Modules sse3

Module	Type	Versions	Description
abaqus	phys	2021	Documentation: Abaqus Description: Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. Homepage: http://www.simulia.com/products/abaqus_fea.html URL: http://www.simulia.com/products/abaqus_fea.html Keyword:phys
abinit	chem	10.0.3	Documentation: ABINIT Description: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Homepage: http://www.abinit.org/ URL: http://www.abinit.org/ Keyword:chem
abseil	-	20230125.3	Description: 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. Homepage: https://abseil.io/ URL: https://abseil.io/
abyss	bio	2.3.7	Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio
actc	-	1.1	Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc
admixture	bio	1.3.0	Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture URL: http://software.genetics.ucla.edu/admixture Keyword:bio
advisor	tools	2020.3	Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe URL: https://software.intel.com/intel-advisor-xe Keyword:tools
afni	bio	24.1.03	Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ URL: http://afni.nimh.nih.gov/ Keyword:bio
alevin-fry	-	0.8.2	Description: alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. Homepage: https://github.com/COMBINE-lab/alevin-fry URL: https://github.com/COMBINE-lab/alevin-fry
amber	chem	22.5-23.5	Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem
ambertools	chem	23.5	Description: 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. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php Keyword:chem
ampl-mp	-	3.1.0	Description: An open-source library for mathematical programming. Homepage: https://github.com/ampl/mp URL: https://github.com/ampl/mp
amrfinderplus	-	3.12.8	Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus
angsd	bio	0.940	Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd URL: http://www.popgen.dk/angsd Keyword:bio
annovar	bio	20191024	Description: 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). Homepage: http://annovar.openbioinformatics.org/en/latest/ URL: http://annovar.openbioinformatics.org/en/latest/ Keyword:bio
anserini	-	0.9.4	Description: An open-source information retreival toolkit built on Lucene that aims to bridge the gap between academic information retrieval and the practice of building real-world search applications. Usage: Binaries located in Anserini's target/appassembler/bin are on path. Anserini's folders bin, collections, docs, indexes, logs, runs, src, target, tools, as well as the files pom.xml and README.md are available at $EBROOTANSERINI. Eg. Indexing command for help: IndexCollection -h Homepage: https://github.com/castorini/anserini URL: https://github.com/castorini/anserini
ansys	phys	2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2	Documentation: Ansys Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys
ansysedt	-	2021R2, 2023R2	Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com
ant	tools	1.9.15, 1.10.8, 1.10.14	Description: 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. Homepage: https://ant.apache.org/ URL: https://ant.apache.org/ Keyword:tools
antlr	-	2.7.7	Description: 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. Homepage: https://www.antlr2.org/ URL: https://www.antlr2.org/
ants	vis	2.5.0	Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: https://stnava.github.io/ANTs/ URL: https://stnava.github.io/ANTs/ Keyword:vis
apptainer	-	1.1.3, 1.1.5, 1.1.6, 1.1.8, 1.2.4	Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org
aragorn	-	1.2.41	Description: a program to detect tRNA genes and tmRNA genes in nucleotide sequences Homepage: http://www.ansikte.se/ARAGORN/ URL: http://www.ansikte.se/ARAGORN/
arcs	bio	1.2.7	Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. Homepage: https://github.com/bcgsc/arcs URL: https://github.com/bcgsc/arcs Keyword:bio
armadillo	math	12.6.4	Description: 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. Homepage: https://arma.sourceforge.net/ URL: https://arma.sourceforge.net/ Keyword:math
arpack-ng	math	3.9.1	Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math
arrayfire	-	3.9.0	Description: ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. Homepage: https://arrayfire.com/ URL: https://arrayfire.com/
arrow	tools	14.0.0, 14.0.1, 15.0.1, 16.1.0	Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools
ascp	tools	3.5.4	Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ URL: http://downloads.asperasoft.com/ Keyword:tools
