Software Modules on the Curie Cluster

Last Updated: Mon Sep 28 01:00:02 CDT

The available software for the Curie cluster is listed in the table. Click on any software package name to get more information such as the available versions, additional documentation if available, etc.

Name Description
ACTCACTC converts independent triangles into triangle strips or fans.
AdapterRemovalAdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.
AGEntAGEnt is a program for identifying accessory genomic elements in bacterial genomes by using an in-silico subtractive hybridization approach against a core genome, such as those generated by the Spine algorithm. URL:
AGFusionAGFusion is a python package for annotating gene fusions from the human or mouse genomes. URL:
aiohttp" Async http client/server framework
ALFAALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism. URL:
Algorithm-LoopsAlgorithm::Loops - Looping constructs: NestedLoops, MapCar*, Filter, and NextPermute* URL:
AmaraLibrary for XML processing in Python, designed to balance the native idioms of Python with the native character of XML. URL:
AMOSThe AMOS consortium is committed to the development of open-source whole genome assembly software
AnnifAnnif is a multi-algorithm automated subject indexing tool for libraries, archives and museums. URL:
ANTLRANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. URL:
any2fastaConvert various sequence formats to FASTA URL:
APRApache Portable Runtime (APR) libraries. URL:
APR-utilApache Portable Runtime (APR) util libraries. URL:
archspecA library for detecting, labeling, and reasoning about microarchitectures URL:
argtableArgtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. URL:
ArmadilloArmadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. URL:
arpack-ngARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. URL:
ArrayFireArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
ARTART is a set of simulation tools to generate synthetic next-generation sequencing reads"
ARTSARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors.
ASAP3ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). URL:
ASEASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. URL:
astropyThe Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
ATKATK 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. URL:
atoolsTools to make using job arrays a lot more convenient. URL:
at-spi2-atkAT-SPI 2 toolkit bridge URL:
at-spi2-coreAssistive Technology Service Provider Interface. URL:
attrCommands for Manipulating Filesystem Extended Attributes URL:
AutoconfAutoconf 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. URL:
AutoDockAutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. URL:
AutomakeAutomake: GNU Standards-compliant Makefile generator URL:
AutotoolsThis bundle collect the standard GNU build tools: Autoconf, Automake and libtool URL:
awscliUniversal Command Line Environment for AWS URL:
BamToolsBamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. URL:
barrnapBarrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.
basemapThe matplotlib basemap toolkit is a library for plotting 2D data on maps in Python
BBMapBBMap short read aligner, and other bioinformatic tools.
BCALMde Bruijn graph compaction in low memory URL:
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 URL:
bcl2fastq2bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
BEDToolsThe 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. URL:
BerkeleyGWThe BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
BFCBFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. URL:
binutilsbinutils: GNU binary utilities URL:
bioawkBioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
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. URL:
BisonBison 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. URL:
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. URL:
BLATBLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Blitz++Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
BlobToolsA modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.
BloscBlosc, an extremely fast, multi-threaded, meta-compressor library URL:
bokehStatistical and novel interactive HTML plots for Python URL:
BoostBoost provides free peer-reviewed portable C++ source libraries. URL:
Boost.PythonBoost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
bsddb3bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
buildenvThis module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show <this module name>
bwidgetThe BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. URL:
bx-pythonThe bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
byaccBerkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.
bzip2bzip2 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. URL:
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 URL:
cairommThe Cairomm package provides a C++ interface to Cairo.
CanuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). URL:
CapnProtoCap’n Proto is an insanely fast data interchange format and capability-based RPC system.
CastXMLCastXML is a C-family abstract syntax tree XML output tool. URL:
CaVEManSNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib URL:
CD-HITCD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. URL:
cdsapiClimate Data Store API URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
CFITSIOCFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. URL:
cftimeTime-handling functionality from netcdf4-python
CGALThe goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. URL:
cgetCmake package retrieval. This can be used to download and install cmake packages URL:
CharLSCharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios.
