Software Modules on the aces Cluster

ACES Software Modules FASTER Software Modules Grace Software Modules

(Last Updated: Thu Jul 10 2025)

Name	Versions available	Description	Notes
ABYSS	ABySS/2.3.7	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
ACTC	ACTC/1.1	ACTC converts independent triangles into triangle strips or fans.
ADIOS2	ADIOS2/2.10.2	The Adaptable Input/Output (I/O) System transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes.
AI-TOOLS-GPU	AI-Tools-GPU/20240816	AI Tools from Intel (formerly referred to as the Intel AI Analytics Toolkit) give data scientists, AI developers, and researchers familiar Python tools and frameworks to accelerate end-to-end data science and analytics pipelines on Intel architecture. The components are built using oneAPI libraries for low-level compute optimizations. The AI Tools maximize performance from preprocessing through machine learning, and provides interoperability for efficient model development.
ANICALCULATOR	ANIcalculator/1.0	This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.
ANTLR	ANTLR/2.7.7-Java-11	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	AOCC/4.0.0	AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
APBS	APBS/3.4.1	APBS (Adaptive Poisson-Boltzmann Solver) solves the equations of continuum electrostatics for large biomolecular assemblages.
APR	APR/1.7.0	Apache Portable Runtime (APR) libraries.
APR-UTIL	APR-util/1.6.1	Apache Portable Runtime (APR) util libraries.
ASE	ASE/3.20.1 ASE/3.22.1	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/2.36.0 ATK/2.38.0	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.
AUGUSTUS	AUGUSTUS/3.5.0	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
ABSEIL	Abseil/20230125.2 Abseil/20230125.3 Abseil/20230802.1 Abseil/20240116.1	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.
ALPHAFOLD	AlphaFold/2.3.2-CUDA-11.8.0	AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
ALPHAFOLD3	AlphaFold3/3.0.1	This module provides details on creating an AlphaFold3 jobscript. Run the following command to see how to create an AlphaFold3 jobscript: alphafold3jobscript --help .
ALPHAPICKLE	AlphaPickle/1.4.1	ALPHAPICKLE is a programme for extracting the outputs of DeepMind's ALPHAFOLD protein prediction algorithm from the pickle (.pkl) file output.
ALPHAPULLDOWN	AlphaPulldown/2.0.0b5-CUDA-11.7.0	AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer
AMBER	Amber/24-NCCL-2.20.5-CUDA-12.4.1	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.
AMBERTOOLS	AmberTools/22.3	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	Anaconda3/2021.11 Anaconda3/2022.05 Anaconda3/2022.10 Anaconda3/2023.03-1 Anaconda3/2023.07-2 Anaconda3/2024.02-1	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.
ARMADILLO	Armadillo/11.4.3 Armadillo/12.6.2 Armadillo/12.8.0	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	Arrow/8.0.0 Arrow/11.0.0 Arrow/14.0.1 Arrow/16.1.0	Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.
AUTOCONF	Autoconf/2.69 Autoconf/2.71 Autoconf/2.72	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/1.16.2 Automake/1.16.3 Automake/1.16.4 Automake/1.16.5	Automake: GNU Standards-compliant Makefile generator
AUTOTOOLS	Autotools/20200321 Autotools/20210128 Autotools/20210726 Autotools/20220317 Autotools/20231222	This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
BBMAP	BBMap/38.90 BBMap/39.01	BBMap short read aligner, and other bioinformatic tools.
BCFTOOLS	BCFtools/1.17 BCFtools/1.19	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/2.31.0	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+	BLAST+/2.12.0 BLAST+/2.13.0 BLAST+/2.14.0 BLAST+/2.14.1	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.
BLAT	BLAT/3.7	BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
BLIS	BLIS/0.8.1 BLIS/0.9.0 BLIS/1.0	BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
BSBOLT	BSBolt/1.6.0	A fast and safe bisulfite sequencing analysis platform BiSuflite Bolt (BSBolt); a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of BWA and WGSIM for read alignment and read simulation respectively. BSBolt is released under the MIT license.
BUSCO	BUSCO/5.4.7	BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
BWA	BWA/0.7.17 BWA/0.7.18	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/2.5.2	BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
BAZEL	Bazel/3.7.2 Bazel/4.2.2 Bazel/5.1.1 Bazel/6.3.1 Bazel/7.4.1	Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
BEAUTIFULSOUP	BeautifulSoup/4.10.0 BeautifulSoup/4.11.1 BeautifulSoup/4.12.2	Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.
BIO-SEARCHIO-HMMER	Bio-SearchIO-hmmer/1.7.3	Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org.
BIOPERL	BioPerl/1.7.8	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/1.79 Biopython/1.81 Biopython/1.82 Biopython/1.83 Biopython/1.84	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/3.0.5 Bison/3.3.2 Bison/3.7.1 Bison/3.7.6 Bison/3.8.2	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/3.5.0-linux-x86_64-CUDA-11.7.0	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.
BLOSC	Blosc/1.21.5	Blosc, an extremely fast, multi-threaded, meta-compressor library
BLOSC2	Blosc2/2.4.3 Blosc2/2.13.2	Blosc, an extremely fast, multi-threaded, meta-compressor library
BOOST	Boost/1.76.0 Boost/1.77.0 Boost/1.79.0 Boost/1.81.0 Boost/1.82.0 Boost/1.83.0 Boost/1.85.0	Boost provides free peer-reviewed portable C++ source libraries.
BOOST.MPI	Boost.MPI/1.79.0	Boost provides free peer-reviewed portable C++ source libraries.
BOOST.PYTHON	Boost.Python/1.79.0 Boost.Python/1.81.0 Boost.Python/1.83.0	Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
BOWTIE	Bowtie/1.3.1	Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
BOWTIE2	Bowtie2/2.4.4 Bowtie2/2.4.5	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/1.0.9 Brotli/1.1.0	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.
BROTLI-PYTHON	Brotli-python/1.0.9	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.
BRUNSLI	Brunsli/0.1	Brunsli is a lossless JPEG repacking library.
CATCH	CATCH/1.5.2	CATCH is a Python package for designing probe sets to use for nucleic acid capture of diverse sequence.
CD-HIT	CD-HIT/4.8.1	CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
CDO	CDO/2.0.5	CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
CESM-DEPS	CESM-deps/2	CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
CFITSIO	CFITSIO/4.2.0 CFITSIO/4.3.0 CFITSIO/4.3.1 CFITSIO/4.4.1	CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
CGAL	CGAL/4.14.3 CGAL/5.5.2 CGAL/5.6 CGAL/5.6.1	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.
CGNS	CGNS/4.4.0	The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.
CLHEP	CLHEP/2.4.6.2	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.
CLIP	CLIP/20230220-CUDA-11.7.0	CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.
CMAKE	CMake/3.12.1 CMake/3.18.4 CMake/3.20.1 CMake/3.21.1 CMake/3.22.1 CMake/3.23.1 CMake/3.24.3 CMake/3.26.3 CMake/3.27.6 CMake/3.29.3	CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CP2K	CP2K/9.1-lib CP2K/9.1 CP2K/2022.1-lib CP2K/2022.1 CP2K/2023.1-CUDA-11.8.0 CP2K/2023.1-lib CP2K/2023.1-PLUMED-2.9.0 CP2K/2023.1	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/11.1.1 CUDA/11.3.1 CUDA/11.4.1 CUDA/11.7.0 CUDA/11.8.0 CUDA/12.0.0 CUDA/12.1.0 CUDA/12.1.1 CUDA/12.2.0 CUDA/12.2.2 CUDA/12.3.0 CUDA/12.3.2 CUDA/12.4.0 CUDA/12.4.1 CUDA/12.5.0 CUDA/12.6.0 CUDA/12.8.0	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.
CUDA-PYTHON	CUDA-Python/12.1.0-CUDA-12.1.1	Python bindings for CUDA
CUDA-SAMPLES	CUDA-Samples/12.1-CUDA-12.1.1	Samples for CUDA Developers which demonstrates features in CUDA Toolkit
CUDACORE	CUDAcore/11.1.1	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.
CUTLASS	CUTLASS/2.11.0-CUDA-11.7.0 CUTLASS/3.4.0-CUDA-12.1.1	CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these "moving parts" into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.
CUNIT	CUnit/2.1-3	Automated testing framework for C.
CAPNPROTO	CapnProto/0.10.2	Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.
CARTOPY	Cartopy/0.20.3 Cartopy/0.22.0	Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.
CATCH2	Catch2/2.13.9 Catch2/2.13.10 Catch2/3.4.0 Catch2/3.8.0	A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later
CEREAL	Cereal/1.3.0	cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
CHAMELEON	Chameleon/1.2.0	Chameleon is a framework written in C which provides routines to solve dense general systems of linear equations, symmetric positive definite systems of linear equations and linear least squares problems, using LU, Cholesky, QR and LQ factorizations.
CHECK	Check/0.15.2	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.
CHECKM	CheckM/1.2.2	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
CHECKM-DATABASE	CheckM-Database/2015_01_16	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. This is the corresponding database.
CHIMERAX	ChimeraX/1.3 ChimeraX/1.6.1 ChimeraX/1.7.1	UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
CLANG	Clang/13.0.1-CUDA-11.7.0 Clang/13.0.1 Clang/15.0.5 Clang/16.0.6-CUDA-12.1.1 Clang/16.0.6 Clang/17.0.6 Clang/18.1.8	C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
CLIMETLAB	CliMetLab/0.12.6	CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats. It is mostly intended to be used in Jupyter notebooks, and be interoperable with all popular data analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.
COLABFOLD	ColabFold/1.5.2-CUDA-11.7.0	Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine.
COORDGENLIBS	CoordgenLibs/3.0.1 CoordgenLibs/3.0.2	Schrodinger-developed 2D Coordinate Generation
CPPUNIT	CppUnit/1.15.1	CppUnit is the C++ port of the famous JUnit framework for unit testing.
CRYOSPARC	CryoSPARC/4.2.1 CryoSPARC/4.7.0 CryoSPARC/4.7.1	CryoSPARC combines powerful innovations in 3D reconstruction algorithms with specially designed software to provide a streamlined end-to-end single particle cryo-EM workflow.
CUPY	CuPy/11.4.0-CUDA-11.4.1	CuPy is an open-source array library accelerated with NVIDIA CUDA.
CUBEGUI	CubeGUI/4.8.2	Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.
CUBELIB	CubeLib/4.8.1 CubeLib/4.8.2	Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.
CUBEWRITER	CubeWriter/4.8.2	Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.
CYTHON	Cython/0.29.33 Cython/3.0.7 Cython/3.0.10	Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
DB	DB/18.1.40	Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DBCSR	DBCSR/2.5.0 DBCSR/2.6.0	DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations.
DB_FILE	DB_File/1.859	Perl5 access to Berkeley DB version 1.x.
DBUS	DBus/1.13.18 DBus/1.14.0 DBus/1.15.2 DBus/1.15.4 DBus/1.15.8	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/3.6.7	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.
DIAMOND	DIAMOND/2.0.15 DIAMOND/2.1.0	Accelerated BLAST compatible local sequence aligner
DATASPACES	DataSpaces/2.2.0	DataSpaces is a distributed framework built on a dynamic set of nodes of a HPC cluster, which implements a virtual shared-space abstraction that can be accessed concurrently by all applications in a coupled simulation workflow.
DATASETS/AISHELL	Datasets/AISHELL	AISHELL speech corpus dataset
DATASETS/CC3M	Datasets/CC3M	Conceptual Captions 3 Million (CC3M) dataset for vision-language models
DATASETS/COCO	Datasets/COCO	COCO 2017 image dataset for detection, segmentation, and captioning tasks
DATASETS/IMAGENET-PYTORCH	Datasets/ImageNet-PyTorch	ImageNet2012 image classification dataset
DATASETS/IMAGENET-TENSORFLOW	Datasets/ImageNet-TensorFlow	ImageNet2012 image classification dataset
DATASETS/JODIE	Datasets/JODIE	ImageNet2012 image classification dataset
DATASETS/QM9	Datasets/QM9	Quantum Machine 9 (QM9) dataset for quantum chemistry and machine learning, containing detailed quantum chemical calculations for a large set of small organic molecules
DELTALAKE	DeltaLake/0.15.1	Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease.
DENDROPY	DendroPy/4.5.2 DendroPy/5.0.1	A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
DESMOND	Desmond/2023-4	Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on NVIDIA GPUs.
DORADO	Dorado/0.5.2-CUDA-11.8.0	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
DOXYGEN	Doxygen/1.8.20 Doxygen/1.9.1 Doxygen/1.9.4 Doxygen/1.9.5 Doxygen/1.9.7 Doxygen/1.9.8 Doxygen/1.11.0	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.
DRACO	Draco/1.5.6	Draco is a library for compressing and decompressing 3D geometric meshes and point clouds. It is intended to improve the storage and transmission of 3D graphics.
ELPA	ELPA/2021.05.001 ELPA/2021.11.001 ELPA/2022.05.001-CUDA-11.8.0 ELPA/2022.05.001 ELPA/2023.05.001 ELPA/2023.11.001 ELPA/2024.05.001	Eigenvalue SoLvers for Petaflop-Applications .
ELSI	ELSI/2.7.1-PEXSI	ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
ESMF	ESMF/8.0.1 ESMF/8.1.1 ESMF/8.3.0 ESMF/8.6.1	The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.
EASYBUILD	EasyBuild/4.7.1 EasyBuild/4.8.0 EasyBuild/4.8.2 EasyBuild/4.9.0 EasyBuild/4.9.2 EasyBuild/4.9.4 EasyBuild/5.0.0 EasyBuild/5.1.1	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-ACES	EasyBuild-aces/0	EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on aces.hprc.tamu.edu
EASYBUILD-ACES-SCRATCH	EasyBuild-aces-SCRATCH/0	User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb
EASYBUILD-ACES-MYEB	EasyBuild-aces-myeb/0	User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb
EASYBUILD-ACES-TMP	EasyBuild-aces-tmp/0	EasyBuild environment variables for building in /tmp and installing in /sw/eb on aces.hprc.tamu.edu
EIGEN	Eigen/3.3.8 Eigen/3.3.9 Eigen/3.4.0	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
EMACS	Emacs/27.2 Emacs/28.2	GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
FASTA	FASTA/36.3.8i	The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
FFTW	FFTW/3.3.8 FFTW/3.3.9 FFTW/3.3.10	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.MPI/3.3.10	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	FFmpeg/4.3.2 FFmpeg/4.4.2 FFmpeg/5.1.2 FFmpeg/6.0	A complete, cross-platform solution to record, convert and stream audio and video.
