<\/a><\/td>\n | A fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n |
\n| Bedtools<\/a><\/td>\n | A fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n |
\n| BGEN (bgenix)<\/a><\/td>\n | Tools to process genome data in BGEN format<\/td>\n<\/tr>\n |
\n| Bioconductor (in R)<\/a><\/td>\n | Tools for analysis and comprehension of high-throughput genomic data<\/td>\n<\/tr>\n |
\n| BioPerl<\/a><\/td>\n | Tools for analysis and comprehension of high-throughput genomic data<\/td>\n<\/tr>\n |
\n| BLAST<\/a><\/td>\n | Nucleotide or protein sequence matching statistics<\/td>\n<\/tr>\n |
\n| BLAT<\/a><\/td>\n | Protein alignment tool<\/td>\n<\/tr>\n |
\n| Block<\/a><\/td>\n | DMRG computational chemistry code<\/td>\n<\/tr>\n |
\n| Bowtie<\/a><\/td>\n | Sequence alignment<\/td>\n<\/tr>\n |
\n| Bowtie2<\/a><\/td>\n | Sequence alignment<\/td>\n<\/tr>\n |
\n| BWA<\/a><\/td>\n | Burrows-Wheeler Aligner, genome sequence mapper<\/td>\n<\/tr>\n |
\n| corHMM<\/a><\/td>\n | Evaluate models of binary character evolution<\/td>\n |
\n
\n| Cufflinks<\/a><\/td>\n | Sequence assembly<\/td>\n<\/tr>\n |
\n| EMIRGE<\/a><\/td>\n | Ribosomal gene reconstruction python scripts<\/td>\n<\/tr>\n |
\n| Ensembl Tools<\/a><\/td>\n | Varient Effect Predictor script in perl<\/td>\n<\/tr>\n |
\n| EVM<\/a><\/td>\n | Gene processing<\/td>\n<\/tr>\n |
\n| Fast-LMM<\/a><\/td>\n | GWAS python tools for large datasets<\/td>\n<\/tr>\n |
\n| FASTA Number<\/a><\/td>\n | FAST processing scripts<\/td>\n<\/tr>\n |
\n| FastQC<\/a><\/td>\n | Sequence data quality control tool<\/td>\n<\/tr>\n |
\n| fastStructure<\/a><\/td>\n | Large SNP genotype data population inference<\/td>\n<\/tr>\n |
\n| FSL<\/a><\/td>\n | Library of analysis tools for FMRI, MRI and DTI brain imaging data<\/td>\n<\/tr>\n |
\n| GATK<\/a><\/td>\n | Genome Analysis Toolkit<\/td>\n<\/tr>\n |
\n| GeneMark-ES<\/a><\/td>\n | Gene prediction<\/td>\n<\/tr>\n |
\n| Geneland<\/a><\/td>\n | Statistical analysis of population genetics data in R<\/td>\n<\/tr>\n |
\n| HiCUP<\/a><\/td>\n | Genome mapping<\/td>\n<\/tr>\n |
\n| HOMER<\/a><\/td>\n | Software for motif discovery and next generation sequencing analysis<\/td>\n<\/tr>\n |
\n| IDBA and IDBA-UD<\/a><\/td>\n | Graph assemblers for second-generation sequencing reads<\/td>\n<\/tr>\n |
\n| LDSC<\/a><\/td>\n | Heritability and genetic correlation estimates<\/td>\n<\/tr>\n |
\n| MACS<\/a><\/td>\n | Model-based Analysis for ChIP-Seq<\/td>\n<\/tr>\n |
\n| MACS2<\/a><\/td>\n | Model-based Analysis for ChIP-Seq<\/td>\n<\/tr>\n |
\n| Marge<\/a><\/td>\n | Model-based Analysis of Regulation of Gene Expression<\/td>\n<\/tr>\n |
\n| MaxBin<\/a><\/td>\n | Binning assembled metagenomic sequences<\/td>\n<\/tr>\n |
\n
\n| MEGAHIT<\/a><\/td>\n | Fast metagenomics assembly tool<\/td>\n<\/tr>\n |
\n| metaVelvet<\/a><\/td>\n | De novo metagenome assembly from short sequence reads<\/td>\n<\/tr>\n |
\n| mmtsb toolset<\/a><\/td>\n | Multiscale Modeling Tools for Structural Biology<\/td>\n<\/tr>\n |
\n| MosaicFinder<\/a><\/td>\n | Gene fusion identification tool<\/td>\n<\/tr>\n |
\n| MrBayes<\/a><\/td>\n | Bayesian Inference of Phylogeny<\/td>\n<\/tr>\n |