autodock_vina	chem	1.1.2	Description: AutoDock Vina is an open-source program for doing molecular docking. Homepage: http://vina.scripps.edu/index.html URL: http://vina.scripps.edu/index.html Keyword:chem
bacio	-	2.6.0	Description: This library performs binary I/O for the NCEP models, processing unformatted byte-addressable data records, and transforming the little endian files and big endian files. This is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-bacio/ URL: https://github.com/NOAA-EMC/NCEPLIBS-bacio/
bamtools	bio	2.5.2	Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools URL: https://github.com/pezmaster31/bamtools Keyword:bio
bbmap	bio	38.86, 39.06	Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio
bcftools	bio	1.18, 1.19	Description: 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 Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio
bcl-convert	-	4.2.4, 4.2.7	Description: The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html URL: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html
beagle	-	5.4, 5.4-240301	Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html
beagle-lib	bio	4.0.1	Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio
bedops	-	2.4.41	Description: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. Homepage: http://bedops.readthedocs.io/en/latest/index.html URL: http://bedops.readthedocs.io/en/latest/index.html
bedtools	bio	2.31.0	Description: 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. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio
beef	chem	0.1.1	Description: BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. Homepage: http://suncat.stanford.edu/facility/software/functional URL: http://suncat.stanford.edu/facility/software/functional Keyword:chem
berkeleygw	phys	4.0	Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org URL: http://www.berkeleygw.org Keyword:phys
bioawk	-	1.0	Description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. Homepage: https://github.com/lh3/bioawk URL: https://github.com/lh3/bioawk
bioperl	bio	1.7.7, 1.7.8	Description: 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. Homepage: https://bioperl.org/ URL: https://bioperl.org/ Extensions: Bio::Procedural-1.7.4, BioPerl-1.7.8, XML::DOM::XPath-0.14, XML::Writer-0.900 Keyword:bio
bismark	-	0.24.1	Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
blast	bio	2.2.26	Description: 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. Homepage: http://blast.ncbi.nlm.nih.gov/ URL: http://blast.ncbi.nlm.nih.gov/ Keyword:bio
blast+	bio	2.14.1	Documentation: BLAST Description: 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. Homepage: https://blast.ncbi.nlm.nih.gov/ URL: https://blast.ncbi.nlm.nih.gov/ Keyword:bio
blender	vis	3.6.0, 4.0.2	Description: 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. Homepage: https://www.blender.org/ URL: https://www.blender.org/ Keyword:vis
blis	-	0.8.1, 0.9.0, 1.0	Description: BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. Homepage: https://github.com/flame/blis/ URL: https://github.com/flame/blis/
blosc	-	1.17.1	Description: Blosc, an extremely fast, multi-threaded, meta-compressor library Homepage: https://www.blosc.org/ URL: https://www.blosc.org/
boost	tools	1.72.0, 1.82.0	Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools
boost-mpi	tools	1.72.0, 1.82.0	Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools
bowtie2	bio	2.5.2, 2.5.4	Description: 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. Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio
breseq	-	0.38.2	Description: breseq is a computational pipeline for the analysis of short-read re-sequencing data Homepage: https://barricklab.org/breseq URL: https://barricklab.org/breseq
brunsli	-	0.1	Description: Brunsli is a lossless JPEG repacking library. Homepage: https://github.com/google/brunsli/ URL: https://github.com/google/brunsli/
btllib	-	1.6.2	Description: Bioinformatics Technology Lab common code library Homepage: https://github.com/bcgsc/btllib URL: https://github.com/bcgsc/btllib
bufr	-	12.0.1	Description: The NCEPLIBS-bufr library contains routines and utilites for working with the WMO BUFR format. It is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-bufr/ URL: https://github.com/NOAA-EMC/NCEPLIBS-bufr/
bustools	-	0.40.0	Description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. Homepage: https://github.com/BUStools/bustools URL: https://github.com/BUStools/bustools
bwa	bio	0.7.17, 0.7.18	Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ URL: http://bio-bwa.sourceforge.net/ Keyword:bio
