Software Modules on the Curie Cluster

Last Updated: Mon Oct 14 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
ABRA2ABRA2 is an updated implementation of ABRA featuring: RNA support, Improved scalability (Human whole genomes now supported), Improved accuracy, Improved stability and usability (BWA is no longer required to run ABRA although we do recommend BWA as the initial aligner for DNA) URL: https://github.com/mozack/abra2
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.
aiohttp" Async http client/server framework
AMOSThe AMOS consortium is committed to the development of open-source whole genome assembly software
antApache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
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: https://www.antlr2.org/
APRApache Portable Runtime (APR) libraries. URL: http://apr.apache.org/
APR-utilApache Portable Runtime (APR) util libraries. URL: http://apr.apache.org/
argtableArgtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. URL: http://argtable.sourceforge.net/
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.
ASEASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.
astropyThe Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.
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: https://developer.gnome.org/ATK/stable/
at-spi2-atkAT-SPI 2 toolkit bridge URL: https://wiki.gnome.org/Accessibility
at-spi2-coreAssistive Technology Service Provider Interface. URL: https://wiki.gnome.org/Accessibility
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.
AutomakeAutomake: GNU Standards-compliant Makefile generator
AutotoolsThis bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BamToolsBamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
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.
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
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.
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.
binutilsbinutils: GNU binary utilities
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.
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.
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.
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: http://www.blosc.org/
bokehStatistical and novel interactive HTML plots for Python
BoostBoost provides free peer-reviewed portable C++ source libraries.
Boost.PythonBoost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
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: https://core.tcl-lang.org/bwidget/home
bx-pythonThe bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
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.
C3DConvert3D Medical Image Processing Tool
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
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).
CapnProtoCap’n Proto is an insanely fast data interchange format and capability-based RPC system.
CD-HITCD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
CFITSIOCFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. URL: https://heasarc.gsfc.nasa.gov/fitsio/
cftimeTime-handling functionality from netcdf4-python
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.
CHARMMCHARMM is a versatile and widely used molecular simulation program with broad application to many-particle sy stems. Use charmm for the serial version and charmm-mpi for the mpi version. Environmental variable $TREXHOME is set to the location of the AdHocTrex directory, which inludes examples and scripts.\\ This module has restricted access.
CheMPS2CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
ClangC, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
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.
coloramaCross-platform colored terminal text.
CppUnitCppUnit is the C++ port of the famous JUnit framework for unit testing.
cramCram is a functional testing framework for command line applications. URL: https://bitheap.org/cram Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
csvkitcsvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. URL: https://github.com/wireservice/csvkit Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
ctagsCtags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.
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: https://www.scalasca.org/software/cube-4.x/download.html
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: https://www.scalasca.org/software/cube-4.x/download.html
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.
cutadaptCutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
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
CythonThe Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.
cyvcf2cython + htslib == fast VCF and BCF processing
daskDask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.
DBBerkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
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.
dbus-glibD-Bus is a message bus system, a simple way for applications to talk to one another. URL: http://dbus.freedesktop.org/doc/dbus-glib
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: https://deepdiff.readthedocs.io/en/latest/
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: https://pypi.org/project/dill/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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.
double-conversionEfficient binary-decimal and decimal-binary conversion routines for IEEE doubles. URL: https://github.com/google/double-conversion
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.
DrakeDrake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies.
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: https://easybuilders.github.io/easybuild
EasyBuild-curieEasyBuild environment variables for building system software on curie.tamu.edu
EasyBuild-curie-REasyBuild environment variables for building software for the experimental R_modules on curie.tamu.edu
EasyBuild-curie-restricted-vaspEasyBuild environment variables for building restricted software VASP on curie.tamu.edu
EasyBuild-curie-SCRATCHUser EasyBuild environment for curie.tamu.edu in $SCRATCH/eb
EigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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.
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: https://github.com/enasequence/enaBrowserTools/
esslIBM Engineering and Scientific Subroutine Library for Linux on POWER Version 5.3.0
esslFFTW3FFTW3 wrappers using the IBM Engineering and Scientific Subroutine Library for Linux on POWER Version 5.3.0
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)
FALCONFalcon: a set of tools for fast aligning long reads for consensus and assembly
fast5A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
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.
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.
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.