\n| Picard<\/a><\/td>\n | Tools for manipulating high-throughput sequence data<\/td>\n<\/tr>\n |
\n| Primer3<\/a><\/td>\n | Design PCR primers for genetics and molecular biology<\/td>\n<\/tr>\n |
\n| Prodigal<\/a><\/td>\n | Protein-coding gene prediction.<\/td>\n<\/tr>\n |
\n| PySnpTools<\/a><\/td>\n | SNP genome data python file processing<\/td>\n<\/tr>\n |
\n| Quast and MetaQuast<\/a><\/td>\n | Evaluation of genome assemblies.<\/td>\n<\/tr>\n |
\n| QIIME<\/a><\/td>\n | Comparison and analysis of microbial communities<\/td>\n<\/tr>\n |
\n| RapMap<\/a><\/td>\n | testing ground for ideas in lightweight \/ quasi \/ pseudo transcriptome alignment<\/td>\n |
\n
\n| RAxML<\/a><\/td>\n | Maximum Likelihood based inference of large phylogenetic trees<\/td>\n<\/tr>\n |
\n| Salmon<\/a><\/td>\n | Fast transcript quantification from RNA-seq data<\/td>\n<\/tr>\n |
\n| SAMtools<\/a><\/td>\n | Sequence alignment and mapping tools<\/td>\n<\/tr>\n |
\n| SCENIC<\/a><\/td>\n | R workflow to process single-cell RNA-seq data.<\/td>\n<\/tr>\n |
\n| Shellfish<\/a><\/td>\n | Analysis of genome-wide SNP data<\/td>\n<\/tr>\n |
\n| STACKS<\/a><\/td>\n | Short-read sequence processing<\/td>\n<\/tr>\n |
\n| Structure<\/a><\/td>\n | Genetics software for investigating population structure<\/td>\n<\/tr>\n |
\n| tabix<\/a><\/td>\n | Generic indexer for TAB-delimited genome position files<\/td>\n<\/tr>\n |
\n| TopHat<\/a><\/td>\n | Splice junction mapper<\/td>\n<\/tr>\n |
\n| Relion<\/a><\/td>\n | Statistical Cryo-EM reconstruction<\/td>\n<\/tr>\n |
\n| USEARCH<\/a><\/td>\n | Sequence analysis<\/td>\n<\/tr>\n |
\n| vcftools<\/a><\/td>\n | Package for working with VCFfiles<\/td>\n<\/tr>\n |
\n| Velvet<\/a><\/td>\n | Genomic assembler<\/td>\n<\/tr>\n |
\n| vsearch<\/a><\/td>\n | Sequence analysis<\/td>\n<\/tr>\n |
\n| Xaim<\/a><\/td>\n | Graphical Molecule tool<\/td>\n<\/tr>\n |
\n| X! Tandem<\/a><\/td>\n | Mass spectra and peptide matching tool<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nComputational Chemistry, Molecular Dynamics<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| ADF<\/a><\/td>\n | Amsterdam Density Functional computational chemistry<\/td>\n<\/tr>\n | \n| Amber<\/a><\/td>\n | A general purpose molecular mechanics\/dynamics suite<\/td>\n<\/tr>\n | \n| Autodock<\/a><\/td>\n | Autodock4 and Vina – Molecular docking tools<\/td>\n<\/tr>\n | \n| CASTEP<\/a><\/td>\n | Computational chemistry<\/td>\n<\/tr>\n | \n| CASTEPconv<\/a><\/td>\n | Script to automate convergence calculations<\/td>\n<\/tr>\n | \n| CHARMM<\/a><\/td>\n | A many-particle molecular simulation program<\/td>\n<\/tr>\n | \n| Chem Shell<\/a><\/td>\n | Interactive shell for computational chemistry calculations<\/td>\n<\/tr>\n | \n| CRYSTAL<\/a><\/td>\n | A general-purpose program for the ab-initio study of crystalline solids<\/td>\n<\/tr>\n | \n| DFTB+<\/a><\/td>\n | Density Functional Tight Binding<\/td>\n<\/tr>\n | \n| DL_MESO<\/a><\/td>\n | General purpose mesoscale simulation package. LBE and DPD.<\/td>\n<\/tr>\n | \n| DL_MONTE<\/a><\/td>\n | Monte Carlo simulation of condensed phases.