bwa-mem2	-	2.2.1	Description: The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. The original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license. Homepage: https://github.com/bwa-mem2/bwa-mem2 URL: https://github.com/bwa-mem2/bwa-mem2
cap3	bio	20151002	Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio
catch2	-	2.11.0	Description: A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) Homepage: https://github.com/catchorg/Catch2 URL: https://github.com/catchorg/Catch2
ccsm	geo	4_0_a02	Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ URL: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo
cdo	geo	2.2.2	Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo URL: https://code.zmaw.de/projects/cdo Keyword:geo
cellranger	bio	2.1.0	Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome URL: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio
cereal	-	1.3.0, 1.3.2	Description: 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. Homepage: https://uscilab.github.io/cereal/ URL: https://uscilab.github.io/cereal/
cesm	geo	2.1.3	Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm2/ URL: http://www.cesm.ucar.edu/models/cesm2/ Keyword:geo
cfitsio	vis	4.3.0	Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/ URL: http://heasarc.gsfc.nasa.gov/fitsio/ Keyword:vis
cfour	chem	2.1	Description: Serial version of CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem
cfour-mpi	chem	2.1	Description: CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem
cgal	math	4.14.3, 5.5.2	Description: 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. Homepage: https://www.cgal.org/ URL: https://www.cgal.org/ Keyword:math
charm-gems	-	1.3.3	Description: This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations. Homepage: https://github.com/simnibs/charm-gems URL: https://github.com/simnibs/charm-gems Compatible modules: python/3.11, python/3.10 Extensions: charm-gems-1.3.3
circos	vis	0.69-9	Description: Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. Homepage: http://www.circos.ca/ URL: http://www.circos.ca/ Keyword:vis
clang	tools	17.0.6	Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/ URL: https://clang.llvm.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools
clhep	math	2.4.6.2, 2.4.7.1	Description: 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. Homepage: https://proj-clhep.web.cern.ch/proj-clhep/ URL: https://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math
cmake	tools	3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7	Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. Homepage: https://www.cmake.org URL: https://www.cmake.org Keyword:tools
code-server	-	3.5.0, 3.12.0	Description: Run VS Code on any machine anywhere and access it in the browser. Homepage: https://github.com/cdr/code-server URL: https://github.com/cdr/code-server
coinmp	-	1.8.4	Description: CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects. Homepage: https://projects.coin-or.org/CoinMP URL: https://projects.coin-or.org/CoinMP
comsol	phys	5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2.0.415	Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys
coordgenlibs	chem	1.4.2	Description: Schrodinger-developed 2D Coordinate Generation Homepage: https://github.com/schrodinger/coordgenlibs URL: https://github.com/schrodinger/coordgenlibs Keyword:chem
corset	bio	1.09	Description: Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. Homepage: https://github.com/Oshlack/Corset/wiki URL: https://github.com/Oshlack/Corset/wiki Keyword:bio
cppzmq	-	4.7.1	Description: cppzmq is a C++ binding for libzmq Homepage: https://github.com/zeromq/cppzmq URL: https://github.com/zeromq/cppzmq
crest	chem	3.0.1	Description: Conformer-Rotamer Ensemble Sampling Tool Homepage: https://github.com/grimme-lab/crest URL: https://github.com/grimme-lab/crest Keyword:chem
cromwell	tools	58	Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/ URL: https://cromwell.readthedocs.io/ Keyword:tools
cst	phys	2020	Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ URL: https://www.cst.com/ Keyword:phys
csvtk	-	0.23.0	Description: Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts. Homepage: https://github.com/shenwei356/csvtk URL: https://github.com/shenwei356/csvtk
cuba	-	4.2.2	Description: Cuba a library for multidimensional numerical integration Homepage: https://feynarts.de/cuba/ URL: https://feynarts.de/cuba/
cudnn	math	8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29	Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn URL: https://developer.nvidia.com/cudnn Keyword:math
