SOFTWAREDESCRIPTIONINFERTINKERCLIFFSHUCKLEBERRYCASCADESDRAGONSTOOTH
guppyGPUSOFTWAREDESCRIPTION
juliaJulia technical computing language
matlabMATLAB Technical Computing
ABAQUSFinite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
ABINITABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
ABySSAssembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
ANSYSANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
APRApache Portable Runtime (APR) libraries.
APR-utilApache Portable Runtime (APR) util libraries.
ATK ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
AUGUSTUSAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
AccelerateCFD_CECommunity Edition of AccelerateCFD platform for creating reduced order models from high fidelity CFD
Anaconda3Anaconda python distribution, python version 3.5
AtomPAWAtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.
Autoconf Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
AutomakeAutomake: GNU Standards-compliant Makefile generator
Autotools This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BCFtoolsSamtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
BEDToolsBEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
BLAST+Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
BUSCOBUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
BamToolsBamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
BazelBazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
BiopythonBiopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
Bison Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. , Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
BoostBoost provides free peer-reviewed portable C++ source libraries.
Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
CGALThe Computational Geometry Algorithms Library is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry.
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CP2KCP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
DBBerkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DBus D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
DaltonThe Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements..
DendroPyA Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
Doxygen Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
ELPAEigenvalue SoLvers for Petaflop-Applications .
EasyBuildEasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way., EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
EigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
FDSFire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.
FFTWFFTW is a C subroutine library for computing the discrete Fourier transform (DFT
FFmpegA complete, cross-platform solution to record, convert and stream audio and video.
FLACFLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
FriBidi The Free Implementation of the Unicode Bidirectional Algorithm.
GCCThe GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GCCcoreThe GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GDALGDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
GEOSGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GLPKThe GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
GLibGLib is one of the base libraries of the GTK+ project
GMP GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
GMTGMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
GObject-IntrospectionGObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds for both single and double precision. It also contains the gmxapi extension for the single precision MPI build.
GSLThe GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
GTK+GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
Gdk-Pixbuf The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
GhostscriptGhostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
GlobalArraysGlobal Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
GoGo is an open source programming language that makes it easy to build simple, reliable, and efficient software.
GuileGuile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.
HDF5HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
HMMERHMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
HMMER2HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.
HPLHPL is a software package that solves a (random) dense linear system in double precision (64 bits
HTSlibA C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
HarfBuzzHarfBuzz is an OpenType text shaping engine.
HypreHypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
ICUICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
ImageMagickImageMagick
JasPer The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
JavaJava Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
JellyfishJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
JsonCpp JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
JuliaJulia is a high-level, high-performance dynamic programming language for numerical computing
LAMELAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LAMMPSLAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
LLVMThe LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler
LMDBLMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
LibTIFFtiff: Library and tools for reading and writing TIFF data files
LibintLibint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
LuaLua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
M4 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. , GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
MATLABMATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
METIS METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPSA parallel sparse direct solver
MakoA super-fast templating language that borrows the best ideas from the existing templating languages
MariaDB-connector-cMariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.
MathematicaMathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.
MesaMesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
MesonMeson is a cross-platform build system designed to be both as fast and as user friendly as possible.
MetaEukMetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
Miniconda3Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.
NAMDNAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NASMNASM: General-purpose x86 assembler
NLopt NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
NSPRNetscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSSNetwork Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
NVHPCC, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
NastranNASTRANDESCRIPTION
NinjaNinja is a small build system with a focus on speed.
OpenBLASOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenFOAMOpen source CFD package
OpenMMOpenMM is a toolkit for molecular simulation.
OpenMPIThe Open MPI Project is an open source MPI-3 implementation.
OpenMolcasOpenMolcas is a quantum chemistry software package
OpenSSLThe OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
PCRE The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PETScPETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
PLUMEDPLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
PMIxProcess Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b
PROJProgram proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
PangoPango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
ParaViewParaView Scientific Visualization
PatranPATRANDESCRIPTION
PerlLarry Wall's Practical Extraction and Report Language
PillowPillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
PyCharmPyCharm Community Edition: Python IDE for Professional Developers
PyTorchTensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
PyYAMLPyYAML is a YAML parser and emitter for the Python programming language.
PysamPysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
PythonPython is a programming language that lets you work more quickly and integrate your systems more effectively.
QIIME2QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
Qt5Qt is a comprehensive cross-platform C++ application framework.
QuantumESPRESSOQuantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
RR For Statistical Computing
RubyRuby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
SAMtoolsSAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SCOTCHSoftware package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SConsSCons is a software construction tool.
SEPPSATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
SLEPcSLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
SQLiteSQLite: SQL Database Engine in a C Library
SWIGSWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
ScaFaCoSScaFaCoS is a library of scalable fast coulomb solvers.
ScaLAPACKThe ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SciPy-bundleBundle of Python packages for scientific software
SerfThe serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
SoXSoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion.
SpaceRanger Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
Subversion Subversion is an open source version control system.
SuiteSparseSuiteSparse is a collection of libraries manipulate sparse matrices.