<\/td>\n<\/tr>\n | \n| DL_POLY<\/a><\/td>\n | DL_POLY_CLASSIC, a general purpose classic MD suite<\/td>\n<\/tr>\n | \n| DL_POLY4<\/a><\/td>\n | A general purpose classic MD suite<\/td>\n<\/tr>\n | \n| DynamO<\/a><\/td>\n | Particle simulation and molecular dynamics<\/td>\n<\/tr>\n | \n| ELK<\/a><\/td>\n | All-electron full-potential linearised augmented-plane wave code<\/td>\n<\/tr>\n | \n| Exciting<\/a><\/td>\n | A full-potential linearised augmented-plane wave code<\/td>\n<\/tr>\n | \n| Gaussian<\/a><\/td>\n | Performs semi-empirical and ab-initio molecular orbital calculations<\/td>\n<\/tr>\n | \n| GoodVibes<\/a><\/td>\n | Quasi-harmonic thermochemical calculation from Gaussian files<\/td>\n<\/tr>\n | \n| Gold Suite<\/a><\/td>\n | Protein Docking<\/td>\n<\/tr>\n | \n| GROMACS<\/a><\/td>\n | GROMACS is a package for computing molecular dynamics of biochemical and non-biological systems<\/td>\n<\/tr>\n | \n| LAMMPS<\/a><\/td>\n | Classical molecular dynamics code<\/td>\n<\/tr>\n | \n| Maestro<\/a><\/td>\n | Molecular modeling tool<\/td>\n<\/tr>\n | \n| MDAnalysis<\/td>\n | Molecular Dynamics trajectory analysis<\/td>\n<\/tr>\n | \n| MGLTools<\/a><\/td>\n | Graphical molecular visualization tools.<\/td>\n<\/tr>\n | \n| MOE<\/a><\/td>\n | Molecular Operating Environment<\/td>\n<\/tr>\n | \n| MOLCAS<\/a><\/td>\n | Ab initio quantum chemistry software<\/td>\n<\/tr>\n | \n| MOLPRO<\/a><\/td>\n | Ab initio quantum chemistry software<\/td>\n<\/tr>\n | \n| MOLDEN<\/a><\/td>\n | Molecular Graphics Visualisation Tool<\/td>\n<\/tr>\n | \n| NAMD<\/a><\/td>\n | Molecular Dynamics code<\/td>\n<\/tr>\n | \n| openbabel<\/a><\/td>\n | Molecular data processing<\/td>\n<\/tr>\n | \n| openeye<\/a><\/td>\n | A portfolio of molecular modeling applications for pharmaceutical research<\/td>\n<\/tr>\n | \n| Ovito<\/a><\/td>\n | Scientific visualization and analysis of atomistic simulation data<\/td>\n<\/tr>\n | \n| ORCA<\/a><\/td>\n | Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry<\/td>\n<\/tr>\n | \n| Packmol<\/a><\/td>\n | Initial configurations for Molecular Dynamics Simulations by packing optimization<\/td>\n<\/tr>\n | \n| pcazip<\/a><\/td>\n | Trajectory compression tools<\/td>\n<\/tr>\n | \n| Phenix and Rosetta<\/a><\/td>\n | Python-based Hierarchical ENvironment for Integrated Xtallography<\/td>\n<\/tr>\n | \n| Plumed<\/a><\/td>\n | Free energy calculations in molecular systems<\/td>\n<\/tr>\n | \n| POLYRATE<\/a><\/td>\n | Chemical reaction rates for polyatomics<\/td>\n<\/tr>\n | \n| PyCoCo<\/a><\/td>\n | Process conformations within an ensemble of molecular structures using Python<\/td>\n<\/tr>\n | \n| pymol<\/a><\/td>\n | Molecular visualization<\/td>\n<\/tr>\n | \n| PyPcaZip<\/a><\/td>\n | Trajectory compression tools using Python<\/td>\n<\/tr>\n | \n| Quantum Espresso<\/a><\/td>\n | Nanoscale materials modelling and electronic-structure calculations.