Software Modules on the Faster Cluster

ACES Software Modules FASTER Software Modules Grace Software Modules Terra Software Modules

Last Updated: Aug 7 11:58:37 CDT

The available software for the FASTER 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
ABINIT'ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. '
ABySS'Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler'
ACTC'ACTC converts independent triangles into triangle strips or fans.'
AFLOW'Automatic FLOW for Materials Discovery'
AMOS'The AMOS consortium is committed to the development of open-source whole genome assembly software'
AMPHORA2'An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.'
ANSYS'ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. '
ANTLR'ANTLR, 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.'
AOCC'AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0'
APR'Apache Portable Runtime (APR) libraries.'
APR-util'Apache Portable Runtime (APR) util libraries.'
ASE'ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.'
ATK'ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. '
Abseil'Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.'
AdapterRemoval'AdapterRemoval 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.'
AlphaFold'AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known'
AlphaPickle'ALPHAPICKLE is a programme for extracting the outputs of DeepMind's ALPHAFOLD protein prediction algorithm from the pickle (.pkl) file output.'
Amber'AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.'
Anaconda3'Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. '
Arcade-Learning-Environment'The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE.'
Archive-Zip'Provide an interface to ZIP archive files.'
Armadillo'Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.'
Arrow'Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.'
ArviZ'Exploratory analysis of Bayesian models with Python'
AutoDock-GPU'OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.'
Autoconf'Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.'
Automake'Automake: GNU Standards-compliant Makefile generator'
Autotools'This bundle collect the standard GNU build tools: Autoconf, Automake and libtool '
BAli-Phy'BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.'
BBMap'BBMap short read aligner, and other bioinformatic tools.'
BCFtools'Samtools 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'
BEDTools'BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.'
BLAST'Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.'
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.'
BLIS'AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.'
BWA'Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. '
BamTools'BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.'
Bazel'Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.'
Beast'BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. '
BeautifulSoup'Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.'
Berkeley-UPC'Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. The programmer is presented with a single shared, partitioned address space, where variables may be directly read and written by any processor, but each variable is physically associated with a single processor.'
Bio-DB-HTS'Read files using HTSlib including BAM/CRAM, Tabix and BCF database files'
BioPerl'Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.'
Biopython'Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. '
Bison'Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.'
Blender'Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. '
BoTorch'GPyTorch is a Gaussian process library implemented using PyTorch.'
Boost'Boost provides free peer-reviewed portable C++ source libraries.'
Boost.Python'Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.'
Bottleneck'Fast NumPy array functions written in C'
Bowtie'Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.'
Bowtie2'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.'
Brotli'Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.'
CD-HIT'CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.'
CDAT'CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems.'
CDO'CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.'
CFITSIO'CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.'
CGAL'The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.'
CLHEP'The 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.'
CMake'CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. '
CNVnator'a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads '
CP2K'CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. '
CUDA'CUDA (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.'
CUDAcore'CUDA (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.'
Cartopy'Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.'
Chapel'Chapel is a programming language designed for productive parallel computing at scale.'
Check'Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.'
ChimeraX'UCSF ChimeraX is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. '
Clang'C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.'
Clang-AOMP'AOMP is an open source Clang/LLVM based compiler with added support for the OpenMP® API on Radeon™ GPUs.'
Clp'Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.'
ClustalW2'ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.'
CoinUtils'CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.'
ColabFold'Making Protein folding accessible to all!'
Compress-Raw-Zlib'Low-Level Interface to zlib or zlib-ng compression library'
CoordgenLibs'Schrodinger-developed 2D Coordinate Generation'
CppUnit'CppUnit is the C++ port of the famous JUnit framework for unit testing. '
CuPy'CuPy is an open-source array library accelerated with NVIDIA CUDA.'
Cython'Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). '
DB'Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.'
DBD-mysql'Perl binding for MySQL'
DB_File'Perl5 access to Berkeley DB version 1.x.'
DBus'D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. '
DCMTK'DCMTK 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.'
DFT-D3'DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.'
DIAMOND'Accelerated BLAST compatible local sequence aligner'
Dalton'=========== Dalton More information ================ - Homepage: '
DendroPy'A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.'
Devito'Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms.'
Doxygen'Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. '
DualSPHysics'DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems.'
ELPA'Eigenvalue SoLvers for Petaflop-Applications.'
EMBOSS'EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.'
ESM'Evolutionary Scale Modeling'
ESMF'The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.'
EasyBuild'EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.'
EasyBuild-faster'EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on'
EasyBuild-faster-SCRATCH'User EasyBuild environment for in $SCRATCH/eb'
EasyBuild-faster-myeb'User EasyBuild environment for in $SCRATCH/eb'
EasyBuild-faster-tmp'EasyBuild environment variables for building in /tmp and installing in /sw/eb on'
Eigen'Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.'