CheMPS2CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. URL:
ChromaprintChromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source. URL:
ClangC, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. URL:
Clang-Python-bindingsPython bindings for libclang URL:
CLHEPThe CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
Clustal-OmegaClustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
ClustalW2ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
CMakeCMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. URL:
coloramaCross-platform colored terminal text.
cornerMake some beautiful corner plots. URL:
covid-simThis is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London. URL:
CppUnitCppUnit is the C++ port of the famous JUnit framework for unit testing. URL:
cramCram is a functional testing framework for command line applications. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
CrossMapCrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. URL:
CRPropaCRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment. URL:
csvkitcsvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
CubeLibCube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools. URL:
CubeWriterCube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. URL:
CUDACUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
CufflinksTranscript assembly, differential expression, and differential regulation for RNA-Seq
cURLlibcurl 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. URL:
cutadaptCutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. URL:
CVXPYCVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers. URL:
CWPSUSeismic Unix is an open source seismic utilities package supported by the Center for Wave Phenomena (CWP) at the Colorado School of Mines (CSM).
CyclerComposable style cycles
CythonCython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). URL:
cyvcf2cython + htslib == fast VCF and BCF processing URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
daskDask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. URL:
datamashGNU datamash performs basic numeric, textual and statistical operations on input data files URL:
DBBerkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. URL:
DBusD-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. URL:
dbus-glibD-Bus is a message bus system, a simple way for applications to talk to one another. URL:
DCMTKDCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
deepdiffDeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. URL:
DendroPyA Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
DIAMONDAccelerated BLAST compatible local sequence aligner
dilldill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
DL_POLY_ClassicDL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package. URL:
DocutilsDocutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.
DorisDelft object-oriented radar interferometric software URL:
double-conversionEfficient binary-decimal and decimal-binary conversion routines for IEEE doubles. URL:
DoxygenDoxygen 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. URL:
dtcmpDatatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. URL:
EasyBuildEasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. URL:
EasyBuild-curieEasyBuild environment variables for building system software on
EasyBuild-curie-REasyBuild environment variables for building software for the experimental R_modules on
EasyBuild-curie-restricted-vaspEasyBuild environment variables for building restricted software VASP on
EasyBuild-curie-SCRATCHUser EasyBuild environment for in $SCRATCH/eb
ecCodesecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). URL:
EigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. URL:
EIGENSOFTThe EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. URL:
EmacsGNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
EMAN2EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
emceeEmcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet! URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
enaBrowserToolenaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. URL:
ETSF_IOA library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
eudeveudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.
ExonerateExonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
expatExpat 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) URL:
FaberFaber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
FALCONFalcon: a set of tools for fast aligning long reads for consensus and assembly
fastpA tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. URL:
FastQCFastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
fastStructurefastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. URL:
FastTreeFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. URL:
FFmpegA complete, cross-platform solution to record, convert and stream audio and video. URL:
FFTWFFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. URL:
FIATThe FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.
fileThe file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.
FLASHFLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
Flask" Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications.
flexFlex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. URL:
FLTKFLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
fmtfmt (formerly cppformat) is an open-source formatting library. URL:
fontconfigFontconfig is a library designed to provide system-wide font configuration, customization and application access. URL:
fossGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. URL:
FRANzA fast and flexible parentage inference program for natural populations. URL:
freeglutfreeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. URL:
freetypeFreeType 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. URL:
FreeXLFreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. URL:
FriBidiThe Free Implementation of the Unicode Bidirectional Algorithm. URL:
FTGLFTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL ( applications. URL:
futurepython-future is the missing compatibility layer between Python 2 and Python 3. It allows you to use a single, clean Python 3.x-compatible codebase to support both Python 2 and Python 3 with minimal overhead.
g2clibLibrary contains GRIB2 encoder/decoder ('C' version). URL:
g2libLibrary contains GRIB2 encoder/decoder and search/indexing routines. URL:
g2logg2log, efficient asynchronous logger using C++11 URL:
GapCloserGapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads. URL:
GATKThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. URL:
gawkgawk: GNU awk
gcThe Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. URL:
GCATemplatesGCATemplates is a collection of HPC template scripts for tools useful for bioinformatics tasks.