<\/td>\n<\/tr>\n | \n| Towhee<\/a><\/td>\n | Monte Carlo molecular simulation code<\/td>\n<\/tr>\n | \n| TURBOMOLE<\/a><\/td>\n | Quantum chemistry – electronic structure calculations<\/td>\n<\/tr>\n | \n| VASP<\/a><\/td>\n | VASP<\/td>\n<\/tr>\n | \n| Visual Colloids<\/a><\/td>\n | Molecular visualization tool<\/td>\n<\/tr>\n | \n| VOTCA<\/a><\/td>\n | Molecular Dynamics<\/td>\n<\/tr>\n | \n| VMD<\/a><\/td>\n | Molecular Graphics Visualisation Tool<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nComputational Fluid Dynamics<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| ABAQUS <\/a><\/td>\n | Finite Element Analysis<\/td>\n<\/tr>\n | \n| ACE<\/a><\/td>\n | Computational Fluid Dynamics<\/td>\n<\/tr>\n | \n| CFX<\/a><\/td>\n | Computational Fluid Dynamics<\/td>\n<\/tr>\n | \n| Code Aster<\/a><\/td>\n | Finite Element Analysis for structural and civil engineering<\/td>\n<\/tr>\n | \n| Code Saturne<\/a><\/td>\n | General Purpose Computational Fluid Dynamics Software<\/td>\n<\/tr>\n | \n| DynamO<\/a><\/td>\n | Particle simulation and molecular dynamics<\/td>\n<\/tr>\n | \n| FDS<\/a><\/td>\n | Fire Dynamics Simulator<\/td>\n<\/tr>\n | \n| Fluent<\/a><\/td>\n | A computational fluid dynamics package<\/td>\n<\/tr>\n | \n| Gerris2D \/ 3D<\/a><\/td>\n | Fluid flow solver<\/td>\n<\/tr>\n | \n| gpyro<\/a><\/td>\n | Generalized Pyrolysis Model for Combustible Solids<\/td>\n<\/tr>\n | \n| OpenFOAM<\/a><\/td>\n | Fluid dynamics platform<\/td>\n<\/tr>\n | \n| PowerFLOW<\/a><\/td>\n | Fluid flow simulation<\/td>\n<\/tr>\n | \n| StarCCM+<\/a><\/td>\n | A computation continuum mechanics application<\/td>\n<\/tr>\n | \n| Star-CD<\/a><\/td>\n | Computational fluid dynamics simulation<\/td>\n<\/tr>\n | \n| Telemac<\/a><\/td>\n | Free-surface flow solvers<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nFinite Element Modelling<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| ABAQUS <\/a><\/td>\n | Finite Element Analysis<\/td>\n<\/tr>\n | \n| LS-DYNA<\/a><\/td>\n | A general purpose explicit solver<\/td>\n<\/tr>\n | \n| Materials Studio<\/a><\/td>\n | Materials modeling and simulation<\/td>\n<\/tr>\n | \n| MUMPS<\/a><\/td>\n | MUltifrontal Massively Parallel sparse direct Solver on AMD Bulldozer compute nodes<\/td>\n<\/tr>\n | \n| Yade<\/a><\/td>\n | C++\/Python DEM framework<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nMathematics<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| FICO Xpress<\/a><\/td>\n | Optimization and data analytics tools<\/td>\n<\/tr>\n | \n| Mathematica<\/a><\/td>\n | Numeric and symbolic computing and programming<\/td>\n<\/tr>\n | \n| MATLAB<\/a><\/td>\n | Numerical computation, visualization and programming.<\/td>\n<\/tr>\n | \n| Octave (GNU)<\/a><\/td>\n | Free MATLAB-like application for numerical calculations<\/td>\n<\/tr>\n | \n| PyGMO<\/a><\/td>\n | Parallel optimization framework in python<\/td>\n<\/tr>\n | \n| R<\/a><\/td>\n | Statistical computing and graphics. Includes bioconductor.