FLAC	FLAC/1.3.3 FLAC/1.3.4 FLAC/1.4.2 FLAC/1.4.3	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/2.2.00	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/1.3.8	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.
FASTANI	FastANI/1.33	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
FASTQC	FastQC/0.11.9-Java-11	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.
FASTTREE	FastTree/2.1.11	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
FIJI	Fiji/2.15.1	Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
FIONA	Fiona/1.8.21 Fiona/1.9.2 Fiona/1.9.5	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/138.0.3	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/1.1.2 Flask/2.2.2	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/3.0.4 FlexiBLAS/3.2.0 FlexiBLAS/3.2.1 FlexiBLAS/3.3.1 FlexiBLAS/3.4.4	FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
FREEXL	FreeXL/1.0.6	FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
FRIBIDI	FriBidi/1.0.10 FriBidi/1.0.12 FriBidi/1.0.13	The Free Implementation of the Unicode Bidirectional Algorithm.
GATB-CORE	GATB-Core/1.4.2	GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly efficient algorithms to analyse NGS data sets
GATK	GATK/4.3.0.0-Java-11 GATK/4.4.0.0-Java-17	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.
GCC	GCC/8.3.0 GCC/10.2.0 GCC/10.3.0 GCC/11.2.0 GCC/11.3.0 GCC/12.2.0 GCC/12.3.0 GCC/13.1.0 GCC/13.2.0 GCC/13.3.0 GCC/14.2.0	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	GCCcore/8.2.0 GCCcore/8.3.0 GCCcore/10.2.0 GCCcore/10.3.0 GCCcore/11.2.0 GCCcore/11.3.0 GCCcore/12.2.0 GCCcore/12.3.0 GCCcore/13.1.0 GCCcore/13.2.0 GCCcore/13.3.0 GCCcore/14.2.0	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,...).
GCONF	GConf/3.2.6	GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.
GDAL	GDAL/3.2.1 GDAL/3.3.0 GDAL/3.3.2 GDAL/3.5.0 GDAL/3.6.2 GDAL/3.7.1 GDAL/3.9.0	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.
GDB	GDB/13.2	The GNU Project Debugger
GDRCOPY	GDRCopy/2.1-CUDA-11.1.1 GDRCopy/2.2 GDRCopy/2.3 GDRCopy/2.3.1 GDRCopy/2.4 GDRCopy/2.4.1	A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
GEOS	GEOS/3.9.1 GEOS/3.10.3 GEOS/3.11.1 GEOS/3.12.0 GEOS/3.12.1	GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GKLIB	GKlib/5.1.1 GKlib/20231211 GKlib/20240119 GKlib/20240321 GKlib/20240329	A library of various helper routines and frameworks used by Karypis Lab software such as METIS.
GL2PS	GL2PS/1.4.2	GL2PS: an OpenGL to PostScript printing library
GLFW	GLFW/3.3.8	GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop
GLM	GLM/0.9.9.8	OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
GLPK	GLPK/5.0	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/2.66.1 GLib/2.68.2 GLib/2.69.1 GLib/2.72.1 GLib/2.75.0 GLib/2.77.1 GLib/2.78.1 GLib/2.81.0	GLib is one of the base libraries of the GTK+ project
GMAP-GSNAP	GMAP-GSNAP/2021-12-17 GMAP-GSNAP/2023-02-17 GMAP-GSNAP/2023-04-20	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
GMP	GMP/6.2.0 GMP/6.2.1 GMP/6.3.0	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
GOBJECT-INTROSPECTION	GObject-Introspection/1.68.0 GObject-Introspection/1.72.0 GObject-Introspection/1.74.0 GObject-Introspection/1.76.1 GObject-Introspection/1.78.1 GObject-Introspection/1.80.1	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.
GPAW	GPAW/24.1.0	GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.
GPAW-SETUPS	GPAW-setups/0.9.20000	PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.
GPFLOW	GPflow/2.9.0-CUDA-11.7.0-TensorFlow-2.11.0 gpflow/2.9.0-CUDA-11.7.0-TensorFlow-2.11.0 gpflow/2.9.0-CUDA-11.7.0	GPflow is a package for building Gaussian process models in python, using TensorFlow.
GPYTORCH	GPyTorch/1.10-CUDA-11.7.0	GPyTorch is a Gaussian process library implemented using PyTorch.
GRASS	GRASS/8.2.0 GRASS/8.3.1	The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
GROMACS	GROMACS/2021.5-CUDA-11.4.1-PLUMED-2.8.0 GROMACS/2023.1-CUDA-11.7.0 GROMACS/2023.1-CUDA-12.2.0 GROMACS/2023.3-CUDA-11.8.0 GROMACS/2023.3-CUDA-12.1.1-PLUMED-2.9.0 GROMACS/2023.3 GROMACS/2024.1	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 GPU enabled 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	GSL/2.6 GSL/2.7	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	GST-plugins-bad/1.20.2 GST-plugins-bad/1.22.5	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	GST-plugins-base/1.18.5 GST-plugins-base/1.20.2 GST-plugins-base/1.22.1 GST-plugins-base/1.22.5	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/1.18.5 GStreamer/1.20.2 GStreamer/1.22.1 GStreamer/1.22.5	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.
GTK2	GTK2/2.24.33	The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
GTK3	GTK3/3.24.31 GTK3/3.24.35 GTK3/3.24.37 GTK3/3.24.39	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	GTK4/4.7.0 GTK4/4.13.1	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/0.7.6	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	Gdk-Pixbuf/2.42.6 Gdk-Pixbuf/2.42.8 Gdk-Pixbuf/2.42.10	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.
GEANT4	Geant4/11.1.2	Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
GEANT4-DATA	Geant4-data/11.1	Datasets for Geant4.
GENERATIVEMODELS	GenerativeModels/0.2.1-CUDA-11.7.0
GHOSTSCRIPT	Ghostscript/9.54.0 Ghostscript/9.56.1 Ghostscript/10.0.0 Ghostscript/10.01.2 Ghostscript/10.02.1	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/3.1.27 GitPython/3.1.40	GitPython is a python library used to interact with Git repositories
GLOBALARRAYS	GlobalArrays/5.8.2	Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
GLOBUS-CLI	Globus-CLI/3.6.0	A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
GNUTLS	GnuTLS/3.7.3 GnuTLS/3.7.8	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/1.18.3 Go/1.22.1	Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
GRAPHBLAS	GraphBLAS/8.2.1	SuiteSparse:GraphBLAS is a complete implementation of the GraphBLAS standard, which defines a set of sparse matrix operations on an extended algebra of semirings using an almost unlimited variety of operators and types. When applied to sparse adjacency matrices, these algebraic operations are equivalent to computations on graphs.
GRAPHENE	Graphene/1.10.8	Graphene is a thin layer of types for graphic libraries
GRAPHICSMAGICK	GraphicsMagick/1.3.36	GraphicsMagick is the swiss army knife of image processing.
GRAPHVIZ	Graphviz/5.0.0	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.
GREENLET	Greenlet/2.0.2 Greenlet/3.0.3	The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.
GUILE	Guile/3.0.7 Guile/3.0.9	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/0.29.1	Gymnasium is an open source Python library for developing and comparing reinforcement learning algorithms by providing a standard API to communicate between learning algorithms and environments, as well as a standard set of environments compliant with that API.
HDF	HDF/4.2.15 HDF/4.2.16-2	HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
HDF-EOS	HDF-EOS/2.20	HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.
HDF-EOS5	HDF-EOS5/1.16	HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.
HDF5	HDF5/1.10.7 HDF5/1.12.1 HDF5/1.12.2 HDF5/1.14.0 HDF5/1.14.2 HDF5/1.14.3 HDF5/1.14.5	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	HH-suite/3.3.0	The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
HIPIFY	HIPIFY/6.2.0	HIPIFY is a set of tools that you can use to automatically translate CUDA source code into portable HIP C++.
HISAT2	HISAT2/2.2.1	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/3.3.2 HMMER/3.4	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.
HPC-X	HPC-X/2.14	NVIDIA HPC-X is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages.
HPL	HPL/2.3	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.
HPRC_UTILS	HPRC_utils/1.0	HPRC_utils is a collection of useful utilities to accompany software modules on the TAMU HPRC clusters.
HTSEQ	HTSeq/2.0.2	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
HTSLIB	HTSlib/1.15.1 HTSlib/1.17 HTSlib/1.18 HTSlib/1.19.1	A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
HUMANN	HUMAnN/3.9 humann/3.6	HUMAnN is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.
HARFBUZZ	HarfBuzz/2.8.1 HarfBuzz/2.8.2 HarfBuzz/4.2.1 HarfBuzz/5.3.1 HarfBuzz/8.2.2	HarfBuzz is an OpenType text shaping engine.
HEFFTE	HeFFTe/2.4.0	Highly Efficient FFT for Exascale (HeFFTe) library
HIGHWAY	Highway/1.0.3 Highway/1.0.4 Highway/1.0.7	Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'.
HOROVOD	Horovod/0.22.1-CUDA-11.3.1-TensorFlow-2.6.0 Horovod/0.28.1-CUDA-11.7.0-TensorFlow-2.11.0 Horovod/0.28.1-CUDA-11.7.0-PyTorch-1.12.1	Horovod is a distributed training framework for TensorFlow.
HYPEROPT	Hyperopt/0.2.7	hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.
HYPRE	Hypre/2.21.0 Hypre/2.25.0 Hypre/2.27.0 Hypre/2.29.0 Hypre/2.31.0	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.
ICON	ICON/2024.01 ICON/2024.07	ICON is a flexible, scalable, high-performance modelling framework for weather, climate and environmental prediction that provides actionable information for society and advances our understanding of the Earth's climate system.
ICU	ICU/67.1 ICU/69.1 ICU/71.1 ICU/72.1 ICU/73.2 ICU/74.1 ICU/75.1	ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
IJULIA	IJulia/1.24.2-Julia-1.10.3	Julia kernel for Jupyter
IML	IML/1.0.5	IML is a free library of C source code which implements algorithms for computing exact solutions to dense systems of linear equations over the integers.
IPYTHON	IPython/7.26.0 IPython/8.5.0 IPython/8.14.0 IPython/8.17.2	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.
IRKERNEL	IRkernel/1.3.2-R-4.3.2	The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.
ISA-L	ISA-L/2.30.0	Intelligent Storage Acceleration Library
ISL	ISL/0.26	isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
ITK	ITK/5.2.1	Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.
IGPROF	IgProf/5.9.18	IgProf is a simple nice tool for measuring and analysing application memory and performance characteristics.
IMAGEJ	ImageJ/1.53t-Java-11	Image Processing and Analysis in Java
IMAGEMAGICK	ImageMagick/7.0.11-14 ImageMagick/7.1.0-4 ImageMagick/7.1.0-37 ImageMagick/7.1.0-53 ImageMagick/7.1.1-15 ImageMagick/7.1.1-34	ImageMagick is a software suite to create, edit, compose, or convert bitmap images
IMATH	Imath/3.1.5 Imath/3.1.6 Imath/3.1.7 Imath/3.1.9	Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
INFERNAL	Infernal/1.1.4	Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.
INTELCLUSTERCHECKER	IntelClusterChecker/2021.5.0	Intel Cluster Checker verifies the configuration and performance of Linux OS-based clusters. Anomalies and performance differences can be identified and practical resolutions provided.
JANSSON	Jansson/2.13.1	Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite
JASPER	JasPer/1.900.1 JasPer/2.0.24 JasPer/2.0.28 JasPer/2.0.33 JasPer/4.0.0	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/1.8.0_371 Java/11.0.16 Java/11.0.18 Java/17.0.6 Java/21.0.2	Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
JELLYFISH	Jellyfish/2.3.0	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
JMOL	Jmol/16.1.59-Java-1.8.0_371 Jmol/16.1.59	Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules
JSONCPP	JsonCpp/1.9.4 JsonCpp/1.9.5	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	Judy/1.0.5	A C library that implements a dynamic array.
JULIA	Julia/1.8.5-linux-x86_64 Julia/1.9.3-linux-x86_64 Julia/1.10.0-musl-x86_64 Julia/1.10.2-linux-x86_64 Julia/1.10.3-linux-x86_64 Julia/1.11.4-linux-x86_64	Julia is a high-level, high-performance dynamic programming language for numerical computing
JULIA_TAMU	Julia_TAMU/1.10.2	Julia is a high-level, high-performance dynamic programming language for numerical computing.. - Homepage: https://julialang.org
JUPYTER-BUNDLE	Jupyter-bundle/20230823	This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub.
JUPYTERHUB	JupyterHub/4.0.2	JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
JUPYTERLAB	JupyterLab/3.5.0 JupyterLab/4.0.3 JupyterLab/4.0.5 JupyterLab/4.2.0	JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.
JUPYTERNOTEBOOK	JupyterNotebook/7.0.2 JupyterNotebook/7.0.3	The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.
KMCP	KMCP/0.9.1	KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
KAHIP	KaHIP/3.14 KaHIP/3.16	The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.
KALEIDO	Kaleido/0.2.1	Fast static image export for web-based visualization libraries with zero dependencies
KALIGN	Kalign/3.3.1 Kalign/3.3.5 Kalign/3.4.0	Kalign is a fast multiple sequence alignment program for biological sequences.
KERAS	Keras/2.4.3-TensorFlow-2.5.0	Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
KRAKEN2	Kraken2/2.1.2	Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
LAME	LAME/3.100	LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LAMMPS	LAMMPS/patch_19Nov2024-intel-kokkos LAMMPS/2Aug2023_update2-CUDA-11.8.0-sm90 LAMMPS/2Aug2023_update2-intel-2023.07 LAMMPS/2Aug2023_update2-kokkos-CUDA-12.1.1 LAMMPS/3Aug2023-intel-2023.07 LAMMPS/23Jun2022_update4-kokkos-CUDA-11.4.1 LAMMPS/23Jun2022-kokkos-CUDA-11.4.1 LAMMPS/23Jun2022-kokkos-extra-pair-styles LAMMPS/23Jun2022-kokkos	LAMMPS is a classical molecular dynamics code with a focus on materials modeling.