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,...). URL:
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,...). URL:
gcccudaGNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
GConfGConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.
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. URL:
GDBThe GNU Project Debugger
GDCHARTEasy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format. URL:
GDCMGrassroots DICOM: Cross-platform DICOM implementation URL:
Gdk-PixbufThe 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.
Geant4Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
gearshifftBenchmark Suite for Heterogenuous FFT Implementations URL:
GEOSGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) URL:
GerrisGerris is a Free Software program for the solution of the partial differential equations describing fluid flow
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 URL:
gffreadGFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. URL:
gflagsThe gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. URL:
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. URL:
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. URL:
gifsicleGifsicle is a command-line tool for creating, editing, and getting information about GIF images and animations. Making a GIF animation with gifsicle is easy. URL:
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. URL:
GizaGiza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.
GL2PSGL2PS: an OpenGL to PostScript printing library URL:
GladeGlade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.
glewThe OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. URL:
GLibGLib is one of the base libraries of the GTK+ project URL:
GLibmmC++ bindings for Glib URL:
GLIMMERGlimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
GlimmerHMMGlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.
GlobalArraysGlobal Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
GLOBUSGlobus Software Package, without GRAM, MyProxy, GSI-SSH
Globus-CLIA Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
glogA C++ implementation of the Google logging module. URL:
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. URL:
GMPGMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. URL:
gmpichgcc and GFortran based compiler toolchain, including MPICH for MPI support.
gmpolfgcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
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. URL:
GNUCompiler-only toolchain with GCC and binutils.
gnuplotPortable interactive, function plotting utility
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. URL:
golfGNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW. URL: (none)
gompiGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. URL: (none)
googletestGoogle's C++ test framework
goolfGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
GPAWGPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. URL:
gperfGNU 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. URL:
gperftoolsgperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. URL:
gradunwarpGradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. URL:
GraphicsMagickGraphicsMagick is the swiss army knife of image processing. URL:
GRASPThe General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. URL:
GROMACSGROMACS 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.
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. URL:
gSOAPThe gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST XML Web services and generic C/C++ XML data bindings. The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C++ code. It also supports exposing (legacy) C and C++ applications as XML Web services by auto-generating XML serialization code and WSDL specifications. Or you can simply use it to automatically convert XML to/from C and C++ data. The toolkit supports options to generate pure ANSI C or C++ with or without STL. URL:
gsportGSPORT command-line tool for accessing GenomeScan Customer Portal URL:
GST-plugins-baseGStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GStreamerGStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
gtestGoogle's framework for writing C++ tests on a variety of platforms URL:
GTK+The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
GTSGTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
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.
gzipgzip (GNU zip) is a popular data compression program as a replacement for compress URL:
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. URL:
HALHAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. URL:
HarfBuzzHarfBuzz is an OpenType text shaping engine.
HDFHDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. URL:
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. URL:
hdf5storageThis Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data. All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
HDF-EOSThe HDF-EOS2 is a software library designed built on HDF4* to support EOS-specific data structures, namely Grid, Point, and Swath.
HelloThe GNU Hello program produces a familiar, friendly greeting. Yes, this is another implementation of the classic program that prints "Hello, world!" when you run it. However, unlike the minimal version often seen, GNU Hello processes its argument list to modify its behavior, supports greetings in many languages, and so on. URL:
help2manhelp2man produces simple manual pages from the '--help' and '--version' output of other commands. URL:
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. URL:
HPLHPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. URL:
HTSeqHTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. URL:
HTSlibA C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix URL:
hunspellHunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. URL:
hwlocThe 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. URL:
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. URL:
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. URL:
ibmatPlaceholder EasyBuild module for IBMs Advanced Toolchain default installation
iCountiCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.