Szip Szip compression software, providing lossless compression of scientific data
TINKERThe TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
Tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
TensorFlowAn open-source software library for Machine Intelligence
TkTk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
TkinterTkinter module, built with the Python buildsystem
TopHatTopHat is a fast splice junction mapper for RNA-Seq reads.
UCXUnified Communication X An open-source production grade communication framework for data centric and high-performance applications
UDUNITSUDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
UnZipUnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality.
VASPThe Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
VTKThe Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
ValgrindValgrind: Debugging and profiling tools
Voro++Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
WRFThe Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.
Wannier90A tool for obtaining maximally-localised Wannier functions
X11The X Window System (X11) is a windowing system for bitmap displays
XML-LibXMLPerl binding for libxml2
XZxz: XZ utilities
XvfbXvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.
YasmYasm: Complete rewrite of the NASM assembler with BSD license
ZipZip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
amd-uprofAMD μProf for performance analysis
archspecA library for detecting, labeling, and reasoning about microarchitectures
aspect-2.2.0AspectDESCRIPTION
aspect-2.3.0AspectDESCRIPTION
at-spi2-atkAT-SPI 2 toolkit bridge
at-spi2-core Assistive Technology Service Provider Interface.
bcl2fastq2bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
binutilsbinutils: GNU binary utilities
bokehStatistical and novel interactive HTML plots for Python
boost-1.58.0BOOSTDESCRIPTION
bzip2 bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
cURL libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
cairoCairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
canuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
daskDask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
dealii-9.2.0SOFTWAREDESCRIPTION
dealii-9.3.1DEALIIDESCRIPTION
double-conversionEfficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
dxaDXA Dislocation Analysis
ea-utilsEA-utils are command line tools for processing biological sequencing data.
expat Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags
flatbuffersFlatBuffers: Memory Efficient Serialization Library
flatbuffers-pythonPython Flatbuffers runtime library.
flexGithub Repository
fontconfig Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
fossGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
freetype FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
gaussianGaussian is a computer program for computational quantum chemistry that includes various methods for electronic structure calculations.
gc The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
gettextGNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
gflagsGoogle command line flags
giflibgiflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
gitGit is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
glm-0.9.8.5SOFTWAREDESCRIPTION
glogGoogle Logging Library
gmsh3D finite element grid generator with a build-in CAD engine and post-processor
gnuplotGNU Plot
gomklGNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL
gompiGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
gperf GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
gperftools gperftools is a collection of a high-performance multi-threaded malloc(
guppyCPUSOFTWAREDESCRIPTION
gzipgzip (GNU zip) is a popular data compression program as a replacement for compress
h5pyHDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
help2man help2man produces simple manual pages from the '--help' and '--version' output of other commands. , help2man produces simple manual pages from the '--help' and '--version' output of other commands.
hwloc The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
hypothesisHypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
iccifortIntel C, C++ & Fortran compilers
iimpiIntel C/C++ and Fortran compilers, alongside Intel MPI.
imklIntel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
impiIntel MPI Library, compatible with MPICH ABI
intelIntel Compilers (C, C++, Fortran)
intltoolintltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
iomklIntel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
iompiIntel C/C++ and Fortran compilers, alongside Open MPI.
kaldiKaldi is a toolkit for speech recognition
kim-apiOpen Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
libGLUThe OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libarchive Multi-format archive and compression library
libcerf libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
libdrmDirect Rendering Manager runtime library.
libepoxyEpoxy is a library for handling OpenGL function pointer management for you
libevent The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
libfabric Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.
libffi The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. , The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
libgdGD is an open source code library for the dynamic creation of images by programmers.
libgeotiffLibrary for reading and writing coordinate system information from/to GeoTIFF files
libglvndlibglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libiconvLibiconv converts from one character encoding to another through Unicode conversion
libjpeg-turbolibjpeg-turbo is a JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems.
libmathevalGNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
liboggOgg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
libpciaccessGeneric PCI access library.
libpnglibpng is the official PNG reference library
libreadline The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
libsndfileLibsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
libtool GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistring This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwindThe primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
libvorbisOgg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
libxcLibrary of exchange-correlation functionals for density-functional theory
libxml2 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxsmmLIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
libyamlLibYAML is a YAML parser and emitter written in C.
lpsolveMixed Integer Linear Programming (MILP) solver
ls-dynaLS-DYNA general-purpose finite element simulation software.
ls-prepostLS-PrePost
lz4LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
matplotlibmatplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
metis-5.1.0METISDESCRIPTION, METIS_DESCRIPTION
minimap2Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.
molmodMolMod is a Python library with many compoments that are useful to write molecular modeling programs.
mpi4pyMPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
nanopolishSoftware package for signal-level analysis of Oxford Nanopore sequencing data.
ncurses The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. , The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
netCDFNetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data., NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netCDF-FortranNetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
nettleNettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
networkxNetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nodejsNode.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
nsyncnsync is a C library that exports various synchronization primitives, such as mutexes
numactl The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
p4estParallel adaptive mesh refinement on forests of octrees
p4est-2.2P4ESTDESCRIPTION
parallelGNU Parallel
parmetis-4.0.3PARMETIS4.0.3DESCRIPTION, PARMETISDESCRIPTION, SOFTWAREDESCRIPTION
picardPicard: A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats
pixman Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.