LASSO-PYTHON	LASSO-Python/2.0.0	This python library is designed for general purpose usage in the field of Computer Aided Engineering (CAE). It's name originates from the original initiator and donator of the project Lasso GmbH. The library is now maintained by an open-source community.
LERC	LERC/4.0.0	LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).
LLVM	LLVM/10.0.1 LLVM/11.1.0 LLVM/12.0.1 LLVM/13.0.1 LLVM/14.0.3 LLVM/14.0.6-llvmlite LLVM/14.0.6 LLVM/15.0.5 LLVM/16.0.6 LLVM/18.1.8	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/0.9.24 LMDB/0.9.28 LMDB/0.9.29 LMDB/0.9.31	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.
LZO	LZO/2.10	Portable lossless data compression library
LEPTONICA	Leptonica/1.83.0 Leptonica/1.84.1	Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
LEVELDB	LevelDB/1.22	LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
LIBSOUP	LibSoup/3.0.7	libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.
LIBSTDCOMPAT	LibStdCompat/20250218-76b61ae	LibStdCompat is a set of compatibility headers for C++ 14, 17, and 20 for C++11.
LIBTIFF	LibTIFF/4.1.0 LibTIFF/4.2.0 LibTIFF/4.3.0 LibTIFF/4.4.0 LibTIFF/4.5.0 LibTIFF/4.6.0	tiff: Library and tools for reading and writing TIFF data files
LIBINT	Libint/2.7.2-lmax-6-cp2k	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	LittleCMS/2.12 LittleCMS/2.13.1 LittleCMS/2.14 LittleCMS/2.15	Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
LUA	Lua/5.4.4 Lua/5.4.6	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	M4/1.4.18 M4/1.4.19	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/7.505-with-extensions MAFFT/7.520-with-extensions	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.
MATIO	MATIO/1.5.23	matio is an C library for reading and writing Matlab MAT files.
MDI	MDI/1.4.26	The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods.
MDTRAJ	MDTraj/1.9.9	Read, write and analyze MD trajectories with only a few lines of Python code.
METIS	METIS/5.1.0	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.
MFEM	MFEM/4.7-CUDA-12.6.0 MFEM/70941b4	MFEM is a modular parallel C++ library for finite element methods. MFEM can be viewed as a finite element toolbox that provides the building blocks for developing finite element algorithms in a manner similar to that of MATLAB for linear algebra methods.
MGARD	MGARD/1.5.2	MGARD (MultiGrid Adaptive Reduction of Data) is a technique for multilevel lossy compression and refactoring of scientific data based on the theory of multigrid methods.
MMSEQS2	MMseqs2/14-7e284	MMseqs2: ultra fast and sensitive search and clustering suite
MOAB	MOAB/20250227-9f72cdd	The Mesh-Oriented datABase (MOAB) is a component for representing and evaluating mesh data. MOAB can store and represent structured and unstructured meshes consisting of elements in the finite element zoo, including polygons and polyhedra.
MONAI	MONAI/1.0.1	MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem.
MPC	MPC/1.2.1 MPC/1.3.1	Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
MPFR	MPFR/4.1.0 MPFR/4.2.0 MPFR/4.2.1	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MPICH	MPICH/4.2.1	MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).
MUMPS	MUMPS/5.4.0-metis MUMPS/5.5.1-metis MUMPS/5.6.1-metis	A parallel sparse direct solver
MUMMER	MUMmer/4.0.0rc1	MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
MVAPICH-PLUS	MVAPICH-Plus/4.0pre-GCC-11.1.0-CUDA-12.2-OFED-5.0 MVAPICH-Plus/4.0-GCC-13.2.0-CUDA-12.4-UCX-SLURM	The new MVAPICH-Plus series is an advanced version of the MVAPICH MPI library. It is targeted to support unified MVAPICH2-GDR and MVAPICH2-X features. It is also targeted to provide optimized support for modern platforms (CPU, GPU, and interconnects) for HPC, Deep Learning, Machine Learning, Big Data and Data Science applications. MVAPICH-Plus 4.0a with support for unified MVAPICH2-GDR and MVAPICH2-X features is available. Features of this release include: support for various HPC fabrics (InfiniBand, Slingshot, Omni-Path, OPX, RoCE, and Ethernet/iWARP), various CPUs (x86, ARM, and OpenPOWER), and various GPUs (NVIDIA, AMD, and Intel), CMA support for intra-node pt2pt communication, CUDA-aware MPI (pt2pt and collective) support, IPC-based support for collectives on Intel GPU, on-the-fly compression support for collectives for NVIDIA GPUs.
MVAPICH2-GDR	MVAPICH2-GDR/2.3.7-GCC-11.2.0-CUDA-11.4.1	MVAPICH2-GDR 2.3.7 binary release is based on MVAPICH2 2.3.7 and incorporates designs that take advantage of GPUDirect RDMA technology enabling direct P2P communication between NVIDIA GPUs and Mellanox InfiniBand adapters.
MAGICS	Magics/4.13.0	Magics is ECMWF's meteorological plotting software and can be either accessed directly through its Python or Fortran interfaces or by using Metview.
MAKO	Mako/1.1.3 Mako/1.1.4 Mako/1.2.0 Mako/1.2.4 Mako/1.3.5	A super-fast templating language that borrows the best ideas from the existing templating languages
MAMBA	Mamba/23.1.0-4	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/10.9.3	MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
MASH	Mash/2.3	Fast genome and metagenome distance estimation using MinHash
MATLAB	Matlab/R2023a Matlab/R2023b Matlab/R2024a Matlab/R2024b	A numerical computing environment and fourth-generation programming language. - Homepage: http://www.mathworks.com/products/matlab/
MAVEN	Maven/3.9.6	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.
MEMORYVIEWER	MemoryViewer/1.0	MemoryViewer software gives system administrators comprehensive insight into the physical memory topology as well as the application memory utilization.
MERCURIAL	Mercurial/6.4.5	Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
MERCURY	Mercury/2.4.0 mercury/2.4.0	Mercury is a Remote Procedure Call (RPC) framework specifically designed for use in High-Performance Computing (HPC) systems with high-performance fabrics.
MESA	Mesa/21.1.1 Mesa/21.1.7 Mesa/22.0.3 Mesa/22.2.4-LLVM-14.0.6 Mesa/22.2.4 Mesa/23.1.4 Mesa/23.1.9 Mesa/24.1.3	Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
MESON	Meson/0.55.3 Meson/0.58.0 Meson/0.58.2 Meson/0.62.1 Meson/0.64.0 Meson/1.1.1 Meson/1.2.3 Meson/1.4.0	Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
METAEUK	MetaEuk/6	MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
METAPHLAN	MetaPhlAn/3.0.14	MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
MINPATH	MinPath/1.6	MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
MINICONDA3	Miniconda3/4.12.0 Miniconda3/22.11.1-1 Miniconda3/23.3.1-0 Miniconda3/23.5.2-0 Miniconda3/23.9.0-0 Miniconda3/23.10.0-1	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.
MINIFORGE3	Miniforge3/24.11.3-0 Miniforge3/25.3.0-3	Miniforge is a free minimal installer for conda and Mamba specific to conda-forge.
MUJOCO	MuJoCo/3.1.4	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	MultiQC/1.14	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/2.14-mpi	NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NAMD-MULTICORE-CUDA	NAMD-multicore-CUDA/3.0b3	A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NAMD-NETLRTS-SMP-CUDA	NAMD-netlrts-smp-CUDA/3.0b3	A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NAMD-VERBS-SMP-CUDA	NAMD-verbs-smp-CUDA/3.0b3	A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NASM	NASM/2.15.05 NASM/2.16.01 NASM/2.16.03	NASM: General-purpose x86 assembler
NCCL	NCCL/2.8.3-CUDA-11.1.1 NCCL/2.10.3-CUDA-11.3.1 NCCL/2.10.3-CUDA-11.4.1 NCCL/2.12.12-CUDA-11.7.0 NCCL/2.12.12-CUDA-11.8.0 NCCL/2.16.2-CUDA-12.0.0 NCCL/2.18.3-CUDA-12.1.1 NCCL/2.20.5-CUDA-12.2.0 NCCL/2.20.5-CUDA-12.4.0 NCCL/2.20.5-CUDA-12.4.1 NCCL/2.20.5-CUDA-12.5.0 NCCL/2.22.3-CUDA-12.6.0	The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
NCL	NCL/6.6.2	NCL is an interpreted language designed specifically for scientific data analysis and visualization.
NCO	NCO/5.0.1	The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.
NEDIT	NEdit/5.7.7	A fast, compact Motif/X11 plain text editor, for most popular Unix systems.
NLTK	NLTK/3.8.1	NLTK is a leading platform for building Python programs to work with human language data.
NLOPT	NLopt/2.7.0 NLopt/2.7.1	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	NSPR/4.32 NSPR/4.34 NSPR/4.35	Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSS	NSS/3.69 NSS/3.79 NSS/3.85 NSS/3.89.1 NSS/3.94	Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
NTL	NTL/11.5.1	NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.
NTPOLY	NTPoly/2.7.0	is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.
NVHPC	NVHPC/21.9 NVHPC/22.9-CUDA-11.7.0 NVHPC/22.11-CUDA-11.7.0 NVHPC/22.11-CUDA-11.8.0 NVHPC/23.1-CUDA-12.0.0 NVHPC/23.7-CUDA-12.1.1 NVHPC/23.7-CUDA-12.2.0 NVHPC/24.1-CUDA-12.3.0 NVHPC/24.9-CUDA-12.6.0 NVHPC/25.1-CUDA-12.6.0	C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
NVSHMEM	NVSHMEM/2.8.0-CUDA-11.7.0 NVSHMEM/2.8.0-CUDA-12.1.1 NVSHMEM/2.8.0-CUDA-12.5.0 NVSHMEM/2.11.0-CUDA-12.5.0 NVSHMEM/3.0.6-CUDA-12.5.0	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.
NEXTFLOW	Nextflow/23.10.0	Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
NIBABEL	NiBabel/4.0.2	NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.
NINJA	Ninja/1.10.1 Ninja/1.10.2 Ninja/1.11.1 Ninja/1.12.1	Ninja is a small build system with a focus on speed.
OCAML	OCaml/5.1.1	OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.
ONNX	ONNX/1.15.0	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/1.16.3	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.
OPARI2	OPARI2/2.0.7 OPARI2/2.0.8	OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
ORCA	ORCA/6.0.1-avx2	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/7.1-1	OSU Micro-Benchmarks
OTF2	OTF2/3.0.3 otf2/3.0.3	The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools.
OPENBLAS	OpenBLAS/0.3.12 OpenBLAS/0.3.15 OpenBLAS/0.3.18 OpenBLAS/0.3.20 OpenBLAS/0.3.21 OpenBLAS/0.3.23 OpenBLAS/0.3.24 OpenBLAS/0.3.27	OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OPENBABEL	OpenBabel/3.1.1	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/4.6.0-contrib OpenCV/4.6.0-CUDA-11.7.0-contrib OpenCV/4.8.1-contrib	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.
OPENEXR	OpenEXR/3.1.5 OpenEXR/3.1.7 OpenEXR/3.2.0	OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications
OPENFOAM	OpenFOAM/v2206 OpenFOAM/v2306 OpenFOAM/v2312 OpenFOAM/v2406 OpenFOAM/10 OpenFOAM/11 OpenFOAM/12	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	OpenFold/1.0.1-CUDA-11.3.1 OpenFold/2.1.0-CUDA-12.1.1	A faithful PyTorch reproduction of DeepMind's AlphaFold 2
OPENIMAGEIO	OpenImageIO/2.3.17.0	OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications.
OPENJPEG	OpenJPEG/2.4.0 OpenJPEG/2.5.0	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/7.5.1-CUDA-11.3.1-DeepMind-patch OpenMM/7.5.1-DeepMind-patch OpenMM/7.7.0 OpenMM/8.0.0-CUDA-11.7.0 OpenMM/8.0.0-CUDA-11.8.0 OpenMM/8.0.0-CUDA-12.1.1 OpenMM/8.0.0 OpenMM/8.2.0	OpenMM is a toolkit for molecular simulation.
OPENMPI	OpenMPI/nostub-4.1.4 OpenMPI/4.0.5 OpenMPI/4.1.1 OpenMPI/4.1.4-CUDA-11.8.0 OpenMPI/4.1.4-PyFR OpenMPI/4.1.4 OpenMPI/4.1.5 OpenMPI/4.1.6-CUDA-12.5.0-PyFR OpenMPI/4.1.6-CUDA-12.5.0 OpenMPI/4.1.6 OpenMPI/5.0.3-CUDA-12.5.0-PyFR OpenMPI/5.0.3-CUDA-12.5.0 OpenMPI/5.0.3	The Open MPI Project is an open source MPI-3 implementation.
OPENPGM	OpenPGM/5.2.122	OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
OPENSSL	OpenSSL/1.1 OpenSSL/1.1.1q OpenSSL/3 OpenSSL/3.1.5	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.
OPENSCENEGRAPH	OpenSceneGraph/3.6.5	The OpenSceneGraph is an open source high performance 3D graphics toolkit, used by application developers in fields such as visual simulation, games, virtual reality, scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating systems. The OpenSceneGraph is now well established as the world leading scene graph technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual reality industries.
OPENSUBDIV	OpenSubdiv/3.6.0	OpenSubdiv is a set of open source libraries that implement high performance subdivision surface (subdiv) evaluation on massively parallel CPU and GPU architectures.
OPTIX	OptiX/7.2.0	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/3.1.0	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.
PAPI	PAPI/7.0.0 PAPI/7.0.1 PAPI/7.1.0	PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
PASA	PASA/2.5.3	PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
PCRE	PCRE/8.44 PCRE/8.45	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2	PCRE2/10.36 PCRE2/10.37 PCRE2/10.40 PCRE2/10.42 PCRE2/10.43	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PDAL	PDAL/2.4.3 PDAL/2.6.0	PDAL is a C++ library for translating and manipulating point cloud data.
PDT	PDT/3.25.1 PDT/3.25.2	Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
PETSC	PETSc/3.15.1 PETSc/3.17.4 PETSc/3.19.2 PETSc/3.19.2-64bit PETSc/3.20.3 PETSc/20231020-CUDA-11.8.0 PETSc/20231023-CUDA-11.8.0 PETSc/20231110-CUDA-11.8.0	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.
PFFT	PFFT/20181230	PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. The library is written in C and MPI. A Fortran interface is also available. Support for hybrid parallelization based on OpenMP and MPI is under development.