cusparselt	-	0.4.0.7, 0.5.0.1	Description: NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix Homepage: https://docs.nvidia.com/cuda/cusparselt/index.html URL: https://docs.nvidia.com/cuda/cusparselt/index.html
custom-ctypes	-	1.1, 1.2	Description: This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names. Homepage: https://github.com/ComputeCanada/custom_ctypes/ URL: https://github.com/ComputeCanada/custom_ctypes/
cutensor	-	1.5.0.3, 1.7.0.1, 2.0.0.7	Description: cuTENSOR is a high-performance CUDA library for tensor primitives. Homepage: https://developer.nvidia.com/cutensor URL: https://developer.nvidia.com/cutensor
cvit	-	1.2.1	Description: A genomic linkage feature visualization tools based on Perl. Homepage: https://sourceforge.net/projects/cvit/ URL: https://sourceforge.net/projects/cvit/ Extensions: Config::IniFiles-3.000002, Data::Dumper-2.173, ExtUtils::PkgConfig-1.16, GD-2.71, GD::Arrow-0.01, GD::SVG-0.33, GD::Text-0.86, SVG-2.84, Test::Fork-0.02
dakota	tools	6.13	Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools
das_tool	-	1.1.6	Description: DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Homepage: https://github.com/cmks/DAS_Tool URL: https://github.com/cmks/DAS_Tool Extensions: data.table-1.14.8, docopt-0.7.1, magrittr-2.0.3
db	-	18.1.32	Description: Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. Homepage: https://www.oracle.com/technetwork/products/berkeleydb URL: https://www.oracle.com/technetwork/products/berkeleydb
dcm2niix	bio	1.0.20230411	Description: dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio
ddt-cpu	tools	20.2, 22.0.1, 23.1.1	Documentation: ARM software Description: Profiler and debugger, combining MAP and DDT. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com
ddt-gpu	tools	20.2, 22.0.1, 23.1.1	Documentation: ARM software Description: Profiler and debugger, combining MAP and DDT, with support for CUDA. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com
delly	-	0.8.5, 1.1.8	Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Homepage: https://github.com/dellytools/delly/ URL: https://github.com/dellytools/delly/
dftd4	chem	3.6.0	Description: Generally Applicable Atomic-Charge Dependent London Dispersion Correction. Homepage: https://github.com/dftd4/dftd4 URL: https://github.com/dftd4/dftd4 Keyword:chem
diamond	bio	2.1.8	Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio
dl_poly4	chem	5.1.0	Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx URL: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem
dorado	-	0.2.1, 0.2.2, 0.3.0, 0.4.1, 0.4.3, 0.5.3, 0.6.1, 0.7.0, 0.7.2	Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Homepage: https://github.com/nanoporetech/dorado URL: https://github.com/nanoporetech/dorado
dotnet-core	-	3.1.8, 5.0.12, 6.0.0	Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. Homepage: https://www.microsoft.com/net/ URL: https://www.microsoft.com/net/
double-conversion	-	3.1.5	Description: Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. Homepage: https://github.com/google/double-conversion URL: https://github.com/google/double-conversion
ecbuild	-	3.8.0	Description: A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems Homepage: https://ecbuild.readthedocs.io/ URL: https://ecbuild.readthedocs.io/
eccodes	geo	2.31.0	Description: 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). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.10, python/3.11 Extensions: cfgrib-0.9.10.4, eccodes-1.6.1 Keyword:geo
edirect	-	20.9.20231210	Description: Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. Homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/ URL: https://www.ncbi.nlm.nih.gov/books/NBK25501/
eigen	math	3.3.7, 3.4.0	Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org URL: https://eigen.tuxfamily.org Keyword:math
elpa	math	2020.05.001, 2023.05.001	Description: Eigenvalue SoLvers for Petaflop-Applications. Homepage: https://elpa.mpcdf.mpg.de/ URL: https://elpa.mpcdf.mpg.de/ Keyword:math
embree	-	3.11.0, 4.3.0	Description: Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. Homepage: https://github.com/embree/embree URL: https://github.com/embree/embree
energyplus	-	9.3.0, 23.2.0	Description: EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings. Homepage: https://energyplus.net/downloads URL: https://energyplus.net/downloads
esmf	geo	8.6.0	Description: The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Homepage: https://www.earthsystemcog.org/projects/esmf/ URL: https://www.earthsystemcog.org/projects/esmf/ Compatible modules: python/3.10, python/3.11 Extensions: esmpy-8.6.0 Keyword:geo