FEMZIP-L'FEMZIP-L is a data compression software package for LS-DYNA result files - Homepage: '
FFTW'FFTW 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.'
FFTW.MPI'FFTW 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.'
FFmpeg'A complete, cross-platform solution to record, convert and stream audio and video.'
FIRESTARTER'FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy.'
FLAC'FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.'
FLASH'FLASH (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. '
FLTK'FLTK 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.'
FSL'FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.'
FastQC'FastQC 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.'
Fiji'Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.'
Fiona'Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.'
Firefox'Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.'
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. This module includes the Flask extensions: Flask-Cors'
FlexiBLAS'FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.'
Foldseek'Foldseek enables fast and sensitive comparisons of large structure sets.'
FreeBayes'freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.'
FreeImage'FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe.'
FriBidi'The Free Implementation of the Unicode Bidirectional Algorithm. '
GATK'The 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.'
GCATools'GCATools is a collection of useful scripts for bioinformatics tasks.'
GCC'The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).'
GCCcore'The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).'
GDAL'GDAL 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.'
GDRCopy'A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.'
GEOS'GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)'
GL2PS'GL2PS: an OpenGL to PostScript printing library'
GLFW'GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop'
GLPK'The 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.'
GLib'GLib is one of the base libraries of the GTK+ project'
GMP'GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. '
GObject-Introspection'GObject 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.'
GPy'GPy is a Gaussian Process (GP) framework written in Python'
GPyTorch'GPyTorch is a Gaussian process library implemented using PyTorch.'
GROMACS'GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds for both single and double precision. It also contains the gmxapi extension for the single precision MPI build next to PLUMED.'
GSL'The 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-bad'GStreamer 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.'
GST-plugins-base'GStreamer 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.'
GStreamer'GStreamer 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.'
GTK+'GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. '
GTK2'The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. '
GTK3'GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. '
GTK4'GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. '
GTS'GTS 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.'
Gdk-Pixbuf'The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. '
GetDist'GetDist is a Python package for analysing Monte Carlo samples, including correlated samples from Markov Chain Monte Carlo (MCMC).'
Ghostscript'Ghostscript 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.'
GitPython'GitPython is a python library used to interact with Git repositories '
GlobalArrays'Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model'
GnuTLS'GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.'
Go'Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.'
GraalVM'GraalVM is a high-performance JDK distribution designed to accelerate the execution of applications written in Java and other JVM languages along with support for JavaScript, Ruby, Python, and a number of other popular languages. whatis([==[Homepage:'
Gradle'Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. '
Graphene'Graphene is a thin layer of types for graphic libraries'
GraphicsMagick'GraphicsMagick is the swiss army knife of image processing.'
Graphviz'Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.'
Guile'Guile 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.'
Gymnasium'Gymnasium is a standard API for reinforcement learning, and a diverse collection of reference environments.'
HDBSCAN'The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering.'
HDF'HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. '
HDF5'HDF5 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.'
HH-suite'The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).'
HISAT2'HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).'
HMMER'HMMER 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.'
HPL'HPL 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.'
HTSeq'HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.'
HTSlib'A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix'
HarfBuzz'HarfBuzz is an OpenType text shaping engine.'
Horovod'Horovod is a distributed training framework for TensorFlow.'
Hypre'Hypre 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.'
ICU'ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.'
IGV'This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.'
IPython'IPython 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.'
ISA-L'Intelligent Storage Acceleration Library'
ITK'Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.'
ImageJ'Image Processing and Analysis in Java'
ImageMagick'ImageMagick is a software suite to create, edit, compose, or convert bitmap images'
Imath'Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics '
InterProScan'InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.'
JAGS'JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation '
JUnit'A programmer-oriented testing framework for Java.'
JasPer'The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. '
Java'Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.'
JsonCpp'JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. '
Judy'A C library that implements a dynamic array.'
Julia'Julia is a high-level, high-performance dynamic programming language for numerical computing'
KaHIP'The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.'
Kalign'Kalign is a fast multiple sequence alignment program for biological sequences.'
Keras'Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. '
Knitro'The Artelys Knitro Solver is a plug-in Solver Engine that extends Analytic Solver Platform, Risk Solver Platform, Premium Solver Platform or Solver SDK Platform to solve nonlinear optimization problems of virtually unlimited size. '
LAME'LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.'
LAMMPS'LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. Homepage: '
LLVM'The 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.'
LMDB'LMDB 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.'
LUMPY'A probabilistic framework for structural variant discovery. '
LZO'Portable lossless data compression library'
LaTeX'TeX Live is a basic implementation of the TeX typesetting system created by Donald Knuth. The main engine is LaTeX which compiles tex code into printable formats. This build includes some scientific packages for labelling plots. Homepage: '
Leptonica'Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.'
LibTIFF'tiff: Library and tools for reading and writing TIFF data files'
Libint'Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.'
LittleCMS'Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. '
Lua'Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.'
M4'GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. '
MAFFT'MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.'
MAGMA'MAGMA 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.'
MAGeCK'Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center.'
MAINMAST'=========== MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map. It is a fully automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. More information ================ - Homepage: '
MCL'The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. '
MEGAHIT'An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph'
METIS'METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. '
MPFR'The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. '
MUMPS'A parallel sparse direct solver'
MUMmer'MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. '
MaSuRCA'The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.'
Mako'A super-fast templating language that borrows the best ideas from the existing templating languages'
Mamba'Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. '
MariaDB'MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.'
Mathematica'Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.'
Matlab'A numerical computing environment and fourth-generation programming language. - Homepage: '
Mauve'Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.'
Maven'Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. '
McCortex'McCortex is a multi-sample de novo assembly and variant calling using Linked de bruijn graphs.'
Mesa'Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.'
Meson'Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.'
Miniconda3'Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.'
Mothur'Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.'
MuJoCo'MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment.'
MultiQC'Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.'
NAMD'NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.'
NASM'NASM: General-purpose x86 assembler'
NCCL'The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.'
NCCL-tests'Tests check both the performance and the correctness of NCCL operations.'
NCO'The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.'
NGS'NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.'
NGSadmix'NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods.'
NLTK'NLTK is a leading platform for building Python programs to work with human language data.'
NLopt'NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. '
NSPR'Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.'
NSS'Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.'
NVBIO'NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA. It contains the nvBowtie and nvLighter applications.'
NVHPC'C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)'
NVSHMEM'NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams. '
NanoFilt'Filtering and trimming of long read sequencing data.'
NextDenovo'NextDenovo is a string graph-based de novo assembler for TGS long reads.'
NextPolish'NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both.'
Nextflow'Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data'
Ninja'Ninja is a small build system with a focus on speed.'
Nuitka'Nuitka is the optimizing Python compiler written in Python that creates executables that run without an need for a separate installer.'
OBITools3'A package for the management of analyses and data in DNA metabarcoding.'
OGDF'OGDF is a self-contained C++ library for graph algorithms, in particular for (but not restricted to) automatic graph drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects.'
ONNX'Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring).'
ONNX-Runtime'ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms.'
ORCA'ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.'
OSU-Micro-Benchmarks'OSU Micro-Benchmarks'
Octave'GNU Octave is a high-level interpreted language, primarily intended for numerical computations.'
Open-Data-Cube-Core'The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems.'
OpenAI-Gym'A toolkit for developing and comparing reinforcement learning algorithms.'
OpenBLAS'OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.'
OpenBabel'Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.'
OpenCV'OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository.'
OpenCensus-python'OpenCensus for Python. OpenCensus provides a framework to measure a server's resource usage and collect performance stats. This repository contains Python related utilities and supporting software needed by OpenCensus.'
OpenEXR'OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications'
OpenFOAM'OpenFOAM 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.'
OpenFold'A faithful PyTorch reproduction of DeepMind's AlphaFold 2'
OpenJPEG'OpenJPEG 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.'
OpenMM'OpenMM is a toolkit for molecular simulation.'
OpenMPI'The Open MPI Project is an open source MPI-3 implementation.'
OpenMX'OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. '
OpenPGM'OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. '
OpenSSL'The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. '
OptiX'OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms.'
Optuna'Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters.'
Osi'Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.'
PCAngsd'PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations.'
PCRE'The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. '
PCRE2'The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. '
PETSc'PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. '
PLINK'Whole-genome association analysis toolset'
PLUMED'PLUMED 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. '
PMIx'Process 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. '
POV-Ray'The 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.'
PROJ'Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates'
Pango'Pango 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.'
ParMETIS'ParMETIS 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.'
ParaView'ParaView is a scientific parallel visualizer.'
ParallelFold'This project is a modified version of DeepMind's AlphaFold2 to achieve high-throughput protein structure prediction.'
Perl'Larry Wall's Practical Extraction and Report Language'
Pillow'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.'
Pillow-SIMD'Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.'
Pilon'Pilon is an automated genome assembly improvement and variant detection tool'
PnetCDF'Parallel netCDF: A Parallel I/O Library for NetCDF File Access'
PostgreSQL'PostgreSQL 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.'