PHYLIP	PHYLIP/3.697	PHYLIP is a free package of programs for inferring phylogenies.
PLINK	PLINK/2.00a3.7	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
PLUMED	PLUMED/2.7.2 PLUMED/2.7.3 PLUMED/2.8.0 PLUMED/2.8.1 PLUMED/2.9.0 PLUMED/2.9.2 PLUMED/2.9.3	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	PMIx/3.1.5 PMIx/3.2.3 PMIx/4.1.0 PMIx/4.1.2 PMIx/4.2.2 PMIx/4.2.4 PMIx/4.2.5 PMIx/4.2.6 PMIx/5.0.1 PMIx/5.0.2	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	POV-Ray/3.7.0.10	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.
PRANK	PRANK/170427	PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.
PROJ	PROJ/7.2.1 PROJ/8.0.1 PROJ/8.1.0 PROJ/9.0.0 PROJ/9.1.1 PROJ/9.2.0 PROJ/9.3.1	Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
PRRTE	PRRTE/3.0.2 PRRTE/3.0.5	The PMIx Reference Runtime Environment is a reference run-time environment that utilizes the PMIx API. It mainly provides run-time environment infrastructure for environments that do not natively have them. In practical terms, this typically means providing infrastructure for non-scheduled environments that have no concept of distributed scheduling, file staging, remote stdout/stderr redirection, and only have ssh to execute commands on remote nodes.
PYTHIA	PYTHIA/8.309	PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a general purpose Monte Carlo event generator.
PADICOTM	PadicoTM/20220531	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
PANDOC	Pandoc/3.1.2	If you need to convert files from one markup format into another, pandoc is your swiss-army knife
PANGO	Pango/1.48.5 Pango/1.48.8 Pango/1.50.7 Pango/1.50.12 Pango/1.50.14 Pango/1.51.0	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/4.0.3	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.
PARAFOLD	ParaFold/2.0-CUDA-11.8.0	This project is a modified version of DeepMind's AlphaFold2 to achieve high-throughput protein structure prediction.
PARAVIEW	ParaView/5.11.1-MPI-Linux64 ParaView/5.11.1 ParaView/5.11.2 ParaView/5.12.0-MPI-Linux64	ParaView is the world’s leading open source post-processing visualization engine.
PARABRICKS	Parabricks/4.1.1	Clara Parabricks is a GPU-accelerated software suite for performing secondary analysis of next generation sequencing DNA and RNA data.
PARSL	Parsl/2023.7.17	Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python's parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available.
PERL	Perl/5.32.0-minimal Perl/5.32.0 Perl/5.32.1-minimal Perl/5.32.1 Perl/5.34.0-minimal Perl/5.34.0 Perl/5.34.1-minimal Perl/5.34.1 Perl/5.36.0-minimal Perl/5.36.0 Perl/5.36.1 Perl/5.38.0 Perl/5.38.2	Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies.
PERL-BUNDLE-CPAN	Perl-bundle-CPAN/5.36.1 Perl-bundle-CPAN/5.38.0 Perl-bundle-CPAN/5.38.2	A set of common packages from CPAN
PERL-BUNDLE1-CPAN	Perl-bundle1-CPAN/5.36.1	A set of common packages from CPAN
PERL-BUNDLE2-CPAN	Perl-bundle2-CPAN/5.36.1	A set of common packages from CPAN
PILLOW	Pillow/8.0.1 Pillow/8.2.0 Pillow/8.3.2 Pillow/9.1.1 Pillow/9.4.0 Pillow/10.0.0 Pillow/10.2.0	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-SIMD/8.2.0 Pillow-SIMD/9.2.0 Pillow-SIMD/9.5.0	Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
PNETCDF	PnetCDF/1.12.3 PnetCDF/1.13.0	Parallel netCDF: A Parallel I/O Library for NetCDF File Access
PORTMIDI	PortMidi/2.0.4	PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA).
POSTGRESQL	PostgreSQL/13.4 PostgreSQL/15.2 PostgreSQL/16.1	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.
PTEX	Ptex/2.4.2	Ptex is a texture mapping system developed by Walt Disney Animation Studios for production-quality rendering.
PUK	Puk/20220531	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
PUKABI	PukABI/20220531	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
PYBIOLIB	PyBioLib/1.1.988	PyBioLib is a Python package for running BioLib applications from Python scripts and the command line. BioLib is a library of biological data science applications. Applications on BioLib range from small bioinformatics utilities to state-of-the-art machine learning algorithms for predicting characteristics of biological molecules.
PYCUDA	PyCUDA/2022.2.2-CUDA-11.8.0	PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.
PYCAIRO	PyCairo/1.21.0 PyCairo/1.25.0	Python bindings for the cairo library
PYFR	PyFR/1.15.0-Python-3.11.5-CUDA-11.8.0 PyFR/2.0.0	PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.
PYGOBJECT	PyGObject/3.42.1 PyGObject/3.46.0	PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.
PYOPENGL	PyOpenGL/3.1.6 PyOpenGL/3.1.7	PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.
PYQT5	PyQt5/5.15.4	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.
PYROSETTA	PyRosetta/4.release-387	PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
PYTENSOR	PyTensor/2.17.1	Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs
PYTORCH	PyTorch/1.10.0-CUDA-11.3.1 PyTorch/1.12.0-CUDA-11.7.0 PyTorch/1.12.0 PyTorch/1.12.1-CUDA-11.3.1 PyTorch/1.12.1-CUDA-11.7.0 PyTorch/1.13.1-CUDA-11.7.0 PyTorch/1.13.1 PyTorch/2.1.2-CUDA-12.1.1 PyTorch/2.1.2 PyTorch/2.7.0-CUDA-12.6.0	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/2.1.0-PyTorch-1.12.0-CUDA-11.7.0	PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.
PYTORCH-LIGHTNING	PyTorch-Lightning/1.5.9-CUDA-11.3.1 PyTorch-Lightning/1.7.7-CUDA-11.7.0 PyTorch-Lightning/1.8.4-CUDA-11.7.0 PyTorch-Lightning/1.8.4 PyTorch-Lightning/2.2.1-CUDA-12.1.1	PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.
PYTORCH-BUNDLE	PyTorch-bundle/2.1.2-CUDA-12.1.1	PyTorch with compatible versions of official Torch extensions.
PYYAML	PyYAML/5.3.1 PyYAML/5.4.1 PyYAML/6.0 PyYAML/6.0.1	PyYAML is a YAML parser and emitter for the Python programming language.
PYZMQ	PyZMQ/24.0.1 PyZMQ/25.1.1 PyZMQ/25.1.2	Python bindings for ZeroMQ
PYCURL	PycURL/7.45.2	PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.
PYSAM	Pysam/0.18.0 Pysam/0.19.1 Pysam/0.20.0 Pysam/0.21.0 Pysam/0.22.0 Pysam/0.22.1	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/2.7.18-bare Python/2.7.18 Python/3.8.6 Python/3.9.5-bare Python/3.9.5 Python/3.9.6-bare Python/3.9.6 Python/3.10.4-bare Python/3.10.4 Python/3.10.8-bare Python/3.10.8 Python/3.11.3 Python/3.11.5 Python/3.12.3	Python is a programming language that lets you work more quickly and integrate your systems more effectively.
PYTHON-BUNDLE-PYPI	Python-bundle-PyPI/2023.06 Python-bundle-PyPI/2023.10 Python-bundle-PyPI/2024.06	Bundle of Python packages from PyPI
QCA	QCA/2.3.5	Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.
QEMU	QEMU/9.0.2	A generic and open source machine emulator and virtualizer.
QGIS	QGIS/3.28.1	QGIS is a user friendly Open Source Geographic Information System (GIS)
QIIME2	QIIME2/2022.11 QIIME2/2023.7.0 QIIME2/2024.10-Amplicon-itsxpress QIIME2/2024.10-Amplicon QIIME2/2024.10-Pathogenome QIIME2/2024.10-Metagenome	QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
QJSON	QJson/0.9.0	QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.
QSCINTILLA	QScintilla/2.11.6	QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control
QUAST	QUAST/5.2.0	QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.
QUDA	QUDA/20250226-f0e46e4-CUDA-12.2.0-magma-2.7.2 QUDA/20250226-f0e46e4-CUDA-12.2.0	QUDA is a library for performing calculations in lattice QCD on graphics processing units (GPUs), leveraging NVIDIA's CUDA platform.
QHULL	Qhull/2020.2	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.
QISKIT	Qiskit/2.0.2	Qiskit is an open-source SDK for working with quantum computers at the level of extended quantum circuits, operators, and primitives.
QT5	Qt5/5.15.2 Qt5/5.15.5 Qt5/5.15.7 Qt5/5.15.10 Qt5/5.15.13	Qt is a comprehensive cross-platform C++ application framework.
QT5WEBKIT	Qt5Webkit/5.212.0-alpha4	Qt Port of WebKit. WebKit is an open source web browser engine.
QT6	Qt6/6.6.3	Qt is a comprehensive cross-platform C++ application framework.
QTKEYCHAIN	QtKeychain/0.13.2	Platform-independent Qt API for storing passwords securely.
QUANTUMESPRESSO	QuantumESPRESSO/7.1 QuantumESPRESSO/7.2 QuantumESPRESSO/7.3.1 QuantumESPRESSO/7.4.1-Environ-3.1 QuantumESPRESSO/7.4.1-NVHPC-24.9-CUDA-12.6.0	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	Qwt/6.2.0	The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
R	R/4.1.0 R/4.2.0 R/4.2.1-stub R/4.2.1 R/4.2.2 R/4.3.1 R/4.3.2 R/4.3.3 R/4.4.1	R is a free software environment for statistical computing and graphics.
R-BUNDLE-BIOCONDUCTOR	R-bundle-Bioconductor/3.15-R-4.2.1	Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
R-BUNDLE-CRAN	R-bundle-CRAN/2023.12	Bundle of R packages from CRAN
RAPIDS	RAPIDS/23.08	Built based on the Apache Arrow columnar memory format, cuDF is a GPU DataFrame library for loading, joining, aggregating, filtering, and otherwise manipulating data.
RAPSEARCH2	RAPSearch2/2.24	RAPSearch stands for Reduced Alphabet based Protein similarity Search
RDFLIB	RDFlib/5.0.0 RDFlib/6.2.0	RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
RDKIT	RDKit/2022.09.4	RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
RE2	RE2/2022-06-01 RE2/2023-03-01 RE2/2023-08-01 RE2/2024-03-01 RE2/2024-07-02 re2/2023-11-01	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.
ROOT	ROOT/6.26.06 ROOT/6.26.10	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	RSEM/1.3.3	RNA-Seq by Expectation-Maximization
RACON	Racon/1.5.0	Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
RAPIDJSON	RapidJSON/1.1.0 RapidJSON/1.1.0-20230928 RapidJSON/1.1.0-20240409	A fast JSON parser/generator for C++ with both SAX/DOM style API
RAVEN	Raven/1.8.1	Raven is a de novo genome assembler for long uncorrected reads.
RAY-PROJECT	Ray-project/2.2.0 Ray-project/2.6.2	Ray is a fast and simple framework for building and running distributed applications.
REFRAME	ReFrame/4.0.5	ReFrame is a framework for writing regression tests for HPC systems.
REDIS	Redis/7.0.8	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.
ROSETTA	Rosetta/3.14-mpi Rosetta/3.14	Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.
RUBY	Ruby/3.0.1 Ruby/3.0.3 Ruby/3.3.0	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/1.52.1 Rust/1.54.0 Rust/1.60.0 Rust/1.65.0 Rust/1.70.0 Rust/1.73.0 Rust/1.75.0 Rust/1.76.0 Rust/1.78.0 Rust/1.81.0 Rust/1.82.0	Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SAMTOOLS	SAMtools/1.11 SAMtools/1.14 SAMtools/1.16.1 SAMtools/1.17 SAMtools/1.18 SAMtools/1.22	SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SCOTCH	SCOTCH/6.1.0 SCOTCH/6.1.2 SCOTCH/7.0.1 SCOTCH/7.0.3 SCOTCH/7.0.4	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/4.4.0	SCons is a software construction tool.
SDL2	SDL2/2.0.20 SDL2/2.0.22 SDL2/2.26.3 SDL2/2.28.2 SDL2/2.28.5 SDL2/2.30.6	SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SDL2_IMAGE	SDL2_image/2.8.2	This is a simple library to load images of various formats as SDL surfaces. It can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP images, depending on build options (see the note below for details.)
SDL2_MIXER	SDL2_mixer/2.8.0	Due to popular demand, here is a simple multi-channel audio mixer. It supports 8 channels of 16 bit stereo audio, plus a single channel of music. It can load FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus audio, depending on build options (see the note below for details.)
SDL2_TTF	SDL2_ttf/2.22.0	This library is a wrapper around the FreeType and Harfbuzz libraries, allowing you to use TrueType fonts to render text in SDL applications.
SEPP	SEPP/4.5.1	SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
SHAP	SHAP/0.41.0	SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions.
SIONLIB	SIONlib/1.7.7-tools SIONlib/1.7.7	SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.
SLEPC	SLEPc/3.15.1 SLEPc/3.17.2	SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
SPADES	SPAdes/3.15.3 SPAdes/3.15.5	Genome assembler for single-cell and isolates data sets
SQLALCHEMY	SQLAlchemy/2.0.25	SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
SQLITE	SQLite/3.33.0 SQLite/3.35.4 SQLite/3.36 SQLite/3.38.3 SQLite/3.39.4 SQLite/3.42.0 SQLite/3.43.1 SQLite/3.44.0 SQLite/3.45.3	SQLite: SQL Database Engine in a C Library
SRA-TOOLKIT	SRA-Toolkit/3.0.3 SRA-Toolkit/3.0.5	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
SSW	SSW/1.1	SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
STAR	STAR/2.7.2b STAR/2.7.10b STAR/2.7.11a	STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
SUNDIALS	SUNDIALS/6.3.0	SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
SWIG	SWIG/4.0.2 SWIG/4.1.1	SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
SAFETENSORS	Safetensors/0.4.3	Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast. This variant of Safetensors is installed with support for numpy and PyTorch
SALMON	Salmon/1.9.0	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
SCAFACOS	ScaFaCoS/1.0.1 ScaFaCoS/1.0.4	ScaFaCoS is a library of scalable fast coulomb solvers.