IDBA-UDIDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
igraphigraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. URL:
imageioImageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
ImageMagickImageMagick is a software suite to create, edit, compose, or convert bitmap images URL:
imbalanced-learnimbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.
IntaRNAEfficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
INTEGRATEINTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform. URL:
intltoolintltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. URL:
iperfiperf - A TCP, UDP, and SCTP network bandwidth measurement tool
IPythonIPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. URL:
JAGSJAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
JasPerThe 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. URL:
JavaThis is a downstream version of the OpenJDK project. It is used to build and maintain a SAP supported version of OpenJDK for SAP customers and partners who wish to use OpenJDK to run their applications. URL:
jbigkitJBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. URL:
JDKIBM Java for 64-bit PowerPCs
JellyfishJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jemallocjemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. URL:
JsonCppJsonCpp 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. URL:
JudyA C library that implements a dynamic array. URL:
JupyterLabJupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. URL:
kallistokallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. URL:
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. URL:
KrakenKraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
Kraken2Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. URL:
KronaToolsKrona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
kwantKwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport. URL:
LAMELAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. URL:
LAPACKLAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
LASTZLASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. URL:
LCovLCOV - the LTP GCOV extension
LevelDBLevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. URL:
libaioAsynchronous input/output library that uses the kernels native interface. URL:
libarchiveMulti-format archive and compression library URL:
libartGraphics routines used by the GnomeCanvas widget and some other applications. libart renders vector paths and the like.
libavLibav is a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts.
libBigWigA C library for handling bigWig files URL:
libcerflibcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. URL:
libcircleAn API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization. URL:
libconfigLibconfig is a simple library for processing structured configuration files
libdapA C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. URL:
libdrmDirect Rendering Manager runtime library. URL:
libdwarfThe DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) URL:
libeditThis BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.
libelflibelf is a free ELF object file access library URL:
libepoxyEpoxy is a library for handling OpenGL function pointer management for you URL:
libeventThe 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. URL:
libfabricLibfabric 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. URL:
libffcallGNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters URL:
libffiThe 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. URL:
libgcryptLibgpg-error is a small library that defines common error values for all GnuPG components. URL:
libgdGD is an open source code library for the dynamic creation of images by programmers. URL:
libgeotiffLibrary for reading and writing coordinate system information from/to GeoTIFF files URL:
libgladeLibglade is a library for constructing user interfaces dynamically from XML descriptions.
libGLUThe OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. URL:
libglvndlibglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. URL:
libgnomecanvasThe canvas widget allows you to create custom displays using stock items such as circles, lines, text, and so on. It was originally a port of the Tk canvas widget but has evolved quite a bit over time.
libgpg-errorLibgpg-error is a small library that defines common error values for all GnuPG components. URL:
libharulibHaru is a free, cross platform, open source library for generating PDF files. URL:
libICEX Inter-Client Exchange library for
libiconvLibiconv converts from one character encoding to another through Unicode conversion URL:
libidnGNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. URL:
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. URL:
libjpeg-turbolibjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. URL:
libmathevalGNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. URL:
libMemcachedlibMemcached is an open source C/C++ client library and tools for the memcached server ( It has been designed to be light on memory usage, thread safe, and provide full access to server side methods.
libpciaccessGeneric PCI access library. URL:
libpnglibpng is the official PNG reference library URL:
libpslC library for the Public Suffix List URL:
libpthread-stubsThe X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libreadlineThe 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. URL:
libsamplerateSecret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio. URL:
libsigc++The libsigc++ package implements a typesafe callback system for standard C++. URL:
libsigsegvGNU libsigsegv is a library for handling page faults in user mode. URL:
libSMX11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.