PyCUDA'PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.'
PyCairo'Python bindings for the cairo library'
PyCharm'PyCharm Community Edition: Python IDE for Professional Developers'
PyGObject'PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.'
PyMC3'Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano'
PyOpenCL'PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.'
PyPy 'PyPy is a replacement for CPython. It implements Python 2.7.18, and 3.7.10. It supports all of the core language, passing the Python 2.7 test suite and almost all of the 3.7 test suite (with minor modifications) It supports most of the commonly used Python standard library modules. whatis([==[Homepage:'
PyQt5'PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.'
PyStan'Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.'
PyTorch'Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.'
PyTorch-Geometric'PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.'
PyTorch-Lightning'PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.'
PyTorch3D'PyTorch3D is FAIR's library of reusable components for deep learning with 3D data.'
PyYAML'PyYAML is a YAML parser and emitter for the Python programming language.'
Pyomo'Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. '
Pysam'Pysam 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.'
Python'Python is a programming language that lets you work more quickly and integrate your systems more effectively.'
QIIME2'QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.'
Qhull'Qhull 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. '
Qt5'Qt is a comprehensive cross-platform C++ application framework.'
QuantumESPRESSO'Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). '
Qwt'The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.'
R'R is a free software environment for statistical computing and graphics.'
R-bundle-Bioconductor'Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.'
RAxML'RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.'
RAxML-NG'RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.'
RDFlib'RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.'
RE2'RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. '
RNAlysis'RNAlysis is a Python-based software for analyzing RNA sequencing data.'
ROCR-Runtime'The user-mode API interfaces and libraries necessary for host applications to launch compute kernels to available HSA ROCm kernel agents'
ROCT-Thunk-Interface'The user-mode API interfaces used to interact with the ROCk driver'
ROCm-CompilerSupport'The compiler support repository provides various Lightning Compiler related services'
ROOT'The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.'
RSEM'RNA-Seq by Expectation-Maximization'
Racon'Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.'
RapidJSON'A fast JSON parser/generator for C++ with both SAX/DOM style API'
Ray-project'Ray is a fast and simple framework for building and running distributed applications.'
Redis'Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.'
Ruby'Ruby 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.'
Rust'Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.'
SAMtools'SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.'
SCNIC'SCNIC is a package for the generation and analysis of cooccurrence (positive correlation) networks with compositional data.'
SCOTCH'Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.'
SCons'SCons is a software construction tool.'
SDL2'SDL: Simple DirectMedia Layer, a cross-platform multimedia library'
SEPP'SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.'
SMRT-Link'PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided'
SPAdes'Genome assembler for single-cell and isolates data sets'
SQLite'SQLite: SQL Database Engine in a C Library'
SRA-Toolkit'The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format'
STAR'STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.'
STAR-CCM+'Software for solving problems involving flow (of fluids or solids), heat transfer and stress. - Homepage: '
STRUMPACK'STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling.'
SUNDIALS'SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers'
SWIG'SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.'
SZ'Error-bounded lossy compressor for HPC data.'
SZ3'A modular error-bounded lossy compression framework for scientific datasets.'
Salmon'Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.'
Sambamba'Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.'
ScaFaCoS'ScaFaCoS is a library of scalable fast coulomb solvers.'
ScaLAPACK'The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.'
SciPy-bundle'Bundle of Python packages for scientific software'
SciPy_tamu'Bundle of Python packages for scientific software'
Seaborn'Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. '
Serf'The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library'
Shapely'Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.'
Spack'Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.'
Spark'Spark is Hadoop MapReduce done in memory'
SpeedSeq'A flexible framework for rapid genome analysis and interpretation.'
Stacks'Stacks 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. '
Structure'The 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.'
Subversion'Subversion is an open source version control system.'
SuiteSparse'SuiteSparse is a collection of libraries manipulate sparse matrices.'
SuperLU_DIST'SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.'
Szip'Szip compression software, providing lossless compression of scientific data '
TCLAP'TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary.'
Taichi'Taichi Lang is an open-source, imperative, parallel programming language for high-performance numerical computation. It is embedded in Python and uses just-in-time (JIT) compiler frameworks, for example LLVM, to offload the compute-intensive Python code to the native GPU or CPU instructions.'
Tcl'Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. '
TensorFlow'An open-source software library for Machine Intelligence'
TensorRT'An SDK for high-performance deep learning inference, includes a deep learning inference optimizer and runtime that delivers low latency and high throughput for inference applications.'
Theano'Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.'
Thermo-Calc'Thermocalc is a software package for thermodynamic calculations. It is widely used for a variety of calculations.'
Tk'Tk 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.'
Tkinter'Tkinter module, built with the Python buildsystem'
Transformers'State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0'
Trim_Galore'Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).'
UCC'UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. '
UCC-CUDA'UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support. '
UCSCtools'Tools from the UCSC browser..'
UCX'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications '
UCX-CUDA'Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. '
UDUNITS'UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.'
UnZip'UnZip 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.'
VCFtools'The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.'
VEP'Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.'
VMD'VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.'
VTK'The 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.'
VTune'Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.'
VirtualGL'VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.'
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.'
WPS'WRF Preprocessing System (WPS) for WRF. The 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.'
WRF'The 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.'
Wannier90'A tool for obtaining maximally-localised Wannier functions'
Wayland'Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. '
WebProxy'WebProxy module sets up web proxy environment variables, http_proxy and https_proxy, for internet acceess from the compute nodes. Wiki page: '
X11'The X Window System (X11) is a windowing system for bitmap displays'
XML-LibXML'Perl binding for libxml2'
XZ'xz: XZ utilities'
XtalOpt'XtalOpt is a free and truly open source evolutionary algorithm designed for a priori crystal structure prediction.'
Xvfb'Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.'
YACS'YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These "configurations" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.'
YAXT'Yet Another eXchange Tool'
Yasm'Yasm: Complete rewrite of the NASM assembler with BSD license'
Z3'Z3 is a theorem prover from Microsoft Research. '
ZEBULON'Zébulon is the state-of-the-art finite element solver of the Z-set suite. - Homepage: '
ZeroMQ'ZeroMQ 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.'
Zip'Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality'
aesara'Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays.'
aiohttp'Asynchronous HTTP client/server framework for asyncio and Python.'
alsa-lib'The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.'
angsd'Program for analysing NGS data.'
ant'Apache 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.'
any2fasta'Convert various sequence formats to FASTA'
archspec'A library for detecting, labeling, and reasoning about microarchitectures'
aria2'aria2-1.15.1: Multi-threaded, multi-protocol, flexible download accelerator'
arpack-ng'ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.'
arrow-R'R interface to the Apache Arrow C++ library'
astropy'The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.'
at-spi2-atk'AT-SPI 2 toolkit bridge '
at-spi2-core'Assistive Technology Service Provider Interface. '
axl'A C/C++ project support library that covers specialized needs for compiler/parser writing, asynchronous IO, device management, cryptography, etc.'
bamkit'Tools for common BAM file manipulations'
beagle-lib'beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.'
binutils'binutils: GNU binary utilities'
bioawk'Bioawk 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. '
biom-format'The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. '
bohrium'Bohrium provides automatic acceleration of array operations in Python/NumPy, C, and C++ targeting multi-core CPUs and GP-GPUs. Forget handcrafting CUDA/OpenCL to utilize your GPU and forget threading, mutexes and locks to utilize your multi-core CPU.'
bokeh'Statistical and novel interactive HTML plots for Python'
bzip2'bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. '
c-ares'c-ares is a C library for asynchronous DNS requests (including name resolves)'
cURL'libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. '
cairo'Cairo 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'
canu'Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing'
ccache'Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again'
charliecloud'Charliecloud provides user-defined software stacks (UDSS) for high-performance computing (HPC) centers.'
cisTEM'cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. '
cobaya'Cobaya (code for bayesian analysis) is a framework for sampling and statistical modelling: it allows you to explore an arbitrary prior or posterior using a range of Monte Carlo samplers (including the advanced MCMC sampler from CosmoMC, and the advanced nested sampler PolyChord).'
code-server'Run VS Code on any machine anywhere and access it in the browser.'
colossalai'Colossal-AI: A Unified Deep Learning System for Big Model Era'
cppy'A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.'
cuDF'Built based on the Apache Arrow columnar memory format, cuDF is a GPU DataFrame library for loading, joining, aggregating, filtering, and otherwise manipulating data.'
cuDNN'The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.'
cuSPARSELt'NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix'
cuSZ'A modular error-bounded lossy compression framework for scientific datasets.'
cuTENSOR'The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.'
cutadapt'Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.'
cytoolz'Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.'
dace'DaCe is a fast parallel programming framework that takes code in Python/NumPy and other programming languages, and maps it to high-performance CPU, GPU, and FPGA programs, which can be optimized to achieve state-of-the-art.'
dask'Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.'
decona'fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads'
dill'dill 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.'
dlib'Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.'
dm-reverb'Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues.'
dm-tree'dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.'
double-conversion'Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.'
ecCodes'ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).'
edlib'Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.'
einops'Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.'
elfutils'The elfutils project provides libraries and tools for ELF files and DWARF data. '
expat'Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) '
expecttest'This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.'
fastcore'Adds to Python features inspired by other languages we've loved, like multiple dispatch from Julia, mixins from Ruby, and currying, binding, and more from Haskell.'
fdasrsf'A python package for functional data analysis using the square root slope framework and curves using the square root velocity framework which performs pair-wise and group-wise alignment as well as modeling using functional component analysis and regression.'
ffnvcodec'FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).'
file'The 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.'
flatbuffers'FlatBuffers: Memory Efficient Serialization Library Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. '
flatbuffers-python'Python Flatbuffers runtime library.'
flex'Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. '
fontconfig'Fontconfig is a library designed to provide system-wide font configuration, customization and application access. '
foss'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
fosscuda'GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.'
freeglut'freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.'
freetype'FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. '
futhark'Futhark is a small programming language designed to be compiled to efficient parallel code. It is a statically typed, data-parallel, and purely functional array language in the ML family, and comes with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, although the language itself is hardware-agnostic and can also run on multicore CPUs'
g2clib'Library contains GRIB2 encoder/decoder ('C' version).'
gRPC'gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems.'
gawk'gawk: GNU awk'
gc'The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. '
gcccuda'GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.'
gdbm'GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.'
geocube'Tool to convert geopandas vector data into rasterized xarray data.'
geopandas'GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations.'
gettext'GNU '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'
gfbf'GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.'
giflib'giflib 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.'
git'Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.'
glew'The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.'
gnuplot'Portable interactive, function plotting utility'
gobff'GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.'
gompi'GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.'
gompic'GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.'
googletest'Google's framework for writing C++ tests on a variety of platforms'
gperf'GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. '
gpustat'A simple command-line utility for querying and monitoring GPU status'
graphite2'Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.'
groff'Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.'
gsd-vmd'HOOMD-blue GSD plugin for VMD'
gzip'gzip (GNU zip) is a popular data compression program as a replacement for compress'
h5py'HDF5 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.'
hatchling'Hatch is a modern, extensible Python project manager.'
help2man'help2man produces simple manual pages from the '--help' and '--version' output of other commands.'
hifiasm'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.'
hipSYCL'hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP'
hipify-clang'Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced.'
hiredis'Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.'
htop'Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. '
hwloc'The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. '
hyphen'Hyphenation library to use converted TeX hyphenation patterns.'
hypothesis'Hypothesis 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.'
iccifort'Intel C, C++ & Fortran compilers'
iccifortcuda'Intel C, C++ & Fortran compilers with CUDA toolkit'
iimkl'Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).'
iimpi'Intel C/C++ and Fortran compilers, alongside Intel MPI.'
iimpic'Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.'
imageio'Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.'
imkl'Intel oneAPI Math Kernel Library'
imkl-FFTW'FFTW interfaces using Intel oneAPI Math Kernel Library'
impi'Intel MPI Library, compatible with MPICH ABI'
intel'Intel Toolkits installed using Anaconda3 2022.10 '
intel-compilers'Intel C, C++ & Fortran compilers (classic and oneAPI)'
intel-python'Intel Python distribution.'
intelcuda'Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit'
intltool'intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.'
iomkl'Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL).'
iompi'Intel C/C++ and Fortran compilers, alongside Open MPI.'
jax'Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more'
jbigkit'JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.'
jemalloc'jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.'
kim-api'Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. '
lDDT'The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.'
lhsmdu'A package for generating latin hypercube samples with multi-dimensional uniformity.'
libFLAME'libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.'
libGLU'The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. '
libaio'Asynchronous input/output library that uses the kernels native interface.'
libarchive'Multi-format archive and compression library '
libcdms'Climate Data Management System Library.'
libcerf'libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. '
libcifpp'This library contains code to work with mmCIF and PDB files.'
libdap'A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.'
libdeflate'Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.'
libdrm'Direct Rendering Manager runtime library.'
libdrs'PCMDI's old DRS format implementation'
libepoxy'Epoxy is a library for handling OpenGL function pointer management for you'
libevent'The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. '
libfabric'Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. '
libffi'The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. '
libgd'GD is an open source code library for the dynamic creation of images by programmers.'
libgeotiff'Library for reading and writing coordinate system information from/to GeoTIFF files'
libgit2'libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.'
libglvnd'libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.'
libgpuarray'Library to manipulate tensors on the GPU.'
libharu'libHaru is a free, cross platform, open source library for generating PDF files.'