etsf_io	io	1.0.4	Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools Keyword:io
expat	tools	2.2.9, 2.2.10	Description: 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) Homepage: https://libexpat.github.io URL: https://libexpat.github.io Keyword:tools
faiss	-	1.7.4, 1.8.0	Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.10, python/3.11
fastahack	-	1.0.0	Description: Utilities for indexing and sequence extraction from FASTA files. Homepage: https://github.com/ekg/fastahack URL: https://github.com/ekg/fastahack
fastqc	bio	0.11.9, 0.12.0, 0.12.1	Description: 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. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio
fastsimcoal2	bio	2.6.0.3, 2.7.0.9	Description: While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/ URL: http://cmpg.unibe.ch/software/fastsimcoal2/ Keyword:bio
fermi-lite	-	20190320	Description: Standalone C library for assembling Illumina short reads in small regions. Homepage: https://github.com/lh3/fermi-lite URL: https://github.com/lh3/fermi-lite
ferret	vis	7.6.0	Description: Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. Ferret 7.6.0 is the final available version of Classic Ferret. The developers recommend using PyFerret instead. Homepage: http://ferret.pmel.noaa.gov/ URL: http://ferret.pmel.noaa.gov/ Keyword:vis
fftw	math	3.3.10	Description: 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. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math
fftw-mpi	math	3.3.10	Description: 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. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math
filevercmp	-	20191210	Description: filevercmp function as in sort --version-sort. Homepage: https://github.com/ekg/filevercmp URL: https://github.com/ekg/filevercmp
filtlong	bio	0.2.0, 0.2.1	Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong URL: https://github.com/rrwick/Filtlong Keyword:bio
flexiblas	-	3.0.4, 3.3.1, 3.4.4	Description: FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release URL: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release
flint	math	3.0.0	Description: FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. Homepage: http://www.flintlib.org/ URL: http://www.flintlib.org/ Keyword:math
fmlrc2	-	0.1.8	Description: FMLRC v2, based on the same methodology used by the original FMLRC. In benchmarks, the results between FMLRC v1 and v2 are nearly identical, but tests have shown that v2 uses approximately 50% of the run and CPU time compared to v1. Homepage: https://github.com/HudsonAlpha/fmlrc2 URL: https://github.com/HudsonAlpha/fmlrc2
fmm3d	-	1.0.4	Description: Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine. Homepage: https://fmm3d.readthedocs.io URL: https://fmm3d.readthedocs.io Compatible modules: python/3.11, python/3.10
fmriprep	-	23.0.2, 23.1.3	Description: fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI). Homepage: https://fmriprep.org/ URL: https://fmriprep.org/
fmt	-	5.3.0, 6.2.1, 7.0.3	Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/
fpc	tools	3.2.2	Description: Free Pascal is a mature, versatile, open source Pascal compiler. Homepage: https://www.freepascal.org URL: https://www.freepascal.org Keyword:tools
fplll	-	5.4.5	Description: fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name. Homepage: https://github.com/fplll/fplll URL: https://github.com/fplll/fplll
freebayes	bio	1.3.7	Description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Homepage: https://github.com/freebayes/freebayes URL: https://github.com/freebayes/freebayes Keyword:bio
freesurfer	bio	5.3.0	Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. Homepage: http://freesurfer.net/ URL: http://freesurfer.net/ Keyword:bio
freexl	tools	2.0.0	Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. Homepage: https://www.gaia-gis.it/fossil/freexl/index URL: https://www.gaia-gis.it/fossil/freexl/index Keyword:tools
fsl	bio	6.0.7.7	Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio
fsom	-	20151117	Description: A tiny C library for managing SOM (Self-Organizing Maps) neural networks. Homepage: https://github.com/ekg/fsom URL: https://github.com/ekg/fsom
g2clib	geo	1.6.0, 1.8.0	Description: This library contains C decoder/encoder routines for GRIB edition 2. This is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2c URL: https://github.com/NOAA-EMC/NCEPLIBS-g2c Keyword:geo
g2lib	geo	3.4.8	Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2/ URL: https://github.com/NOAA-EMC/NCEPLIBS-g2/ Keyword:geo
gamess-us	chem	20230930-R2	Documentation: GAMESS-US Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS-US is built with Intel compilers, mixed DDI, and OpenMPI 4.1. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem
gate	bio	9.3	Description: GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography Homepage: http://www.opengatecollaboration.org/ URL: http://www.opengatecollaboration.org/ Keyword:bio
gatk	bio	4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0	Description: 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. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio
gblocks	-	0.91b	Description: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Homepage: http://molevol.cmima.csic.es/castresana/Gblocks.html URL: http://molevol.cmima.csic.es/castresana/Gblocks.html
gcc	tools	8.4.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3, 13.3	Description: 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,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools
gd	-	2.77	Description: GD.pm - Interface to Gd Graphics Library Homepage: https://github.com/lstein/Perl-GD URL: https://github.com/lstein/Perl-GD Extensions: ExtUtils::PkgConfig-1.16, GD-2.77
gdal	geo	3.7.2, 3.9.1	Description: 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. Homepage: https://www.gdal.org/ URL: https://www.gdal.org/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12, python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12 Extensions: osgeo-3.9.1 Keyword:geo
gdrcopy	-	2.3.1, 2.4.1	Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy
geant4	phys	11.1.2	Description: 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. Homepage: https://geant4.web.cern.ch/ URL: https://geant4.web.cern.ch/ Keyword:phys
geant4-data	-	10.7.3, 11.1.0, 11.1.2	Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/
gemma	bio	0.98.5	Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio
gentoo	-	2020, 2023	Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix
geos	geo	3.12.0	Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: https://trac.osgeo.org/geos URL: https://trac.osgeo.org/geos Keyword:geo
git-annex	tools	8.20200810, 10.20221003, 10.20231129	Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools
git-lfs	-	2.11.0, 3.3.0, 3.4.0	Description: 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 Homepage: https://git-lfs.github.com URL: https://git-lfs.github.com
glew	-	2.2.0	Description: 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. Homepage: http://glew.sourceforge.net/ URL: http://glew.sourceforge.net/
glfw	-	3.3.2, 3.3.8	Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Extensions: glfw-2.6.2
glm	vis	0.9.9.8	Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm URL: https://github.com/g-truc/glm Keyword:vis
glost	tools	0.3.1	Description: This is GLOST, the Greedy Launcher Of Small Tasks. Homepage: https://github.com/cea-hpc/glost URL: https://github.com/cea-hpc/glost Keyword:tools
gmsh	phys	4.12.2, 4.13.1	Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys
gmt	geo	6.5.0	Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: https://www.generic-mapping-tools.org/ URL: https://www.generic-mapping-tools.org/ Keyword:geo
gnuplot	vis	5.2.8, 5.4.8	Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net URL: http://gnuplot.sourceforge.net Keyword:vis
go	tools	1.14.1, 1.18.3, 1.21.3	Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: https://www.golang.org URL: https://www.golang.org Keyword:tools
googlebenchmark	-	1.8.3	Description: Google's library to benchmark code snippets, similar to unit tests. Homepage: https://github.com/google/benchmark URL: https://github.com/google/benchmark
googletest	tools	1.14.0	Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools
gromacs	chem	2023.3, 2024.1	Documentation: GROMACS Description: 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. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem
gromacs-swaxs	chem	2021.7-0.5.1	Documentation: GROMACS Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem
gsl	math	2.6, 2.7	Description: 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. Homepage: https://www.gnu.org/software/gsl/ URL: https://www.gnu.org/software/gsl/ Keyword:math
gsl-lite	-	0.40.0, 0.41.0	Description: A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later Homepage: https://github.com/gsl-lite/gsl-lite URL: https://github.com/gsl-lite/gsl-lite
gurobi	math	9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0, 11.0.1	Description: The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. Homepage: https://www.gurobi.com URL: https://www.gurobi.com Keyword:math