FFmpegA complete, cross-platform solution to record, convert and stream audio and video. URL: https://www.ffmpeg.org/
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.
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.
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: http://fmtlib.net/
fontconfigFontconfig is a library designed to provide system-wide font configuration, customization and application access.
fossGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
freeglutfreeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
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.
FreeXLFreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
FriBidiThe Free Implementation of the Unicode Bidirectional Algorithm.
FTGLFTGL is a free cross-platform Open Source C++ library that uses Freetype2 to simplify rendering fonts in OpenGL applications. FTGL supports bitmaps, pixmaps, texture maps, outlines, polygon mesh, and extruded polygon rendering modes.
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.
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: http://www.broadinstitute.org/gatk/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
gawkgawk: GNU awk
gcThe Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
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,...).
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,...).
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.
GDBThe GNU Project Debugger
GDCHARTEasy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format. URL: http://users.fred.net/brv/chart
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.
GEOSGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
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
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: https://github.com/gflags/gflags
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.
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: http://libungif.sourceforge.net/
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.
GizaGiza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.
GladeGlade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.
GLibGLib is one of the base libraries of the GTK+ project
GLibmmC++ bindings for Glib URL: http://www.gtk.org/
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
glogA C++ implementation of the Google logging module. URL: https://github.com/google/glog
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.
GMPGMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
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.
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.
golfGNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.
gompiGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
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.
GPAW-setupsPAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.
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.
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.
GraphicsMagickGraphicsMagick is the swiss army knife of image processing.
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.
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: https://github.com/google/googletest
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
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.
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.
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.
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: https://www.gnu.org/software/hello/
help2manhelp2man produces simple manual pages from the '--help' and '--version' output of other commands.
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.
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.
HTSeqA framework to process and analyze data from high-throughput sequencing (HTS) assays
HTSlibA C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
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: http://hunspell.github.io/
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.
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: https://github.com/HypothesisWorks/hypothesis Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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.
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++.
ImageMagickImageMagick is a software suite to create, edit, compose, or convert bitmap images
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: https://sourceforge.net/p/integrate-fusion/wiki/Home/
intltoolintltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
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.
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.
JavaJava Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
JBIGKIT(description not available)
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: http://jemalloc.net
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: http://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html
JudyA C library that implements a dynamic array. URL: http://judy.sourceforge.net/
JUnitA programmer-oriented testing framework for Java.
kallistokallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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.
KronaToolsKrona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
LAMELAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. URL: http://lame.sourceforge.net/
LAMMPSLAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. installed packages: ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MISC MOLECULE MPIIO PERI POEMS PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD USER-ATC USER-AWPMD USER-CGDNA USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MGPT USER-MOLFILE USER-PHONON USER-QMMM USER-QTB USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY VORONOI non-installed packages: GPU KIM KOKKOS LATTE MSCG OPT USER-CGSDK USER-INTEL USER-MEAMC USER-MESO USER-MISC USER-NETCDF USER-OMP USER-QUIP USER-UEF USER-VTK installed packages: ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MEAM MISC MOLECULE MPIIO PERI POEMS PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD USER-ATC USER-AWPMD USER-CGDNA USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MGPT USER-MOLFILE USER-PHONON USER-QMMM USER-QTB USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY VORONOI non-installed packages: GPU KIM KOKKOS LATTE MSCG OPT USER-CGSDK USER-INTEL USER-MEAMC USER-MESO USER-MISC USER-NETCDF USER-OMP USER-QUIP USER-UEF USER-VTK
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.
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: https://github.com/google/leveldb
libaioAsynchronous input/output library that uses the kernels native interface. URL: https://pagure.io/libaio
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.
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.
libconfigLibconfig is a simple library for processing structured configuration files
libdrmDirect Rendering Manager runtime library. URL: http://dri.freedesktop.org
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: http://www.prevanders.net/dwarf.html
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: http://www.mr511.de/software/english.html
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: https://libevent.org/
libffcallGNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters
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.
libgcryptLibgpg-error is a small library that defines common error values for all GnuPG components. URL: https://gnupg.org/related_software/libgcrypt/index.html
libgdGD is an open source code library for the dynamic creation of images by programmers.
libgeotiffLibrary for reading and writing coordinate system information from/to GeoTIFF files
libgladeLibglade is a library for constructing user interfaces dynamically from XML descriptions.
libGLUThe OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
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: https://gnupg.org/related_software/libgpg-error/index.html
libharulibHaru is a free, cross platform, open source library for generating PDF files.
libICEX Inter-Client Exchange library for freedesktop.org
libiconvLibiconv converts from one character encoding to another through Unicode conversion
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.
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.
libmathevalGNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
libMemcachedlibMemcached is an open source C/C++ client library and tools for the memcached server (http://danga.com/memcached). It has been designed to be light on memory usage, thread safe, and provide full access to server side methods.
libpciaccessGeneric PCI access library.
libpnglibpng is the official PNG reference library
libpslC library for the Public Suffix List URL: https://rockdaboot.github.io/libpsl
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.
libsigc++The libsigc++ package implements a typesafe callback system for standard C++. URL: https://libsigcplusplus.github.io/libsigcplusplus/
libsigsegvGNU libsigsegv is a library for handling page faults in user mode.
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: http://www.mega-nerd.com/libsndfile
libsodiumSodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. URL: https://doc.libsodium.org/
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: https://wiki.gnome.org/Projects/libsoup
libspatialindexC++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API
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: https://www.gnu.org/software/libtasn1/
LibTIFFtiff: Library and tools for reading and writing TIFF data files
libtoolGNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistringThis library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwindThe primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications URL: http://www.nongnu.org/libunwind/
LibUUIDPortable uuid C library URL: http://sourceforge.net/projects/libuuid/
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.
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: https://developers.google.com/speed/webp/
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.
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.
libXdmcpThe libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.
libxml++libxml++ is a C++ wrapper for the libxml XML parser library. URL: http://libxmlplusplus.sourceforge.net
libxml2Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxsltLibxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
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: http://pyyaml.org/wiki/LibYAML
LittleCMSLittle CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
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.
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: https://symas.com/lmdb
LoFreqFast and sensitive variant calling from next-gen sequencing data
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: http://www.lua.org/
lxmlThe lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. URL: http://lxml.de/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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: https://lz4.github.io/lz4/
LZOPortable lossless data compression library URL: http://www.oberhumer.com/opensource/lzo/
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.
MACS2Model Based Analysis for ChIP-Seq data
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.
makedependThe makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
MakoA super-fast templating language that borrows the best ideas from the existing templating languages
MariaDB-connector-cMariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. URL: https://downloads.mariadb.org/connector-c/
MarkupSafePython http for humans
MashFast genome and metagenome distance estimation using MinHash
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.
mawkmawk is an interpreter for the AWK Programming Language.
MEGAHITAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
MesaMesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. URL: http://www.mesa3d.org/
MesonMeson is a cross-platform build system designed to be both as fast and as user friendly as possible.
MesquiteMesh-Quality Improvement Library
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: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
MINCMedical Image NetCDF or MINC isn't netCDF.
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.
MothurMothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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.
MPFRThe MPFR library is a C library for multiple-precision floating-point computations with correct rounding. URL: http://www.mpfr.org
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.
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.
MRIcronMRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.
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.
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-15.1.0.0.484
NAMDNAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NASMNASM: General-purpose x86 assembler
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.
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: http://www.unidata.ucar.edu/software/netcdf/
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: http://www.unidata.ucar.edu/software/netcdf/
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.
netMHCpanThe NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs).
nettleNettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
networkxNetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
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.
NIfTINiftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format.
NimNim is a systems and applications programming language.
NinjaNinja is a small build system with a focus on speed.
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.
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: http://nodejs.org
NSPRNetscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSSNetwork Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
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.
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.
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.
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: https://www.score-p.org
OpenBLASOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
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: http://www.openjpeg.org/
OpenMPIThe Open MPI Project is an open source MPI-3 implementation.
OpenPGMOpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. 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: http://code.google.com/p/openpgm/
openpyxlA Python library to read/write Excel 2010 xlsx/xlsm files URL: https://openpyxl.readthedocs.io Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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: https://www.score-p.org
PandocIf you need to convert files from one markup format into another, pandoc is your swiss-army knife
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: http://icl.cs.utk.edu/projects/papi/
parallelparallel: Build and execute shell commands in parallel URL: http://savannah.gnu.org/projects/parallel/
ParaViewParaView is a scientific parallel visualizer. URL: http://www.paraview.org
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.
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.
PCRE2The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. URL: http://www.pcre.org/
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: http://www.cs.uoregon.edu/research/pdt/
PerlLarry Wall's Practical Extraction and Report Language
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.
PillowPillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. URL: http://pillow.readthedocs.org/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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.
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: http://github.com/matze/pkgconfig Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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).
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.
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: https://pmix.org/
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: https://www.postgresql.org/
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.
PROJProgram proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
protobufGoogle Protocol Buffers URL: https://github.com/google/protobuf/
protobuf-pythonPython Protocol Buffers runtime library.
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: https://github.com/giampaolo/psutil 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.
pullseqUtility program for extracting sequences from a fasta/fastq file
pybedtoolspybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
pyBigWigA python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.
PyCairoPython bindings for the cairo library
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.
pyEGA3A basic Python-based EGA download client URL: https://github.com/EGA-archive/ega-download-client
PyGObjectPython Bindings for GLib/GObject/GIO/GTK+
PyGTKPyGTK lets you to easily create programs with a graphical user interface using the Python programming language.
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.
pyprojPython interface to PROJ4 library for cartographic transformations URL: https://pyproj4.github.io/pyproj Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
PyQtPyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.
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.
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.
pytestpytest: simple powerful testing with Python
PythonPython is a programming language that lets you work more quickly and integrate your systems more effectively.
python-igraphPython interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
PyYAMLPyYAML is a YAML parser and emitter for the Python programming language. URL: https://pypi.python.org/pypi/PyYAML/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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.
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.
QScintillaQScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control
QtQt is a comprehensive cross-platform C++ application framework.
QwtThe Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
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
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: http://re2c.org/
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).
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: https://www.ruby-lang.org
SAMtoolsSAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
ScaLAPACKThe ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
scikit-imageScikit-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.
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.
SConsSCons is a software construction tool. URL: http://www.scons.org/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
SCOTCHSoftware package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SDL2SDL: Simple DirectMedia Layer, a cross-platform multimedia library URL: http://www.libsdl.org/
SeabornSeaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
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)
SeqAnSeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
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.
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: http://serf.apache.org/
setuptoolsDownload, build, install, upgrade, and uninstall Python packages -- easily!
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: http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html
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: https://github.com/google/snappy
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: http://www.dest-unreach.org/socat
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.
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
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: http://creskolab.uoregon.edu/stacks/
STARSTAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. URL: https://github.com/alexdobin/STAR
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 provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration.
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.
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.
SubreadSubread: an accurate and efficient aligner for mapping both genomic DNA-seq reads and RNA-seq reads (for the purpose of expression analysis).
SubversionSubversion is an open source version control system. URL: http://subversion.apache.org/
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
SuperLUSuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SWIGSWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. URL: http://www.swig.org/ Compatible modules: Python/3.7.2-GCCcore-8.2.0 (default), Python/2.7.15-GCCcore-8.2.0
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
tabixGeneric indexer for TAB-delimited genome position files
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.
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.
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.
TkTk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
TkinterTkinter module, built with the Python buildsystem
tqdmA fast, extensible progress bar for Python and CLI URL: https://github.com/tqdm/tqdm Compatible modules: Python/2.7.15-GCCcore-8.2.0 (default), Python/3.7.2-GCCcore-8.2.0
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.
UCLUSTUCLUST: Extreme high-speed sequence clustering, alignment and database search.
UCXUnified Communication X An open-source production grade communication framework for data centric and high-performance applications URL: http://www.openucx.org/
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: http://www.unidata.ucar.edu/software/udunits/
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: http://www.info-zip.org/UnZip.html
utf8procutf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. URL: https://github.com/JuliaStrings/utf8proc
util-linuxSet of Linux utilities
ValgrindValgrind: Debugging and profiling tools
VASPThe Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Includes VTST from: http://theory.cm.utexas.edu/vtsttools/index.html
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: http://www.vim.org
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.
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.
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.
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
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: http://www.videolan.org/developers/x264.html
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: http://x265.org/
xbitmapsprovides bitmaps for x
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.
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.
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.
xorg-macrosX.org macros utilities.
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: http://www.x.org/wiki/
xprotoX protocol and ancillary headers
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
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: http://www.tortall.net/projects/yasm/
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: http://www.zeromq.org/
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.
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: https://facebook.github.io/zstd