libiconv'Libiconv converts from one character encoding to another through Unicode conversion'
libidn'GNU 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-turbo'libjpeg-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. '
libmatheval'GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.'
libnsl'The libnsl package contains the public client interface for NIS(YP).'
libogg'Ogg is a multimedia container format, and the native file and stream format for the multimedia codecs.'
libopus'Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.'
libpciaccess'Generic PCI access library.'
libpng'libpng is the official PNG reference library'
libreadline'The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. '
librsvg'Librsvg is a library to render SVG files using cairo.'
libsigsegv'GNU libsigsegv is a library for handling page faults in user mode.'
libsndfile'Libsndfile 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.'
libsodium'Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. '
libssh'Multiplatform C library implementing the SSHv2 protocol on client and server side'
libtasn1'Libtasn1 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.'
libtirpc'Libtirpc is a port of Suns Transport-Independent RPC library to Linux.'
libtool'GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. '
libunistring'This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. '
libunwind'The 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'
libvorbis'Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format'
libvori'C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.'
libwebp'WebP 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.'
libxc'Libxc 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.'
libxml2'Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). '
libxslt'Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).'
libxsmm'LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).'
libyaml'LibYAML is a YAML parser and emitter written in C.'
libzip'libzip is a C library for reading, creating, and modifying zip archives.'
likwid'Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. '
lis'Lis (Library of Iterative Solvers for linear systems, pronounced [lis]) is a parallel software library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. '
lmod'Lmod: An Environment Module System'
loopy'Loopy lets you easily generate the tedious, complicated code that is necessary to get good performance out of GPUs and multi-core CPUs. Loopy's core idea is that a computation should be described simply and then transformed into a version that gets high performance..'
lxml'The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.'
lz4'LZ4 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.'
maeparser'maeparser is a parser for Schrodinger Maestro files.'
magma'The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.'
make'GNU version of make utility'
makeinfo'makeinfo is part of the Texinfo project, the official documentation format of the GNU project.'
matplotlib'matplotlib 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.'
mbuffer'mbuffer is a tool for buffering data streams with a large set of unique features.'
mcOutbryk'mcOutbryk is a SNP calling pipeline using mccortex'
medaka'medaka is a tool to create a consensus sequence from nanopore sequencing data.'
minimap2'Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.'
mkl-service'Python hooks for Intel(R) Math Kernel Library runtime control settings.'
molmod'MolMod is a Python library with many compoments that are useful to write molecular modeling programs.'
mpi4py'MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.'
mujoco-py'MuJoCo is a physics engine for detailed, efficient rigid body simulations with contacts. mujoco-py allows using MuJoCo from Python 3.'
multichoose'generate multiset combinations (n multichoose k).'
ncbi-vdb'The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.'
ncurses'The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.'
netCDF'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netCDF-C++4'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netCDF-Fortran'NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.'
netCDF-combined'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.'
netcdf4-python'Python/numpy interface to netCDF.'
nettle'Nettle 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.'
networkx'NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.'
newick_utils'The Newick Utilities are a suite of programs for working with Newick-formatted phylogenetic trees.'
nlohmann_json'JSON for Modern C++'
nodejs'Node.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.'
nsync'nsync is a C library that exports various synchronization primitives, such as mutexes'
numactl'The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. '
numba'Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.'
numexpr'The 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.'
nv-codec-headers'FFmpeg version of headers required to interface with Nvidias codec APIs.'
nvCOMP'A CUDA library that features generic compression interfaces to enable developers to use high-performance GPU compressors and decompressors in their applications.'
nvidia-container-cli'NVIDIA container command line tools provides a list of locally installed libraries that Charliecloud needs to interface to the local NVIDIA GPUs.'
nvtop'htop-like GPU usage monitor'
oneAPI'=========== Intel® oneAPI Base Toolkit The Intel® oneAPI Base Toolkit (Base Kit) is a core set of tools and libraries for developing high-performance, data-centric applications across diverse architectures. It features an industry-leading C++ compiler that implements SYCL*, an evolution of C++ for heterogeneous computing. See for more information. z More information ================ - Homepage: - Examples: '
p11-kit'Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process.'
pandas'pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.'
parabricks'Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing DNA and RNA data.'
parallel'parallel: Build and execute shell commands in parallel'
parasail'parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. '
patchelf'PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.'
pftoolsV3'A suite of tools to build and search generalized profiles (protein and DNA).'
php'PHP is a popular general-purpose scripting language that is especially suited to web development.'
physics-tenpy'TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks.'
picard'A set of tools (in Java) for working with next generation sequencing data in the BAM format.'