SCALAPACK	ScaLAPACK/2.1.0-fb ScaLAPACK/2.1.0 ScaLAPACK/2.2.0-fb	The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SCALASCA	Scalasca/2.6.1	Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.
SCALENE	Scalene/1.5.26	Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information.
SCHRODINGER	Schrodinger/2023-4	Schrodinger software is a physics-based computational platform that integrates differentiated solutions for predictive modeling, data analytics, and collaboration to enable rapid exploration of chemical space.
SCIPY-BUNDLE	SciPy-bundle/2020.11 SciPy-bundle/2021.05 SciPy-bundle/2021.10 SciPy-bundle/2022.05 SciPy-bundle/2023.02 SciPy-bundle/2023.07 SciPy-bundle/2023.11	Bundle of Python packages for scientific software
SCORE-P	Score-P/8.3 Score-P/8.4	The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
SEABORN	Seaborn/0.12.1 Seaborn/0.13.2	Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
SENTENCEPIECE	SentencePiece/0.1.97 SentencePiece/0.2.0	Unsupervised text tokenizer for Neural Network-based text generation.
SEQLIB	SeqLib/1.2.0	C++ interface to HTSlib, BWA-MEM and Fermi.
SERF	Serf/1.3.9	The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
SHAPELY	Shapely/1.8.2 Shapely/2.0.1	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.
SOX	SoX/14.4.2	Sound eXchange, the Swiss Army knife of audio manipulation
SPFFT	SpFFT/1.1.0	Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.
SPACK	Spack/0.21.2	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/3.5.1-Java-17	Spark is Hadoop MapReduce done in memory
STARPU	StarPU/1.3.11	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
SUBVERSION	Subversion/1.14.2	Subversion is an open source version control system.
SUITESPARSE	SuiteSparse/5.10.1-METIS-5.1.0 SuiteSparse/5.13.0-METIS-5.1.0 SuiteSparse/7.1.0 SuiteSparse/7.7.0-METIS-5.1.0 SuiteSparse/7.8.2-METIS-5.1.0	SuiteSparse is a collection of libraries manipulate sparse matrices.
SUPERLU	SuperLU/6.0.1	SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SUPERLU_DIST	SuperLU_DIST/8.1.0 SuperLU_DIST/8.1.2 SuperLU_DIST/8.2.1	SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SZIP	Szip/2.1.1	Szip compression software, providing lossless compression of scientific data
TCL	Tcl/8.6.10 Tcl/8.6.11 Tcl/8.6.12 Tcl/8.6.13 Tcl/8.6.14	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	TensorFlow/2.5.0 TensorFlow/2.5.3-CUDA-11.3.1 TensorFlow/2.6.0-CUDA-11.3.1 TensorFlow/2.7.1-CUDA-11.4.1 TensorFlow/2.8.4 TensorFlow/2.11.0-CUDA-11.7.0 TensorFlow/2.13.0-CUDA-11.8.0 TensorFlow/2.13.0	An open-source software library for Machine Intelligence
TENSORRT	TensorRT/8.6.0.12-CUDA-11 TensorRT/8.6.0.12-CUDA-12 TensorRT/8.6.1.6-CUDA-11 TensorRT/8.6.1.6-CUDA-12	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/1.1.2-PyMC	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
TK	Tk/8.6.10 Tk/8.6.11 Tk/8.6.12 Tk/8.6.13 Tk/8.6.14	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/3.8.6 Tkinter/3.9.5 Tkinter/3.9.6 Tkinter/3.10.4 Tkinter/3.10.8 Tkinter/3.11.3 Tkinter/3.11.5	Tkinter module, built with the Python buildsystem
TRANSDECODER	TransDecoder/5.5.0	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
TRANSFORMERS	Transformers/4.39.3	State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0
TRANSRATE	Transrate/1.0.3	Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.
TRILINOS	Trilinos/13.4.1	The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
TRIM_GALORE	Trim_Galore/0.6.10	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).
TRIMMOMATIC	Trimmomatic/0.39-Java-17	Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
TRINITY	Trinity/2.15.1	Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
TRINOTATE	Trinotate/4.0.1	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
TRITON	Triton/1.1.1-CUDA-11.7.0	Triton is a language and compiler for parallel programming. It aims to provide a Python-based programming environment for productively writing custom DNN compute kernels capable of running at maximal throughput on modern GPU hardware.
TWISTED	Twisted/22.4.0	Twisted is an event-based framework for internet applications, supporting Python 3.6+.
UCC	UCC/1.0.0 UCC/1.1.0 UCC/1.2.0 UCC/1.3.0	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-CUDA/1.0.0-CUDA-11.7.0 UCC-CUDA/1.1.0-CUDA-12.0.0 UCC-CUDA/1.3.0-CUDA-12.6.0	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.
UCX	UCX/1.9.0-CUDA-11.1.1 UCX/1.9.0 UCX/1.10.0 UCX/1.11.2 UCX/1.12.1 UCX/1.13.1 UCX/1.14.0 UCX/1.14.1 UCX/1.15.0-rc4 UCX/1.15.0-CUDA-12.5.0 UCX/1.15.0 UCX/1.16.0	Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
UCX-CUDA	UCX-CUDA/1.10.0-CUDA-11.3.1 UCX-CUDA/1.11.2-CUDA-11.4.1 UCX-CUDA/1.12.1-CUDA-11.7.0 UCX-CUDA/1.12.1-CUDA-11.8.0 UCX-CUDA/1.12.1-CUDA-12.2.0 UCX-CUDA/1.13.1-CUDA-12.0.0 UCX-CUDA/1.14.1-CUDA-11.8.0 UCX-CUDA/1.14.1-CUDA-12.1.1 UCX-CUDA/1.14.1-CUDA-12.2.0 UCX-CUDA/1.15.0-rc4-CUDA-12.4.1 UCX-CUDA/1.15.0-CUDA-12.2.0 UCX-CUDA/1.15.0-CUDA-12.2.2 UCX-CUDA/1.15.0-CUDA-12.3.0 UCX-CUDA/1.15.0-CUDA-12.4.0 UCX-CUDA/1.15.0-CUDA-12.4.1 UCX-CUDA/1.15.0-CUDA-12.5.0 UCX-CUDA/1.16.0-CUDA-12.6.0	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/2.2.26 UDUNITS/2.2.28	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/6.0	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.
UNI-CORE	Uni-Core/0.0.3-CUDA-11.7.0	An efficient distributed PyTorch framework
UNIFRAC	UniFrac/1.3.2	UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation.
UNICYCLER	Unicycler/0.5.0	Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline.
VCFTOOLS	VCFtools/0.1.16	The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
VESTA	VESTA/3.5.8-gtk3	VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.
VMD	VMD/1.9.4a57	VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
VSCODE	VSCode/1.85.0	Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.
VSEARCH	VSEARCH/2.22.1	VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
VTK	VTK/9.0.1 VTK/9.1.0 VTK/9.2.2 VTK/9.2.6 VTK/9.3.0	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	VTune/2022.3.0 VTune/2025.0.0	Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
VALGRIND	Valgrind/3.21.0 Valgrind/3.23.0	Valgrind: Debugging and profiling tools
VELVET	Velvet/1.2.10-mt-kmer_191	Sequence assembler for very short reads
VIRTUALGL	VirtualGL/3.1	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++/0.4.6	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.
VULKANSDK	VulkanSDK/1.3.239.0 VulkanSDK/1.3.283.0	The Khronos Vulkan API is an explicit, low-overhead, cross-platform graphics and compute API.
WFA2	WFA2/2.3.4	The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.
WPS	WPS/4.4-dmpar	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	WRF/4.2.2-dmpar WRF/4.4-dmpar WRF/4.4.1-dmpar WRF/4.5.1-dmpar	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.
WAYLAND	Wayland/1.20.0 Wayland/1.21.0 Wayland/1.22.0 Wayland/1.23.0	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.
WAYLANDPP	Waylandpp/1.0.0	Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland.
WEBKITGTK+	WebKitGTK+/2.37.1	WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit's full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.
WEBPROXY	WebProxy/0000	WebProxy module sets up web proxy environment variables, http_proxy and https_proxy, for internet acceess from the compute nodes. Wiki page: https://hprc.tamu.edu/wiki/SW:WebProxy
X11	X11/20201008 X11/20210518 X11/20210802 X11/20220504 X11/20221110 X11/20230603 X11/20231019 X11/20240607	The X Window System (X11) is a windowing system for bitmap displays
XGBOOST	XGBoost/1.7.2	XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.
XML-LIBXML	XML-LibXML/2.0207 XML-LibXML/2.0208 XML-LibXML/2.0209	Perl binding for libxml2
XZ	XZ/5.2.5 XZ/5.2.7 XZ/5.4.2 XZ/5.4.4 XZ/5.4.5	xz: XZ utilities
XERCES-C++	Xerces-C++/3.2.4 Xerces-C++/3.2.5	Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
XLSXWRITER	XlsxWriter/3.0.8	A Python module for creating Excel XLSX files
XVFB	Xvfb/1.20.11 Xvfb/1.20.13 Xvfb/21.1.3 Xvfb/21.1.6 Xvfb/21.1.8 Xvfb/21.1.9	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/0.1.8	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.
YASM	Yasm/1.3.0	Yasm: Complete rewrite of the NASM assembler with BSD license
Z3	Z3/4.8.12 Z3/4.10.2-Python-3.10.4 Z3/4.10.2 Z3/4.12.2-Python-3.11.3 Z3/4.12.2 Z3/4.13.0	Z3 is a theorem prover from Microsoft Research.
ZEROMQ	ZeroMQ/4.3.4 ZeroMQ/4.3.5	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/3.0	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
ZOLTAN	Zoltan/3.901	Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit
ABSL-PY	absl-py/2.1.0	absl-py is a collection of Python library code for building Python applications. The code is collected from Google's own Python code base, and has been extensively tested and used in production.
ACCELERATE	accelerate/0.33.0-CUDA-12.1.1	A simple way to launch, train, and use PyTorch models on almost any device and distributed configuration, automatic mixed precision (including fp8), and easy-to-configure FSDP and DeepSpeed support.
AIOHTTP	aiohttp/3.8.3 aiohttp/3.8.5 aiohttp/3.9.5	Asynchronous HTTP client/server framework for asyncio and Python.
ALSA-LIB	alsa-lib/1.2.8 alsa-lib/1.2.9	The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.
ANADAMA2	anadama2/0.10.0	AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to create reproducible workflows and execute them efficiently.
ANNOVAR	annovar/20200607	ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
ANT	ant/1.10.11-Java-11 ant/1.10.12-Java-11 ant/1.10.14-Java-11	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.
ARCHSPEC	archspec/0.1.2 archspec/0.1.3 archspec/0.1.4 archspec/0.2.0 archspec/0.2.1	A library for detecting, labeling, and reasoning about microarchitectures
ARGOBOTS	argobots/1.2	Argobots is a lightweight, low-level threading and tasking framework.
ARIA2	aria2/1.35.0	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
ARM-GNU-TOOLCHAIN	arm-gnu-toolchain/12.3	Arm GNU Toolchain is a community supported pre-built GNU compiler toolchain for Arm based CPUs.
ARM-GNU-TOOLCHAINT	arm-gnu-toolchainT/12.3	Arm GNU Toolchain is a community supported pre-built GNU compiler toolchain for Arm based CPUs.
ARPACK-NG	arpack-ng/3.8.0 arpack-ng/3.9.0 arpack-ng/3.9.1	ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
ARROW-R	arrow-R/8.0.0-R-4.2.1 arrow-R/11.0.0.3-R-4.2.2 arrow-R/14.0.1-R-4.3.2	R interface to the Apache Arrow C++ library
ASSIMP	assimp/5.2.5 assimp/5.3.1	Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.
AT-SPI2-ATK	at-spi2-atk/2.38.0	AT-SPI 2 toolkit bridge
AT-SPI2-CORE	at-spi2-core/2.40.3 at-spi2-core/2.44.1 at-spi2-core/2.46.0 at-spi2-core/2.49.91 at-spi2-core/2.50.0	Assistive Technology Service Provider Interface.
ATTR	attr/2.5.1	Commands for Manipulating Filesystem Extended Attributes
ATTRDICT3	attrdict3/2.0.2	AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
AWSCLI	awscli/2.11.21	Universal Command Line Environment for AWS
BAZELISK	bazelisk/1.25.0	Bazelisk is a wrapper for Bazel written in Go.
BCRYPT	bcrypt/4.0.1	Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)
BENCHMARK	benchmark/1.9.0	A microbenchmark support library.
BINUTILS	binutils/2.31.1 binutils/2.32 binutils/2.35 binutils/2.36.1 binutils/2.37 binutils/2.38 binutils/2.39 binutils/2.40 binutils/2.42	binutils: GNU binary utilities
BIOM-FORMAT	biom-format/2.1.12	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.
BOKEH	bokeh/2.4.1 bokeh/2.4.2 bokeh/2.4.3 bokeh/3.2.2 bokeh/3.4.1	Statistical and novel interactive HTML plots for Python
BOTO3	boto3/1.28.70	Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2.
BTLLIB	btllib/1.7.0	Bioinformatics Technology Lab common code library
BWIDGET	bwidget/1.9.15	The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.
BZIP2	bzip2/1.0.8	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/1.17.2 c-ares/1.18.1	c-ares is a C library for asynchronous DNS requests (including name resolves)
CURL	cURL/7.72.0 cURL/7.76.0 cURL/7.78.0 cURL/7.83.0 cURL/7.86.0 cURL/8.0.1 cURL/8.3.0 cURL/8.7.1	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/1.16.0 cairo/1.17.4 cairo/1.17.8 cairo/1.18.0	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
CAPSTONE	capstone/5.0.1	Capstone is a disassembly framework with the target of becoming the ultimate disasm engine for binary analysis and reversing in the security community.
CAPTUM	captum/0.5.0	Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.
CCACHE	ccache/4.6.1 ccache/4.6.3	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
CDSAPI	cdsapi/0.5.1	Climate Data Store API
CFFI	cffi/1.15.1 cffi/1.16.0	C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.
CHARLIECLOUD	charliecloud/0.33	Charliecloud provides user-defined software stacks (UDSS) for high-performance computing (HPC) centers.
CHEMPROP	chemprop/1.5.2-CUDA-11.7.0	Message Passing Neural Networks for Molecule Property Prediction
CIMFOMFA	cimfomfa/22.273	This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically.