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. URL:
libsodiumSodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. URL:
LibSouplibsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications. URL:
libspatialindexC++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API URL:
libspatialiteSpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
libtarC library for manipulating POSIX tar files
libtasn1Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package. URL:
LibTIFFtiff: Library and tools for reading and writing TIFF data files URL:
libtirpcLibtirpc is a port of Suns Transport-Independent RPC library to Linux. URL:
libtoolGNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. URL:
libunistringThis library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. URL:
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 URL:
LibUUIDPortable uuid C library URL:
libvdwxclibvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. URL:
libwebpWebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. URL:
libX11X11 client-side library
libXauThe libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.
libxcLibxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. URL:
libxcbThe X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libxml++libxml++ is a C++ wrapper for the libxml XML parser library. URL:
libxml2Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). URL:
libxsltLibxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). URL:
libXtlibXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).
libyamlLibYAML is a YAML parser and emitter written in C. URL:
LittleCMSLittle CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. URL:
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) to use LLVM as an optimizer and code generator. URL:
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. URL:
LoFreqFast and sensitive variant calling from next-gen sequencing data
lpsolveMixed Integer Linear Programming (MILP) solver URL:
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. URL:
lwgrpThe Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups URL:
lxmlThe lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
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. URL:
LZOPortable lossless data compression library URL:
M4GNU 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. URL:
MACS2Model Based Analysis for ChIP-Seq data URL:
MAFFTMAFFT 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 <∼10,000 sequences), etc.
MAGMAMAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
MagresPythonMagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes.
makeGNU version of make utility URL:
makedependThe makedepend package contains a C-preprocessor like utility to determine build-time dependencies. URL:
MakoA super-fast templating language that borrows the best ideas from the existing templating languages URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0
MariaDB-connector-cMariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. URL:
MarkupSafePython http for humans
MashFast genome and metagenome distance estimation using MinHash
Math-DerivativeMath::Derivative - Numeric 1st and 2nd order differentiation URL:
Math-SplineMath::Spline - Cubic Spline Interpolation of data URL:
Math-UtilsMath::Utils - Useful mathematical functions not in Perl. URL:
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. URL:
MavericKMavericK is a program for inferring population structure on the basis of genetic information. The mixture modelling framework used by MavericK is identical to that used in the program STRUCTURE by Pritchard et al. (2000), which remains one of the most powerful and widely used programs in population genetics. URL:
mawkmawk is an interpreter for the AWK Programming Language.
mbuffermbuffer is a tool for buffering data streams with a large set of unique features. URL:
MCLThe MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. URL:
MEGAHITAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
memory-profilermemory-profiler is a Python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
MesaMesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. URL:
MesonMeson is a cross-platform build system designed to be both as fast and as user friendly as possible. URL:
MesquiteMesh-Quality Improvement Library URL:
METISMETIS 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. URL:
MINCMedical Image NetCDF or MINC isn't netCDF.
Minimac4Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality. URL:
MinPathMinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
MIRAMIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). URL:
MITObimThe MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. URL:
MoldenMolden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac URL:
molmodMolMod is a Python library with many compoments that are useful to write molecular modeling programs. URL:
MonoAn open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. URL:
MothurMothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. URL:
motifMotif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. URL:
MoviePyMoviePy (full documentation) is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects. URL:
MPFRThe MPFR library is a C library for multiple-precision floating-point computations with correct rounding. URL:
MPICHMPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
MPICH2MPICH2 is a high-performance and widely portable implementation of the MPI-2.2 standard from the Argonne National Laboratory.
mpifileutilsMPI-Based File Utilities For Distributed Systems URL:
mpmathmpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work.
MRtrixMRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. URL:
MultiQCAggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
MUMmerMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. URL:
MUMPSA parallel sparse direct solver URL:
muParsermuParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.
myEBUser EasyBuild built modules in $SCRATCH/eb
MySQLMySQL is one of the world's most widely used open-source relational database management system (RDBMS).
NAGNAG Fortran Library for XLF compiler version xlf-
NAMDNAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NASMNASM: General-purpose x86 assembler URL:
NCOmanipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 URL:
ncompressCompress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files.
ncursesThe 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. URL:
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. URL:
netCDF-C++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. URL:
netCDF-C++4NetCDF (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. URL:
networkxNetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. URL:
NFFTThe NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data. URL:
ngspiceNgspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. URL:
NiBabelNiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
NIfTINiftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format.