pigz'pigz, 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. '
pixman'Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. '
pkg-config'pkg-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). '
pkgconf'pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from'
pkgconfig'pkgconfig is a Python module to interface with the pkg-config command line tool''An open-source, interactive graphing library for Python'
pocl'Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard'
poetry'Python packaging and dependency management made easy'
poppler'Poppler is a PDF rendering library'
popt'Popt is a C library for parsing command line parameters. '
probtorch'Probabilistic Torch is library for deep generative models that extends PyTorch.'
protobuf'Google Protocol Buffers'
protobuf-python'Python Protocol Buffers runtime library.'
pscom'ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. '
psycopg2'Psycopg is the most popular PostgreSQL adapter for the Python programming language.'
pyBigWig'A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.'
pybind11'pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.'
pydantic'Data validation and settings management using Python type hinting.'
pyfaidx'pyfaidx: efficient pythonic random access to fasta subsequences'
pyproj'Python interface to PROJ4 library for cartographic transformations'
pyro-api'Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.'
pyro-ppl'Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.'
pyspoa'Python bindings to spoa.'
pytest'The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.'
pytest-xdist'xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.'
python-isal'Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. '
python-parasail'Python Bindings for the Parasail C Library'
qcat'qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files'
qchem'Q-Chem 5.4.0 release environment module'
qrupdate'qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.'
ragel'Ragel compiles executable finite state machines from regular languages.'
rasterio'Rasterio reads and writes geospatial raster data.'
re2c're2c 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.'
redis-py'The Python interface to the Redis key-value store.'
rioxarray'geospatial xarray extension powered by rasterio'
rlwrap'rlwrap is a 'readline wrapper', a small utility that uses the GNU readline library to allow the editing of keyboard input for any command. I couldn't find anything like it when I needed it, so I wrote this one back in 1999. By now, there are (and, in hindsight, even then there were) a number of good readline wrappers around, like rlfe, distributed as part of the GNU readline library, and the amazing socat ( You should consider rlwrap especially when you need user-defined completion (by way of completion word lists) and persistent history, or if you want to program 'special effects' using the filter mechanism. rlwrap compiles and runs on a fairly wide range of Unix-like systems. '
rocm-cmake'ROCM cmake modules provides cmake modules for common build tasks needed for the ROCM software stack'
rocm-smi'The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications.'
samblaster'samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.'
scikit-bio'scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.'
scikit-build'Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.'
scikit-fda'This package offers classes, methods and functions to give support to Functional Data Analysis in Python. Includes a wide range of utils to work with functional data, and its representation, exploratory analysis, or preprocessing, among other tasks such as inference, classification, regression or clustering of functional data.'
scikit-image'scikit-image is a collection of algorithms for image processing.'
scikit-learn'Scikit-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.'
scipy'SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.'
segmentation-models'Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow.'
snappy'Snappy 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.'
sparsehash'An 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. '
spglib-python'Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.'
spoa'Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences'
spython'Singularity Python is a Python API to work with the Singularity open source software. '
statsmodels'Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.'
svtyper'Bayesian genotyper for structural variants'
tbb'Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.'
tcsh'Tcsh 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.'
tensorboard'TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.'
tensorboardX'Tensorboard for PyTorch.'
tensorflow-probability'TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.'
time'The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.'
torchinfo'" Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. '
torchvision'Datasets, Transforms and Models specific to Computer Vision'
tqdm'A fast, extensible progress bar for Python and CLI'
trimAl'EVB, FEP and LIE simulator.'
typing-extensions'Typing Extensions – Backported and Experimental Type Hints for Python'
ucsctest'Tools from the UCSC browser..'
unison'Unison is a file-synchronization tool. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other.'
upcxx'UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, C++/POSIX threads, CUDA, ROCm/HIP and other HPC frameworks. It leverages GASNet-EX to deliver low-overhead, fine-grained communication, including Remote Memory Access (RMA) and Remote Procedure Call (RPC).'
utf8proc'utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.'
util-linux'Set of Linux utilities'
vasp'The 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. VASP 6.3.2 - Homepage:'
vawk'An awk-like VCF parser. vawk command syntax is exactly the same as awk syntax with a few additional features. '
visit'VisIt is a free, open source, platform independent, distributed, parallel, visualization tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes.'
wxWidgets'wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.'
x264'x264 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. '
x265'x265 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. '
xarray'xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.'
xorg-macros' macros utilities.'
xprop'The 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.'
xxd'xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.'
yaff'Yaff stands for 'Yet another force field'. It is a pythonic force-field code.'
zarr'Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.'
zfp'zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and write large data sets to and from disk.'
zlib'zlib 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.'
zstd'Zstandard 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.'