CISTEM	cisTEM/1.0.0-beta-Linux64	cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
CKDMIP	ckdmip/1.0	Software for the Correlated K-Distribution Model Intercomparison Project (CKDMIP).
COLORIZE	colorize/0.7.7	Ruby gem for colorizing text using ANSI escape sequences. Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.
COLOSSALAI	colossalai/0.1.8-CUDA-11.3.1 colossalai/0.3.0-CUDA-12.1.1	Colossal-AI: A Unified Deep Learning System for Big Model Era
CONFIGURABLE-HTTP-PROXY	configurable-http-proxy/4.5.6	HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
CPIO	cpio/2.15	The cpio package contains tools for archiving.
CPPY	cppy/1.1.0 cppy/1.2.1	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.
CRB-BLAST	crb-blast/0.6.9	Conditional Reciprocal Best BLAST - high confidence ortholog assignment.
CRYPTOGRAPHY	cryptography/41.0.1 cryptography/41.0.4 cryptography/41.0.5 cryptography/42.0.8	cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
CUDF	cuDF/23.04.0 cuDF/23.08.00	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	cuDNN/8.0.4.30-CUDA-11.1.1 cuDNN/8.2.1.32-CUDA-11.3.1 cuDNN/8.2.2.26-CUDA-11.4.1 cuDNN/8.4.1.50-CUDA-11.7.0 cuDNN/8.5.0.96-CUDA-11.7.0 cuDNN/8.6.0.163-CUDA-11.8.0 cuDNN/8.7.0.84-CUDA-11.8.0 cuDNN/8.8.0.121-CUDA-12.0.0 cuDNN/8.9.2.26-CUDA-12.1.1 cuDNN/8.9.2.26-CUDA-12.2.0 cuDNN/8.9.7.29-CUDA-12.3.0 cuDNN/9.5.0.50-CUDA-12.6.0	The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
CUSPARSELT	cuSPARSELt/0.5.0.1-CUDA-12.2.2 cuSPARSELt/0.6.0.6-CUDA-12.1.1	NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix
CUTENSOR	cuTENSOR/1.6.1.5-CUDA-11.4.1 cuTENSOR/1.6.1.5-CUDA-11.7.0 cuTENSOR/1.7.0.1-CUDA-12.0.0 cuTENSOR/2.0.1.2-CUDA-12.1.1 cuTENSOR/2.0.2.5-CUDA-12.6.0	The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.
CUDA_PYTHON	cuda_python/0.2.0	CUDA Python is the home for accessing NVIDIA’s CUDA platform from Python.
CUTADAPT	cutadapt/3.5 cutadapt/4.2	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
CYTHON-BLIS	cython-blis/0.9.1	Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension.
DREP	dRep/3.4.2	dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more.
DACE	dace/1.0.2	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/2021.9.1 dask/2022.1.0 dask/2022.10.0 dask/2023.9.2 dask/2024.5.1	Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
DASK-LABEXTENSION	dask-labextension/7.0.0	This package provides a JupyterLab extension to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.
DBUS-GLIB	dbus-glib/0.112	D-Bus is a message bus system, a simple way for applications to talk to one another.
DEEPDIFF	deepdiff/5.7.0 deepdiff/5.8.1 deepdiff/6.7.1	DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
DILL	dill/0.3.4 dill/0.3.6 dill/0.3.7	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.
DM-TREE	dm-tree/0.1.6 dm-tree/0.1.8	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.
DOCKER-USER	docker-user/202311	Rootless mode allows running the Docker daemon and containers as a non-root user to mitigate potential vulnerabilities in the daemon and the container runtime. Rootless mode executes the Docker daemon and containers inside a user namespace. To start the daemon: 'dockerd-rootless-setuptool.sh install --skip-iptables'. To test it: 'docker run hello-world'. To stop the daemon: 'dockerd-rootless-setuptool.sh uninstall --skip-iptables'
DOUBLE-CONVERSION	double-conversion/3.1.5 double-conversion/3.2.0 double-conversion/3.2.1 double-conversion/3.3.0	Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
ECBUILD	ecBuild/3.7.0 ecBuild/3.8.0	A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems
ECCODES	ecCodes/2.24.2 ecCodes/2.27.0 ecCodes/2.31.0	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).
EGGNOG-MAPPER	eggnog-mapper/2.1.9	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
EINOPS	einops/0.4.1 einops/0.7.0	Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
ELFUTILS	elfutils/0.187 elfutils/0.189	The elfutils project provides libraries and tools for ELF files and DWARF data.
ENCHANT-2	enchant-2/2.3.3	Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.
EXIV2	exiv2/0.27.5	Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata.
EXPAT	expat/2.2.9 expat/2.4.1 expat/2.4.8 expat/2.4.9 expat/2.5.0 expat/2.6.2	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)
EXPECT	expect/5.45.4	Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.
EXPECTTEST	expecttest/0.1.3 expecttest/0.1.5	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.
EZTRACE	eztrace/2.1	EZTrace is a tool that aims at generating automatically execution trace from HPC programs.
FASTAHACK	fastahack/1.0.0	Utilities for indexing and sequence extraction from FASTA files.
FASTAI	fastai/2.7.10	The fastai deep learning library.
FERMI-LITE	fermi-lite/20190320	Standalone C library for assembling Illumina short reads in small regions.
FETK	fetk/1.5	FETK The Finite Element ToolKit (FETK) is a collaboratively developed, evolving collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE).
FFNVCODEC	ffnvcodec/11.1.5.2 ffnvcodec/12.0.16.0 ffnvcodec/12.1.14.0	FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).
FILE	file/5.43	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.
FILEVERCMP	filevercmp/20191210	filevercmp function as in sort --version-sort.
FLATBUFFERS	flatbuffers/1.12.0 flatbuffers/2.0.0 flatbuffers/2.0.7 flatbuffers/23.1.4 flatbuffers/23.5.26	FlatBuffers: Memory Efficient Serialization Library
FLATBUFFERS-PYTHON	flatbuffers-python/1.12 flatbuffers-python/2.0 flatbuffers-python/23.1.4 flatbuffers-python/23.5.26	Python Flatbuffers runtime library.
FLEX	flex/2.6.4	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.
FLIT	flit/3.9.0	A simple packaging tool for simple packages.
FMT	fmt/10.1.0 fmt/10.2.0	fmt (formerly cppformat) is an open-source formatting library.
FONTCONFIG	fontconfig/2.13.92 fontconfig/2.13.93 fontconfig/2.13.94 fontconfig/2.14.0 fontconfig/2.14.1 fontconfig/2.14.2 fontconfig/2.15.0	Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
FOSS	foss/2020b foss/2021a foss/2021b foss/2022a foss/2022b foss/2023a foss/2023b foss/2023.09 foss/2024a foss/2024.05	GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
FOSSCUDA	fosscuda/2020b	GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
FREEBAYES	freebayes/1.3.7-R-4.3.2	Bayesian haplotype-based genetic polymorphism discovery and genotyping.
FREEGLUT	freeglut/3.2.1 freeglut/3.2.2 freeglut/3.4.0	freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
FREETYPE	freetype/2.10.3 freetype/2.10.4 freetype/2.11.0 freetype/2.12.1 freetype/2.13.0 freetype/2.13.2	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.
FSOM	fsom/20151117	A tiny C library for managing SOM (Self-Organizing Maps) neural networks.
G2CLIB	g2clib/1.6.3 g2clib/1.7.0	Library contains GRIB2 encoder/decoder ('C' version).
G2LIB	g2lib/3.2.0	Library contains GRIB2 encoder/decoder and search/indexing routines.
GC	gc/8.2.0 gc/8.2.4	The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
GCCCUDA	gcccuda/2020b	GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
GDOWN	gdown/5.2.0	Google Drive Public File Downloader when curl/wget Fails
GENOMEPY	genomepy/0.16.1	genomepy is designed to provide a simple and straightforward way to download and use genomic data
GEOCUBE	geocube/0.4.3	Tool to convert geopandas vector data into rasterized xarray data.
GEOPANDAS	geopandas/0.12.2 geopandas/0.14.2	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	gettext/0.21 gettext/0.21.1 gettext/0.22 gettext/0.22.5	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	gfbf/2022a gfbf/2022b gfbf/2023a gfbf/2023b gfbf/2023.09 gfbf/2024a gfbf/2024.05	GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
GIFLIB	giflib/5.2.1	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/2.28.0-nodocs git/2.32.0-nodocs git/2.33.1-nodocs git/2.36.0-nodocs git/2.38.1-nodocs git/2.41.0-nodocs git/2.42.0 git/2.45.1	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.
GIT-LFS	git-lfs/3.2.0 git-lfs/3.3.0 git-lfs/3.5.1	Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
GLEW	glew/2.2.0-egl glew/2.2.0-osmesa	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.
GLIB-NETWORKING	glib-networking/2.72.1	Network extensions for GLib
GMPY2	gmpy2/2.1.2 gmpy2/2.1.5	GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x
GNUPLOT	gnuplot/5.4.4 gnuplot/5.4.6 gnuplot/5.4.8	Portable interactive, function plotting utility
GOMKL	gomkl/2022a	GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL
GOMPI	gompi/2020b gompi/2021a gompi/2021b gompi/2022a gompi/2022b gompi/2023a gompi/2023b gompi/2023.05 gompi/2023.09 gompi/2024a gompi/2024.05	GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
GOMPIC	gompic/2020b	GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
GOOGLETEST	googletest/1.11.0 googletest/1.12.1 googletest/1.13.0 googletest/1.14.0	Google's framework for writing C++ tests on a variety of platforms
GPERF	gperf/3.1	GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
GPERFTOOLS	gperftools/2.10 gperftools/2.12 gperftools/2.13	gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
GPFLOW	GPflow/2.9.0-CUDA-11.7.0-TensorFlow-2.11.0 gpflow/2.9.0-CUDA-11.7.0-TensorFlow-2.11.0 gpflow/2.9.0-CUDA-11.7.0	GPflow is a package for building Gaussian process models in python, using TensorFlow.
GPGME	gpgme/1.23.2	GnuPG Made Easy (GPGME) is a library designed to make access to GnuPG easier for applications. It provides a High-Level Crypto API for encryption, decryption, signing, signature verification and key management.
GPUSTAT	gpustat/1.1	A simple command-line utility for querying and monitoring GPU status
GRAPHITE2	graphite2/1.3.14	Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.
GRAPHVIZ-PYTHON	graphviz-python/0.20.1	Simple Python interface for Graphviz
GREAT_TABLES	great_tables/0.17.0	Make awesome display tables using Python.
GROFF	groff/1.22.4 groff/1.23.0	Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
GRPCIO	grpcio/1.57.0	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.
GSLIB	gslib/1.0.8	A sparse communication library.
GZIP	gzip/1.10 gzip/1.12 gzip/1.13	gzip (GNU zip) is a popular data compression program as a replacement for compress
H5PY	h5py/3.1.0 h5py/3.2.1 h5py/3.6.0 h5py/3.7.0 h5py/3.8.0 h5py/3.9.0 h5py/3.10.0	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.
HATCH-JUPYTER-BUILDER	hatch-jupyter-builder/0.9.1	Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.
HATCHLING	hatchling/1.16.1 hatchling/1.18.0 hatchling/1.24.2	Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.
HELP2MAN	help2man/1.47.7 help2man/1.47.8 help2man/1.47.16 help2man/1.48.3 help2man/1.49.2 help2man/1.49.3	help2man produces simple manual pages from the '--help' and '--version' output of other commands.
HIREDIS	hiredis/1.0.2	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.
HUGGINGFACE_HUB	huggingface_hub/0.27.1	The official Python client for the Huggingface Hub.
HUMANN	HUMAnN/3.9 humann/3.6	HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)?
HUNSPELL	hunspell/1.7.1	Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding.
HWLOC	hwloc/2.2.0 hwloc/2.4.1 hwloc/2.5.0 hwloc/2.7.1 hwloc/2.8.0 hwloc/2.9.1 hwloc/2.9.2 hwloc/2.10.0	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.
HYPOTHESIS	hypothesis/5.41.2 hypothesis/6.13.1 hypothesis/6.14.6 hypothesis/6.46.7 hypothesis/6.68.2 hypothesis/6.82.0 hypothesis/6.88.1 hypothesis/6.90.0 hypothesis/6.103.1	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.
IIMPI	iimpi/2021b iimpi/2022a iimpi/2022b iimpi/2022.12 iimpi/2023a iimpi/2023b iimpi/2023.03 iimpi/2023.07 iimpi/2024a	Intel C/C++ and Fortran compilers, alongside Intel MPI.
IMAGEIO	imageio/2.22.2 imageio/2.33.1	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.
IMAKE	imake/1.0.8	imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems.
IMBALANCED-LEARN	imbalanced-learn/0.10.1	imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.
IMKL	imkl/2021.4.0 imkl/2022.1.0 imkl/2022.2.1 imkl/2023.0.0 imkl/2023.1.0 imkl/2023.2.0 imkl/2024.0.0 imkl/2024.2.0	Intel oneAPI Math Kernel Library
IMKL-FFTW	imkl-FFTW/2021.4.0 imkl-FFTW/2022.1.0 imkl-FFTW/2022.2.1 imkl-FFTW/2023.0.0 imkl-FFTW/2023.1.0 imkl-FFTW/2023.2.0 imkl-FFTW/2024.2.0	FFTW interfaces using Intel oneAPI Math Kernel Library
IMPI	impi/2021.4.0 impi/2021.6.0 impi/2021.7.1 impi/2021.8.0 impi/2021.9.0 impi/2021.10.0 impi/2021.11.0 impi/2021.13.0	Intel MPI Library, compatible with MPICH ABI
INTEL	intel/2021b intel/2022a intel/2022b intel/2022.11 intel/2022.12 intel/2023a intel/2023b intel/2023.03 intel/2023.07 intel/2024a	Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
INTEL-COMPILERS	intel-compilers/2021.2.0 intel-compilers/2021.4.0 intel-compilers/2022.1.0 intel-compilers/2022.2.0 intel-compilers/2022.2.1 intel-compilers/2023.0.0 intel-compilers/2023.1.0 intel-compilers/2023.2.1 intel-compilers/2024.0.0 intel-compilers/2024.2.0 intel-compilers/2025.0.0	Intel C, C++ & Fortran compilers (classic and oneAPI)
INTEL/AIKIT	intel/AIKit intel/AIKit intel/AIKit	Intel AI Analytic Toolkit installed using Miniconda3
INTELPYTHON	intelpython/2024.1.0_814	This is the Intel Python distribution.
INTERVALTREE	intervaltree/0.1	An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.
INTLTOOL	intltool/0.51.0	intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
JAX	jax/0.2.20 jax/0.3.25-CUDA-11.7.0 jax/0.3.25 jax/0.4.4-CUDA-11.8.0 jax/0.4.4	Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
JBIGKIT	jbigkit/2.1	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.
JEDI	jedi/0.19.1	Jedi - an awesome autocompletion, static analysis and refactoring library for Python.
JEMALLOC	jemalloc/5.2.1 jemalloc/5.3.0	jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
JSON-C	json-c/0.16 json-c/0.17	JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
JUPYTER-RESOURCE-USAGE	jupyter-resource-usage/1.0.0	Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)
JUPYTER-SERVER	jupyter-server/1.21.0 jupyter-server/2.7.0 jupyter-server/2.7.2 jupyter-server/2.14.0	The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.
JUPYTER-SERVER-PROXY	jupyter-server-proxy/4.0.0 jupyter-server-proxy/4.1.2	Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.
JUPYTERLMOD	jupyterlmod/4.0.3 jupyterlmod/5.2.1	Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod's Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc.
KALLISTO	kallisto/0.48.0	kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
KBLAS-GPU	kblas-gpu/20231024-CUDA-11.8.0	KAUST BLAS (KBLAS) is a high performance CUDA library implementing a subset of BLAS as well as Linear Algebra PACKage (LAPACK) routines on NVIDIA GPUs.
KIM-API	kim-api/2.2.1 kim-api/2.3.0	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.
KINETO	kineto/0.4.0	A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters
LIBGLU	libGLU/9.0.1 libGLU/9.0.2 libGLU/9.0.3	The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
LIBROM	libROM/93ca278	A free, lightweight, scalable C++ library for data-driven physical simulation methods from the intrusive projection-based reduced order models to non-intrusive black-box approaches.
LIBAEC	libaec/1.0.6	Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
LIBAIO	libaio/0.3.112	Asynchronous input/output library that uses the kernels native interface.
LIBARCHIVE	libarchive/3.4.3 libarchive/3.5.1 libarchive/3.6.1 libarchive/3.6.2 libarchive/3.7.2 libarchive/3.7.4	Multi-format archive and compression library
LIBASSUAN	libassuan/2.5.7	Libassuan is a small library implementing the so-called Assuan protocol. This protocol is used for IPC between most newer GnuPG components. Both, server and client side functions are provided.
LIBATOMIC_OPS	libatomic_ops/7.8.2	This package provides semi-portable access to hardware-provided atomic memory update operations on a number of architectures.
LIBCERF	libcerf/2.1 libcerf/2.3	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.
LIBDAP	libdap/3.20.7	A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.
LIBDEFLATE	libdeflate/1.10 libdeflate/1.15 libdeflate/1.18 libdeflate/1.19 libdeflate/1.20	Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
LIBDIVSUFSORT	libdivsufsort/2.0.1	libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.
LIBDRM	libdrm/2.4.106 libdrm/2.4.107 libdrm/2.4.110 libdrm/2.4.114 libdrm/2.4.115 libdrm/2.4.117 libdrm/2.4.122	Direct Rendering Manager runtime library.
LIBEPOXY	libepoxy/1.5.8 libepoxy/1.5.10	Epoxy is a library for handling OpenGL function pointer management for you
LIBEV	libev/4.33	A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs.
LIBEVENT	libevent/2.1.12	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/1.11.0 libfabric/1.12.1 libfabric/1.13.2 libfabric/1.15.1 libfabric/1.16.1 libfabric/1.18.0 libfabric/1.19.0 libfabric/1.21.0	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	libffi/3.3 libffi/3.4.2 libffi/3.4.4 libffi/3.4.5	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.
LIBFYAML	libfyaml/0.9	Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the full YAML testsuite.
LIBGCRYPT	libgcrypt/1.9.3	Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG
LIBGD	libgd/2.3.3	GD is an open source code library for the dynamic creation of images by programmers.
LIBGEOTIFF	libgeotiff/1.6.0 libgeotiff/1.7.0 libgeotiff/1.7.1 libgeotiff/1.7.3	Library for reading and writing coordinate system information from/to GeoTIFF files
LIBGIT2	libgit2/1.1.0 libgit2/1.1.1 libgit2/1.4.3 libgit2/1.5.0 libgit2/1.7.1 libgit2/1.7.2 libgit2/1.8.1	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/1.3.3 libglvnd/1.4.0 libglvnd/1.6.0 libglvnd/1.7.0	libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
LIBGPG-ERROR	libgpg-error/1.42 libgpg-error/1.49	Libgpg-error is a small library that defines common error values for all GnuPG components.
LIBGPUARRAY	libgpuarray/0.7.6	Library to manipulate tensors on the GPU.
LIBICONV	libiconv/1.16 libiconv/1.17	Libiconv converts from one character encoding to another through Unicode conversion
LIBIDN	libidn/1.38	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.
LIBIDN2	libidn2/2.3.2 libidn2/2.3.7	Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.
LIBJPEG-TURBO	libjpeg-turbo/2.0.5 libjpeg-turbo/2.0.6 libjpeg-turbo/2.1.3 libjpeg-turbo/2.1.4 libjpeg-turbo/2.1.5.1 libjpeg-turbo/3.0.1	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.
LIBMAD	libmad/0.15.1b	MAD is a high-quality MPEG audio decoder.
LIBNSL	libnsl/2.0.0	The libnsl package contains the public client interface for NIS(YP).
LIBOGG	libogg/1.3.4 libogg/1.3.5	Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
LIBOPUS	libopus/1.3.1 libopus/1.4 libopus/1.5.2	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	libpciaccess/0.16 libpciaccess/0.17 libpciaccess/0.18.1	Generic PCI access library.
LIBPNG	libpng/1.6.37 libpng/1.6.38 libpng/1.6.39 libpng/1.6.40 libpng/1.6.43	libpng is the official PNG reference library
LIBPRESSIO	libpressio/20250303-11a1edf	LibPressio is a C++ library with C compatible bindings to abstract between different lossless and lossy compressors and their configurations.
LIBPSL	libpsl/0.21.1	C library for the Public Suffix List
LIBREADLINE	libreadline/8.0 libreadline/8.1 libreadline/8.1.2 libreadline/8.2	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.
LIBROSA	librosa/0.10.1	Audio and music processing in Python
LIBRSVG	librsvg/2.55.1	Librsvg is a library to render SVG files using cairo.
LIBRTTOPO	librttopo/1.1.0	The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores.
LIBSECCOMP	libseccomp/2.5.5	The libseccomp library provides an easy to use, platform independent, interface to the Linux Kernel's syscall filtering mechanism. The libseccomp API is designed to abstract away the underlying BPF based syscall filter language and present a more conventional function-call based filtering interface that should be familiar to, and easily adopted by, application developers.
LIBSHARP2	libsharp2/20240830	Library for efficient spherical harmonic transforms at arbitrary spins, supporting CPU vectorization, OpenMP and MPI.
LIBSNDFILE	libsndfile/1.0.31 libsndfile/1.1.0 libsndfile/1.2.0 libsndfile/1.2.2	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	libsodium/1.0.18 libsodium/1.0.19	Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
LIBSPATIALINDEX	libspatialindex/1.9.3	C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API
LIBSPATIALITE	libspatialite/5.0.1	SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
LIBTASN1	libtasn1/4.18.0 libtasn1/4.19.0	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/1.3.1 libtirpc/1.3.2 libtirpc/1.3.3 libtirpc/1.3.4	Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
LIBTOOL	libtool/2.4.6 libtool/2.4.7	GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
LIBUNISTRING	libunistring/1.0 libunistring/1.1	This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
LIBUNWIND	libunwind/1.4.0 libunwind/1.5.0 libunwind/1.6.2 libunwind/1.8.1	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
LIBVDWXC	libvdwxc/0.4.0	libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.
LIBVORBIS	libvorbis/1.3.7	Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
LIBVORI	libvori/220621	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	libwebp/1.2.0 libwebp/1.2.4 libwebp/1.3.1 libwebp/1.3.2	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.
LIBWPE	libwpe/1.13.3	WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.
LIBXC	libxc/5.2.3 libxc/6.1.0 libxc/6.2.2	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	libxml2/2.9.10 libxml2/2.9.13 libxml2/2.10.3 libxml2/2.11.4 libxml2/2.11.5 libxml2/2.12.7	Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
LIBXSLT	libxslt/1.1.34 libxslt/1.1.37 libxslt/1.1.38	Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
LIBXSMM	libxsmm/1.17	LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
LIBYAML	libyaml/0.2.5	LibYAML is a YAML parser and emitter written in C.
LIBZIP	libzip/1.7.3	libzip is a C library for reading, creating, and modifying zip archives.
LIFELINES	lifelines/0.27.4	lifelines is a complete survival analysis library, written in pure Python.
LIT	lit/18.1.7	lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures.
LMOD	lmod/	Lmod: An Environment Module System
LPSOLVE	lpsolve/5.5.2.11	Mixed Integer Linear Programming (MILP) solver
LXML	lxml/4.6.3 lxml/4.9.1 lxml/4.9.2 lxml/4.9.3	The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
LZ4	lz4/1.9.2 lz4/1.9.3 lz4/1.9.4	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/1.3.0 maeparser/1.3.1	maeparser is a parser for Schrodinger Maestro files.
MAGMA	magma/2.6.1-CUDA-11.3.1 magma/2.6.2-CUDA-11.7.0 magma/2.6.2-CUDA-11.8.0 magma/2.7.1-CUDA-12.0.0 magma/2.7.2-CUDA-12.1.1 magma/2.7.2-CUDA-12.2.0	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	make/4.3 make/4.4.1	GNU version of make utility
MAKEDEPEND	makedepend/1.0.6 makedepend/1.0.7 makedepend/1.0.9	The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
MAKEINFO	makeinfo/6.7-minimal makeinfo/7.0.3 makeinfo/7.1	makeinfo is part of the Texinfo project, the official documentation format of the GNU project. This is a minimal build with very basic functionality. Should only be used for build dependencies.
MARGO	margo/0.19.0	Margo provides Argobots-aware bindings to the Mercury RPC library.
MATPLOTLIB	matplotlib/3.3.3 matplotlib/3.4.2 matplotlib/3.4.3 matplotlib/3.5.2 matplotlib/3.7.0 matplotlib/3.7.2 matplotlib/3.8.2	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.
MATURIN	maturin/1.1.0 maturin/1.3.1 maturin/1.4.0-Rust-1.75.0 maturin/1.5.0-Rust-1.76.0 maturin/1.6.0	This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support.
MERCURY	Mercury/2.4.0 mercury/2.4.0	Mercury is an RPC framework specifically designed for use in HPC systems that allows asynchronous transfer of parameters and execution requests, as well as direct support of large data arguments.
MESON-PYTHON	meson-python/0.13.2 meson-python/0.15.0 meson-python/0.16.0	Python build backend (PEP 517) for Meson projects
MICROMAMBA	micromamba/2.1.0-0	A statically-linked single file version of Mamba.
MINIMAP2	minimap2/2.26	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.
MINIZIP	minizip/1.1	Mini zip and unzip based on zlib
ML-COLLECTIONS	ml-collections/0.1.1	ML Collections is a library of Python Collections designed for ML use cases.
ML_DTYPES	ml_dtypes/0.3.2	ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz
MODULAR	modular/0.8.0	The Modular command-line interface.
MOLD	mold/1.3.0 mold/1.11.0 mold/2.4.0	mold is a high-performance drop-in replacement for existing Unix linkers.
MOTIF	motif/2.3.8	Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
MPI4PY	mpi4py/3.1.4 mpi4py/3.1.5 mpi4py/4.0.1	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.
MRCFILE	mrcfile/1.5.0	mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.
MULTICHOOSE	multichoose/1.0.3	generate multiset combinations (n multichoose k).
MUSL	musl/1.2.4	An implementation of the C standard library built on top of the Linux system call API, including interfaces defined in the base language standard, POSIX, and widely agreed-upon extensions.
MYGENE	mygene/3.2.2	Python Client for MyGene.Info services.
NANO	nano/8.1	a simple editor, inspired by Pico
NANOGET	nanoget/1.19.3	Functions to extract information from Oxford Nanopore sequencing data and alignments
NANOMATH	nanomath/1.3.0	A few simple math functions for other Oxford Nanopore processing scripts
NBCLASSIC	nbclassic/1.0.0	NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.
NCBI-VDB	ncbi-vdb/3.0.2 ncbi-vdb/3.0.5	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
NCURSES	ncurses/6.1 ncurses/6.2 ncurses/6.3 ncurses/6.4 ncurses/6.5	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/4.7.4 netCDF/4.8.0 netCDF/4.8.1 netCDF/4.9.0 netCDF/4.9.2	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-C++4/4.3.1	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-Fortran/4.5.3 netCDF-Fortran/4.6.0 netCDF-Fortran/4.6.1	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	netcdf4-python/1.6.1 netcdf4-python/1.6.4	Python/numpy interface to netCDF.
NETTLE	nettle/3.7.2 nettle/3.7.3 nettle/3.8 nettle/3.8.1 nettle/3.9.1	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/2.6.3 networkx/2.8.4 networkx/3.0 networkx/3.1 networkx/3.2.1	NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
NGHTTP2	nghttp2/1.48.0	This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API.
NGHTTP3	nghttp3/0.6.0	nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation.
NGTCP2	ngtcp2/0.7.0	'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol.
NLOHMANN_JSON	nlohmann_json/3.10.5 nlohmann_json/3.11.2 nlohmann_json/3.11.3	JSON for Modern C++
NMAD	nmad/20220531	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
NODEJS	nodejs/14.17.0 nodejs/14.17.6 nodejs/16.15.1 nodejs/18.12.1 nodejs/18.17.1 nodejs/20.9.0	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/1.24.0 nsync/1.25.0 nsync/1.26.0	nsync is a C library that exports various synchronization primitives, such as mutexes
NUMACTL	numactl/2.0.13 numactl/2.0.14 numactl/2.0.16 numactl/2.0.18	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/0.52.0 numba/0.53.1 numba/0.54.1-CUDA-11.4.1 numba/0.56.4-CUDA-11.7.0 numba/0.56.4 numba/0.58.1	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.
NUMPY	numpy/1.26.4	NumPy is the fundamental package for scientific computing with Python.