NilearnNilearn is a Python module for fast and easy statistical learning on NeuroImaging data. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
NimNim is a systems and applications programming language. URL:
NinjaNinja is a small build system with a focus on speed. URL:
NipypeNipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
NLoptNLopt 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. URL:
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. URL:
NOVOPlastyNOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. URL:
NSPRNetscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. URL:
NSSNetwork Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. URL:
numactlThe 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. URL:
numexprThe numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. URL:
numpyNumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
NxTrimNxTrim is a software to remove Nextera Mate Pair junction adapters and categorise reads according to the orientation implied by the adapter location. URL:
oneTBBOfficial Threading Building Blocks (TBB) GitHub repository. Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. For Commercial Intel® TBB distribution, please see: URL:
OOF2OOF: Finite Element Analysis of Microstructures
OOF3DOOF: Finite Element Analysis of Microstructures
OPARI2OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. URL:
OpenBLASOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. URL:
OpenEXROpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications URL:
OpenFOAMOpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
OpenJPEGOpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. URL:
openkim-modelsOpen Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild installs the models. The API itself is in the kim-api package. URL:
OpenMPIThe Open MPI Project is an open source MPI-3 implementation. URL:
OpenMXOpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. URL:
OpenPGMOpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. URL:
OpenPyXLA Python library to read/write Excel 2010 xlsx/xlsm files URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
OptiTypeOptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
OTF2The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. URL:
packmolPacking Optimization for Molecular Dynamics Simulations URL:
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.
PAPIPAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. URL:
parallelparallel: Build and execute shell commands in parallel URL:
ParaViewParaView is a scientific parallel visualizer. URL:
ParFlowParFlow is an integrated, parallel watershed model that makes use of high-performance computing to simulate surface and subsurface fluid flow.
ParMETISParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. URL:
ParMGridGenParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods.
patchelfPatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
PCREThe PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. URL:
PCRE2The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. URL:
PDTProgram Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. URL:
PerlLarry Wall's Practical Extraction and Report Language URL:
phyxphyx performs phylogenetics analyses on trees and sequences. URL:
picardA set of tools (in Java) for working with next generation sequencing data in the BAM format.
pigzpigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. URL:
PILThe Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. URL:
PillowPillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. URL:
PilonPilon is an automated genome assembly improvement and variant detection tool URL:
pixmanPixman 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. URL:
pizzlyPizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.
pkgconfigpkgconfig is a Python module to interface with the pkg-config command line tool URL:
pkg-configpkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). URL:
plcplc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). URL:
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. URL:
plyPython Lex & Yacc
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) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. URL:
polymakepolymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects. URL:
PostgreSQLPostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. URL:
POV-RayThe Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
preseqSoftware for predicting library complexity and genome coverage in high-throughput sequencing.
pretty-yamlPyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
prodigalProdigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. URL:
PROJProgram proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates URL:
protobufGoogle Protocol Buffers URL:
protobuf-pythonPython Protocol Buffers runtime library.
psmcThis software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. URL:
PSolverPoisson Solver from the BigDFT code compiled as a standalone library.
pstoeditpstoedit translates PostScript and PDF graphics into other vector formats
psutilA cross-platform process and system utilities module for Python URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
psycopg2Psycopg is the most popular PostgreSQL adapter for the Python programming language. URL:
ptemceeptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey's wonderful emcee to implement parallel tempering more robustly. If you're trying to characterise awkward, multi-model probability distributions, then ptemcee is your friend. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
pullseqUtility program for extracting sequences from a fasta/fastq file
PyAPS3Python 3 Atmospheric Phase Screen URL:
pybedtoolspybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
pyBigWigA python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
pybind11pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. URL:
PyCairoPython bindings for the cairo library URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
PyCogentPyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.
pydicomPure python package for DICOM medical file reading and writing. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
pyEGA3A basic Python-based EGA download client URL:
PyGObjectPyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. URL:
pygribPython interface for reading and writing GRIB data URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
PyGTKPyGTK lets you to easily create programs with a graphical user interface using the Python programming language.
pyhdfPython wrapper around the NCSA HDF version 4 library URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
PylintPylint is a tool that checks for errors in Python code, tries to enforce a coding standard and looks for code smells. It can also look for certain type errors, it can recommend suggestions about how particular blocks can be refactored and can offer you details about the code's complexity.
PyNASTPyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation.
PyomoPyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.
PyOpenGLPyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
pyparsingThe pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. URL:
pyprojPython interface to PROJ4 library for cartographic transformations URL:
PyQtPyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.
PyRePyRe (Python Reliability) is a Python module for structural reliability analysis. URL:
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. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
PyTablesPyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. URL:
pytestpytest: simple powerful testing with Python
PythonPython is a programming language that lets you work more quickly and integrate your systems more effectively. URL:
python-igraphPython interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
pythranPythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster. URL:
PyYAMLPyYAML is a YAML parser and emitter for the Python programming language. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0
QCATaking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.
QhullQhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. URL:
QJsonQJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.
qrupdateqrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. URL:
QScintillaQScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control
QtQt is a comprehensive cross-platform C++ application framework. URL:
Qt5Qt is a comprehensive cross-platform C++ application framework. URL:
QwtThe Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. URL:
QwtPolarThe QwtPolar library contains classes for displaying values on a polar coordinate system.
RR is a free software environment for statistical computing and graphics.
randfoldMinimum free energy of folding randomization test software
RDFlibRDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. URL: Compatible modules: Python/2.7.16-GCCcore-8.3.0 (default), Python/3.7.4-GCCcore-8.3.0
re2cre2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. URL:
RELIONRELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
REMORAREsource MOnitoring for Remote Applications URL:
requestsPython http for humans
R_modulesAn experiemental TAMU HPRC module to study an alternative approch to the R_tamu module. Features include fine-detailed module control and strict version control for reproducible results (changes to R_tamu can happen at anytime). This is NOT meant for most users unless they have strict need for reproducible results.
RNAzRNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.
RSeQCRSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
R_tamuR is a free software environment for statistical computing and graphics.
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. URL:
RustRust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. URL:
SAMtoolsSAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. URL:
ScaLAPACKThe ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. URL:
scikit-buildScikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. URL:
scikit-imagescikit-image is a collection of algorithms for image processing. URL:
scikit-learnScikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. URL:
scikit-optimizeScikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. URL:
SciPy-bundleBundle of Python packages for scientific software URL:
SConsSCons is a software construction tool. URL: Compatible modules: Python/3.8.2-GCCcore-9.3.0 (default), Python/2.7.18-GCCcore-9.3.0
SCOTCHSoftware package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. URL:
ScytheScythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. URL:
SDL2SDL: Simple DirectMedia Layer, a cross-platform multimedia library URL:
SeabornSeaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. URL:
segemehlsegemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.
sepPython and C library for Source Extraction and Photometry. (this easyconfig provides python library only)
SEPPSATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. URL:
SeqAnSeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. URL:
SeqmagickWe often have to convert between sequence formats and do little tasks on them, and it's not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments. URL:
seqtkSeqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
SerfThe serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library URL:
setuptoolsDownload, build, install, upgrade, and uninstall Python packages -- easily!
ShapelyShapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. URL:
shrinkwrapA std::streambuf wrapper for compression formats. URL:
SibeliaSibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.
SiloSilo is a library for reading and writing a wide variety of scientific data to binary, disk files
SIONlibSIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. URL:
SIPSIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
sixPython 2 and 3 compatibility utilities
snappySnappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. URL:
SNPomaticHigh throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping. URL:
SOAPfuseSOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.
socatsocat is a relay for bidirectional data transfer between two independent data channels. URL:
sparsehashAn extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. URL:
SphinxSphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.
SPLASHSPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations.
SQLiteSQLite: SQL Database Engine in a C Library URL:
StacksStacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. URL:
STARSTAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. URL:
STAR-FusionSTAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
statsmodelsStatsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. URL: Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
StrAutoAutomation and Parallelization of STRUCTURE Analysis. StrAuto is used to streamline population structure analysis using parallel computing.
STREAMThe STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.
strelkaStrelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
StringTieStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. URL:
StructureThe program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
StructureHarvesterStructure Harvester is a program for parsing the output of Pritchard's STRUCTURE and for performing the Evanno method.
SubversionSubversion is an open source version control system. URL:
SuiteSparseSuiteSparse is a collection of libraries manipulate sparse matrices.
SUMOSUMO allows modelling of intermodal traffic systems including road vehicles, public transport and pedestrians. Included with SUMO is a wealth of supporting tools which handle tasks such as route finding, visualization, network import and emission calculation.
SUNDIALSSUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers URL:
SuperLUSuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SVGPerl binding for SVG URL:
SWIGSWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. URL:
sympySymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
SzipSzip compression software, providing lossless compression of scientific data URL:
tabixGeneric indexer for TAB-delimited genome position files
TagLibTagLib is a library for reading and editing the meta-data of several popular audio formats. URL:
tbbIntel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. URL:
TclTcl (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. URL:
tcshTcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. URL:
TetGenA Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator
texinfoTexinfo is the official documentation format of the GNU project.
TheanoTheano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. URL:
timeThe `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. URL:
TinyDBTinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server. URL: Compatible modules: Python/3.7.4-GCCcore-8.3.0 (default), Python/2.7.16-GCCcore-8.3.0
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. URL:
TkinterTkinter module, built with the Python buildsystem URL:
ToglA Tcl/Tk widget for OpenGL rendering. URL:
tqdmA fast, extensible progress bar for Python and CLI URL: Compatible modules: Python/2.7.16-GCCcore-8.3.0 (default), Python/3.7.4-GCCcore-8.3.0
TriangleTriangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. The latter can be generated with no small or large angles, and are thus suitable for finite element analysis. URL:
TrimmomaticTrimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
UCXUnified Communication X An open-source production grade communication framework for data centric and high-performance applications URL:
UDUNITSUDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. URL:
unrarRAR is a powerful archive manager.
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. URL:
utf8procutf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. URL:
util-linuxSet of Linux utilities URL:
ValgrindValgrind: Debugging and profiling tools
VCFtoolsThe aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
VelvetSequence assembler for very short reads
version_requiredA TAMU HPRC module to force users to specify a version when loading certain modules
ViennaRNAThe Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
VimVim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. URL:
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. URL:
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.
VXLA multi-platform collection of C++ software libraries for Computer Vision and Image Understanding. URL:
wgetGNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. URL:
wheelA built-package format for Python.
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.
wxPythonwxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++.
X11The X Window System (X11) is a windowing system for bitmap displays URL:
x264x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. URL:
x265x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. URL:
xcb-protoThe X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
XCfunXCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. URL:
Xerces-C++Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. URL:
xlcbaseIBM XL C/C++ for Linux (SLES11/RHEL6)
xlfbaseIBM XL FORTRAN for Linux (SLES11/RHEL6)
xlmassIBM Mathematical Acceleration Subsystem (MASS) package (SLES10)
xlsmpIBM SMP support packages (SLES10)
XMDS2The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations.
XML-ParserThis is a Perl extension interface to James Clark's XML parser, expat. macros utilities. URL:
xpropThe xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. URL:
xprotoX protocol and ancillary headers URL:
xtransxtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.
XZxz: XZ utilities URL:
yaml-cppyaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec.
YasmYasm: Complete rewrite of the NASM assembler with BSD license URL:
ZeroMQZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. URL:
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 URL:
zlibzlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. URL:
zstdZstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. URL: