Difference between revisions of "Applications"
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| MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. | | MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. | ||
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| + | | [[applications/Miniconda|Miniconda]] | ||
| + | | Miniconda is a lite version of anaconda used for creating virtual environments. | ||
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| [[applications/Minimap2|Minimap2]] | | [[applications/Minimap2|Minimap2]] | ||
| Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. | | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. | ||
Revision as of 14:29, 27 June 2019
Application Support
- Applications listed here refer to those list in the apps section of typing module avail..
- Jump to Development, Libraries, Test Modules.
Click on the links below for support on the individual applications:
| Package | Description |
| ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. |
| Albacore | Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms |
| Anaconda | Anaconda is the leading open data science platform powered by Python. |
| Ansys | ANSYS Fluent software includes broad physical modelling capabilities to model flow, turbulence, heat transfer, and reactions for industrial applications. |
| Avizo | Avizo data visualisation and analysis tool |
| BayesTraits | BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. |
| Blender | Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. |
| Bowtie1 | The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences. |
| Bowtie2 | Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method. |
| Bridger | Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference. |
| Centrifuge | Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species. |
| CMake | CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method. |
| CP2K | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. |
| CUDA | CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes. |
| Cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| Delft3D | Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. |
| FDS-SMV | Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations. |
| FDTD | 3D/2D Maxwell's solver for nanophotonic devices |
| Ffmpeg | ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source. |
| Flex | Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text. |
| Fiji | Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community. |
| Gcc | gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more. |
| GNUplot | Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. |
| Grace | Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr. |
| Guppy | Local accelerated basecalling for Nanopore data. |
| Java | Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented. |
| Julia | Julia is a high-level general-purpose dynamic programming language that was originally designed to address the needs of high-performance numerical analysis and computational science |
| HPL | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
| HyPhy | HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. |
| IDL | IDL, short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging. |
| Intel Parallel Studio | Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing. |
| IQtree | stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood. |
| Libwid | Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. |
| LS-DYNA | General-purpose finite element program capable of simulating complex real world problems. |
| Mafft | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences). |
| Maker | MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. |
| Mathematica | Symbolic mathematical computation program. |
| Matlab | Numerical Computing Environment. |
| Mercurial | Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independent of network access or a central server. Committing, branching and merging are fast and cheap. |
| Mpich | MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. |
| Miniconda | Miniconda is a lite version of anaconda used for creating virtual environments. |
| Minimap2 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. |
| MIKE | MIKE coastal modelling tool (restricted license) |
| Mono | .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime. |
| MrBayes | MrBayes: Bayesian Inference of Phylogeny |
| Mvapich2 | MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance. |
| Ncbi blast | It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. |
| Ncurses | ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner. |
| Nwchem | NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems. |
| Obitools | The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information. |
| Openfoam | OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. |
| OpenMPI | Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes. |
| Orca | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. |
| Packmol | PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. |
| Paraview | ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques. |
| Perl | Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large amount of libraries. |
| PGI | PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran . |
| Prinseq-lite | PRINSEQ can be used to filter, reformat, or trim genomic and meta-genomic sequence data. |
| Python | Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython. |
| Qiime2 | QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
| Quantum Package Shell | Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). |
| R | R is an open source programming language and software environment for statistical computing and graphics. |
| RaXML | RaXML is an open source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. |
| Readline | GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash. |
| RStudio | RStudio provides popular open source and enterprise-ready professional software for the R statistical computing environment. |
| Samtools | Tools (written in C using htslib) for manipulating next-generation sequencing data |
| Savu | Python package to assist with the processing and reconstruction of parallel-beam tomography data. |
| Scalapack | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers |
| SSW | Integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics |
| STAR | Ultrafast universal RNA-seq aligner. |
| Star-ccm+ | Computational Fluid Package. |
| Stata | Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics. |
| Tophat | It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons. |
| Transabyss | Software pipeline for analysing ABySS-assembled transcriptome contigs |
| Transrate | Transrate is software for de-novo transcriptome assembly quality analysis |
| Trinityrnaseq | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
| Utilities | General utilities module including zip, wget and git utilities. |
| Voxfe | VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised easily. |
| Yt | yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically-meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography. |
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