NVIDIA-CONTAINER-CLI	nvidia-container-cli/1.13.2-1-hprc	NVIDIA container command line tools provides a list of locally installed libraries that Charliecloud needs to interface to the local NVIDIA GPUs.
NVTOP	nvtop/3.0.1 nvtop/3.0.2	htop-like GPU usage monitor
OPENPYXL	openpyxl/3.1.2	A Python library to read/write Excel 2010 xlsx/xlsm files
OTF2	OTF2/3.0.3 otf2/3.0.3	The OTF2 library provides an interface to write and read trace data.
P11-KIT	p11-kit/0.24.1 p11-kit/0.25.3	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.
P7ZIP	p7zip/17.04	p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
PARALLEL	parallel/20210722 parallel/20230722	parallel: Build and execute shell commands in parallel
PARAMETERIZED	parameterized/0.9.0	Parameterized testing with any Python test framework
PATCHELF	patchelf/0.15.0 patchelf/0.17.2 patchelf/0.18.0	PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
PBLAT	pblat/2.5.1	When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence.
PETSC4PY	petsc4py/3.20.3	petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.
PHYSICS-TENPY	physics-tenpy/0.10.0	TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks.
PICARD	picard/2.25.1-Java-11	A set of tools (in Java) for working with next generation sequencing data in the BAM format.
PIGZ	pigz/2.6 pigz/2.7	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.
PIOMAN	pioman/20220531	PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately.
PIPENV	pipenv/2025.0.2	Pipenv is a Python virtualenv management tool that supports a multitude of systems and nicely bridges the gaps between pip, python (using system python, pyenv or asdf) and virtualenv. Pipenv automatically creates and manages a virtualenv for your projects, as well as adds/removes packages from your Pipfile as you install/uninstall packages.
PIXMAN	pixman/0.40.0 pixman/0.42.2	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/0.29.2	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/1.8.0 pkgconf/1.9.3 pkgconf/1.9.5 pkgconf/2.0.3 pkgconf/2.2.0	pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
PKGCONFIG	pkgconfig/1.5.1-python pkgconfig/1.5.4-python pkgconfig/1.5.5-python	pkgconfig is a Python module to interface with the pkg-config command line tool
PLOTLY.PY	plotly.py/5.12.0 plotly.py/5.13.1 plotly.py/5.18.0 plotly.py/5.23.0	An open-source, interactive graphing library for Python
POCL	pocl/1.8 pocl/4.0-CUDA-12.1.1 pocl/4.0	Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard
PODMAN	podman/5.1.0-rc1	Podman is an open source container, pod, and container image management engine. Podman makes it easy to find, run, build, and share containers.
POETRY	poetry/1.5.1 poetry/1.6.1 poetry/1.7.1 poetry/1.8.3	Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere.
POLARS	polars/0.20.2 polars/0.47.1	Polars is a blazingly fast DataFrame library for manipulating structured data. The core is written in Rust and this module provides its interface for Python.
POPPLER	poppler/22.12.0 poppler/23.09.0	Poppler is a PDF rendering library
PPLACER	pplacer/1.1.alpha19	Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
PRODIGAL	prodigal/2.6.3	Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
PROKKA	prokka/1.14.5	Prokka is a software tool for the rapid annotation of prokaryotic genomes.
PROTOBUF	protobuf/3.14.0 protobuf/3.17.3 protobuf/3.19.4 protobuf/23.0 protobuf/24.0 protobuf/25.3	Google Protocol Buffers
PROTOBUF-PYTHON	protobuf-python/3.14.0 protobuf-python/3.17.3 protobuf-python/3.19.4 protobuf-python/4.23.0 protobuf-python/4.24.0	Python Protocol Buffers runtime library.
PSUTIL	psutil/5.9.8	A cross-platform process and system utilities module for Python
PSYCOPG2	psycopg2/2.9.5 psycopg2/2.9.9	Psycopg is the most popular PostgreSQL adapter for the Python programming language.
PUGIXML	pugixml/1.12.1	pugixml is a light-weight C++ XML processing library
PY-CPUINFO	py-cpuinfo/9.0.0	py-cpuinfo gets CPU info with pure Python.
PY3DMOL	py3Dmol/2.0.1.post1 py3Dmol/2.1.0	A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook.
PYBIND11	pybind11/2.6.0 pybind11/2.6.2 pybind11/2.7.1 pybind11/2.9.2 pybind11/2.10.3 pybind11/2.11.1 pybind11/2.12.0 pybind11/2.13.6	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	pydantic/1.10.4 pydantic/2.5.3 pydantic/2.7.4	Data validation and settings management using Python type hinting.
PYDICOM	pydicom/2.3.0	Pure python package for DICOM medical file reading and writing.
PYFAIDX	pyfaidx/0.8.1.1	pyfaidx: efficient pythonic random access to fasta subsequences
PYGAME	pygame/2.5.2	Pygame is a set of Python modules designed for writing video games. Pygame adds functionality on top of the excellent SDL library. This allows you to create fully featured games and multimedia programs in the python language.
PYPROJ	pyproj/3.5.0 pyproj/3.6.0	Python interface to PROJ4 library for cartographic transformations
PYTESSERACT	pytesseract/0.3.10	Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and "read" the text embedded in images. Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, Python-tesseract will print the recognized text instead of writing it to a file.
PYTEST	pytest/7.2.2 pytest/7.4.2	The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.
PYTEST-FLAKEFINDER	pytest-flakefinder/1.1.0	Runs tests multiple times to expose flakiness.
PYTEST-RERUNFAILURES	pytest-rerunfailures/11.1 pytest-rerunfailures/12.0	pytest plugin to re-run tests to eliminate flaky failures.
PYTEST-SHARD	pytest-shard/0.1.2	pytest plugin to support parallelism across multiple machines. Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method).
PYTEST-XDIST	pytest-xdist/2.3.0 pytest-xdist/2.5.0 pytest-xdist/3.3.1	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	python-isal/0.11.1 python-isal/1.1.0	Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.
RASTERIO	rasterio/1.3.9	Rasterio reads and writes geospatial raster data.
RE2	RE2/2022-06-01 RE2/2023-03-01 RE2/2023-08-01 RE2/2024-03-01 RE2/2024-07-02 re2/2023-11-01	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.
RE2C	re2c/2.2 re2c/3.0 re2c/3.1	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	redis-py/4.5.1	The Python interface to the Redis key-value store.
RIOXARRAY	rioxarray/0.15.0	Geospatial xarray extension powered by rasterio
RISING	rising/0.2.2	Provides everything needed for high performance data loading and augmentation in PyTorch.
RNAQUAST	rnaQUAST/2.2.2	rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
RPMREBUILD	rpmrebuild/2.11	rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use
RUAMEL.YAML	ruamel.yaml/0.17.21 ruamel.yaml/0.17.32	ruamel.yaml is a YAML 1.2 loader/dumper package for Python.
SCIKIT-BIO	scikit-bio/0.5.7	scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.
SCIKIT-BUILD	scikit-build/0.11.1 scikit-build/0.15.0 scikit-build/0.17.2 scikit-build/0.17.6	Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
SCIKIT-BUILD-CORE	scikit-build-core/0.9.3	Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake.
SCIKIT-CUDA	scikit-cuda/0.5.3-CUDA-11.8.0	SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIA's CUDA Programming Toolkit.
SCIKIT-IMAGE	scikit-image/0.19.3 scikit-image/0.22.0	scikit-image is a collection of algorithms for image processing.
SCIKIT-LEARN	scikit-learn/0.24.2 scikit-learn/1.1.2 scikit-learn/1.2.1 scikit-learn/1.3.1 scikit-learn/1.4.0	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.
SDSL-LITE	sdsl-lite/2.1.1	The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operation performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical.
SETTARG	settarg/	The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
SETUPTOOLS	setuptools/64.0.3	Easily download, build, install, upgrade, and uninstall Python packages
SETUPTOOLS-RUST	setuptools-rust/1.6.0 setuptools-rust/1.7.0 setuptools-rust/1.8.0 setuptools-rust/1.9.0	setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.
SMITHWATERMAN	smithwaterman/20160702	smith-waterman-gotoh alignment algorithm.
SNAPPY	snappy/1.1.8 snappy/1.1.9 snappy/1.1.10 snappy/1.2.1	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.
SPACY	spaCy/3.4.4	Industrial-strength Natural Language Processing (NLP) in Python.
SPARSEHASH	sparsehash/2.0.4	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	spglib/2.0.2	Spglib is a C library for finding and handling crystal symmetries.
SPGLIB-PYTHON	spglib-python/1.16.0 spglib-python/2.0.0	Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
SPYTHON	spython/0.3.0	Singularity Python is a Python API to work with the Singularity open source software.
SQUASHENV	squashenv/0 squashenv/0.1
SST-CORE	sst-core/14.0.0	The Structural Simulation Toolkit (SST) was developed to explore innovations in highly concurrent systems where the ISA, microarchitecture, and memory interact with the programming model and communications system.
STATSMODELS	statsmodels/0.13.1 statsmodels/0.14.1	Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
STRACE	strace/6.6	strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state.
SYMPY	sympy/1.9 sympy/1.10.1 sympy/1.12	SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
SYNTHCITY	synthcity/0.2.4	A library for generating and evaluating synthetic tabular data.
TABIXPP	tabixpp/1.1.2	C++ wrapper to tabix indexer
TALLOC	talloc/2.4.3	A hierarchical, reference counted memory pool system with destructors.
TBB	tbb/2021.5.0 tbb/2021.11.0	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.
TBL2ASN	tbl2asn/20230713-linux64	Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
TCSH	tcsh/6.22.03 tcsh/6.24.01 tcsh/6.24.07 tcsh/6.24.10	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/2.8.0 tensorboard/2.10.0 tensorboard/2.15.1	TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.
TENSORBOARDX	tensorboardX/2.5.1 tensorboardX/2.6.2.2	Tensorboard for PyTorch.
TENSORFLOW-PROBABILITY	tensorflow-probability/0.19.0-CUDA-11.7.0	TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.
TENSORSTORE	tensorstore/0.1.65	TensorStore is an open-source C++ and Python software library designed for storage and manipulation of large multi-dimensional arrays.
TESSERACT	tesseract/5.3.0 tesseract/5.3.4	Tesseract is an optical character recognition engine
TEXLIVE	texlive/20230313	TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
TIME	time/1.9	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.
TMUX	tmux/3.3a	tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
TOKENIZERS	tokenizers/0.15.2	Fast State-of-the-Art Tokenizers optimized for Research and Production
TORCHSAMPLER	torchsampler/0.1.2	A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones.
TORCHTEXT	torchtext/0.14.1-PyTorch-1.12.0	Data loaders and abstractions for text and NLP
TORCHVISION	torchvision/0.11.1-CUDA-11.3.1 torchvision/0.13.1-CUDA-11.7.0 torchvision/0.13.1 torchvision/0.16.0-CUDA-12.1.1	Datasets, Transforms and Models specific to Computer Vision
TORNADO	tornado/6.3.2 tornado/6.4	Tornado is a Python web framework and asynchronous networking library.
TQDM	tqdm/4.61.2 tqdm/4.64.0 tqdm/4.64.1 tqdm/4.66.1 tqdm/4.66.2 tqdm/4.67.1	A fast, extensible progress bar for Python and CLI
TURM	turm/0.7.3	A text-based user interface (TUI) for the Slurm Workload Manager, which provides a convenient way to manage your cluster jobs.
TYPING-EXTENSIONS	typing-extensions/3.7.4.3 typing-extensions/3.10.0.0 typing-extensions/3.10.0.2 typing-extensions/4.3.0 typing-extensions/4.9.0 typing-extensions/4.10.0	Typing Extensions – Backported and Experimental Type Hints for Python
UMAP-LEARN	umap-learn/0.5.3	Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
UMOCI	umoci/0.5.0	A reference implementation of the OCI image specification and provides users with the ability to create, manipulate, and otherwise interact with container images.
UTF8PROC	utf8proc/2.7.0 utf8proc/2.8.0 utf8proc/2.9.0	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	util-linux/2.36 util-linux/2.37 util-linux/2.38 util-linux/2.38.1 util-linux/2.39 util-linux/2.40	Set of Linux utilities
VASP	vasp/6.3.2	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 - gpu compile - Homepage: http://www.vasp.at
VCFLIB	vcflib/1.0.9-R-4.3.2	vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
VIRTUALENV	virtualenv/20.23.1 virtualenv/20.24.6 virtualenv/20.26.2	A tool for creating isolated virtual python environments.
WANDB	wandb/0.13.4 wandb/0.13.6 wandb/0.16.1	CLI and Python API for Weights and Biases: a tool for visualizing and tracking your machine learning experiments.
WGET	wget/1.21.3	GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
WPEBACKEND-FDO	wpebackend-fdo/1.13.1	WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance.
WXPYTHON	wxPython/4.2.0	Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code.
WXWIDGETS	wxWidgets/3.2.0 wxWidgets/3.2.2.1	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	x264/20210414 x264/20210613 x264/20220620 x264/20230226 x264/20231019	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	x265/3.5	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/0.20.1 xarray/2022.6.0 xarray/2022.9.0 xarray/2023.4.2 xarray/2023.9.0	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.
XMLTODICT	xmltodict/0.13.0	Python module that makes working with XML feel like you are working with JSON.
XORG-MACROS	xorg-macros/1.19.2 xorg-macros/1.19.3 xorg-macros/1.20.0 xorg-macros/1.20.1	X.org macros utilities.
XPMEM	xpmem/61c39ef	XPMEM is a Linux kernel module that enables a process to map the memory of another process into its virtual address space.
XPROP	xprop/1.2.5 xprop/1.2.6	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.
XPROTO	xproto/7.0.31	X protocol and ancillary headers
XXD	xxd/8.2.4220 xxd/9.0.1696 xxd/9.0.2112 xxd/9.1.0307	xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.
YAXT	yaxt/0.11.2	A library built on top of MPI for redistributing data between two sets of processes.
YELL	yell/2.2.2	Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.
ZARR	zarr/2.13.3 zarr/2.16.0	Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.
ZFP	zfp/1.0.0 zfp/20250218-bb76298	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/1.2.11 zlib/1.2.12 zlib/1.2.13 zlib/1.3.1	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	zstd/1.4.5 zstd/1.4.9 zstd/1.5.0 zstd/1.5.2 zstd/1.5.5 zstd/1.5.6	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.