<\/td>\n<\/tr>\n | \n| RStudio<\/a><\/td>\n | GUI-based development environment for R<\/td>\n<\/tr>\n | \n| Stata<\/a><\/td>\n | Data analysis and statistical software<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nMultiphysics and Solvers<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| ANSWERS<\/a><\/td>\n | A suite of monte-carlo nuclear simulation tools<\/td>\n<\/tr>\n | \n| LS-DYNA<\/a><\/td>\n | A general purpose explicit solver<\/td>\n<\/tr>\n | \n| Elmer<\/a><\/td>\n | multiphysical simulation<\/td>\n<\/tr>\n | \n| Materials Studio<\/a><\/td>\n | Materials modeling and simulation<\/td>\n<\/tr>\n | \n| PyGMO<\/a><\/td>\n | Parallel optimization framework in python<\/td>\n<\/tr>\n | \n| Serpent<\/a><\/td>\n | Monte-carlo Nuclear reactor physics<\/td>\n<\/tr>\n | \n| StarCCM+<\/a><\/td>\n | A computation continuum mechanics application<\/td>\n<\/tr>\n | \n| WRF (and WPS)<\/a><\/td>\n | WRF weather research and forecasting model<\/td>\n<\/tr>\n | \n| WRF-Chem<\/a><\/td>\n | Weather Research and Forecasting (WRF) model coupled with Chemistry<\/td>\n<\/tr>\n | \n| Yade<\/a><\/td>\n | C++\/Python DEM framework<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nNeural Networks and Machine Learning<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| Chainer<\/a><\/td>\n | Neural netowrks in python<\/td>\n<\/tr>\n | \n| Keras<\/a><\/td>\n | Neural Network python API using Tensorflow<\/td>\n<\/tr>\n | \n| LENS<\/a><\/td>\n | Neural Network Simulator<\/td>\n<\/tr>\n | \n| TensorFlow<\/a><\/td>\n | Data flow graph processing<\/td>\n<\/tr>\n | \n| Theano<\/a><\/td>\n | Multi-dimensional array processing<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\nVisualization<\/h2>\n\n\n\n| PACKAGE<\/th>\n | NOTES<\/th>\n<\/tr>\n | \n| EMAN2<\/a><\/td>\n | Greyscale scientific image processing<\/td>\n<\/tr>\n | \n| ffmpeg<\/a><\/td>\n | Image processing<\/td>\n<\/tr>\n | \n| Freesurfer<\/a><\/td>\n | Visualisation of structural and functional brain imaging data<\/td>\n<\/tr>\n | \n| FSL<\/a><\/td>\n | Analysis of structural and functional brain imaging data<\/td>\n<\/tr>\n | \n| Gephi<\/a><\/td>\n | Graph visualization and analysis<\/td>\n<\/tr>\n | \n| IDL<\/a><\/td>\n | Data visualization programming language<\/td>\n<\/tr>\n | \n| MGLTools<\/a><\/td>\n | Graphical molecular visualization tools.<\/td>\n<\/tr>\n | \n| Ovito<\/a><\/td>\n | Scientific visualization and analysis of atomistic simulation data<\/td>\n<\/tr>\n | \n| Povray<\/a><\/td>\n | Raytracer for rendering 3D models<\/td>\n<\/tr>\n | \n| ParaView<\/a><\/td>\n | Scientific Visualization application based on VTK<\/td>\n<\/tr>\n | \n| Visual Colloids<\/a><\/td>\n | Molecular visualization tool<\/td>\n<\/tr>\n | \n| VMD<\/a><\/td>\n | Molecular Graphics Visualisation Tool<\/td>\n<\/tr>\n | \n| XCrySDen<\/a><\/td>\n | Molecular visualisation tool<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":" 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.. 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-31","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31","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=31"}],"version-history":[{"count":24,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31\/revisions"}],"predecessor-version":[{"id":4830,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31\/revisions\/4830"}],"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=31"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}} | | | | | | | |