hapgen2	-	2.2.0	Description: 'HAPGEN2' simulates case control datasets at SNP markers. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
haploview	-	4.2	Description: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Homepage: https://www.broadinstitute.org/haploview/haploview URL: https://www.broadinstitute.org/haploview/haploview
hdf	io	4.2.16	Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: https://www.hdfgroup.org/products/hdf4/ URL: https://www.hdfgroup.org/products/hdf4/ Keyword:io
hdf5	io	1.10.6, 1.14.2	Description: 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. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io
hdf5-mpi	io	1.10.6, 1.14.2, 1.14.4	Description: 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. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: blosc2-2.7.0, cached-property-1.5.2, h5py-3.11.0, ndindex-1.8, numexpr-2.10.1, py-cpuinfo-9.0.0, tables-3.9.2 Keyword:io
hdfview	-	2.14	Description: HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. Homepage: https://support.hdfgroup.org/products/java/hdfview/ URL: https://support.hdfgroup.org/products/java/hdfview/
healpix	-	3.82	Description: Hierarchical Equal Area isoLatitude Pixelation of a sphere. Homepage: http://healpix.sourceforge.net/ URL: http://healpix.sourceforge.net/
hh-suite	bio	3.3.0	Description: HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Homepage: https://github.com/soedinglab/hh-suite URL: https://github.com/soedinglab/hh-suite Keyword:bio
highfive	-	2.9.0	Description: HighFive is a modern header-only C++11 friendly interface for libhdf5. Homepage: https://github.com/BlueBrain/HighFive URL: https://github.com/BlueBrain/HighFive
hisat2	bio	2.2.1	Description: 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). Homepage: https://daehwankimlab.github.io/hisat2/ URL: https://daehwankimlab.github.io/hisat2/ Keyword:bio
hmmer	bio	3.4	Description: 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. Homepage: http://hmmer.org/ URL: http://hmmer.org/ Keyword:bio
htslib	bio	1.18, 1.19	Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio
hwloc	-	2.4.0, 2.7.1, 2.9.1, 2.10.0	Description: 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. Homepage: https://www.open-mpi.org/projects/hwloc/ URL: https://www.open-mpi.org/projects/hwloc/
igblast	bio	1.17.0, 1.18.0	Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html URL: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio
igraph	math	0.10.7	Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: https://igraph.org URL: https://igraph.org Compatible modules: python/3.10, python/3.11 Extensions: python-igraph-0.11.2 Keyword:math
igv	-	2.9.2	Description: This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. Homepage: https://www.broadinstitute.org/software/igv/ URL: https://www.broadinstitute.org/software/igv/
imb	-	2021.3	Description: The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes Homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks
imkl	math	2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0, 2023.2.0, 2024.1.0	Description: Intel oneAPI Math Kernel Library Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html Keyword:math
impute2	bio	2.3.2	Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html URL: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio
impute5	-	1.1.5	Description: IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1 Homepage: https://jmarchini.org/software/#impute-5 URL: https://jmarchini.org/software/#impute-5
infernal	bio	1.1.5	Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ URL: http://eddylab.org/infernal/ Keyword:bio
intel	tools	2020.1.217, 2021.2.0, 2022.1.0, 2023.2.1	Description: Intel C, C++ and Fortran compilers (classic and oneAPI) Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html Keyword:tools
intel-opencl	-	2021.2.0	Description: Intel's OpenCL CPU runtime Homepage: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html URL: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html
intelmpi	mpi	2021.9.0	Description: Intel MPI Library, compatible with MPICH ABI Homepage: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html URL: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html
intelxed	-	12.0.1	Description: The X86 Encoder Decoder (XED), is a software library (and associated headers) for encoding and decoding X86 (IA32 and Intel64) instructions. Homepage: https://intelxed.github.io/ URL: https://intelxed.github.io/
interproscan	bio	5.52-86.0, 5.50-84.0, 5.64-96.0, 5.53-87.0, 5.55-88.0, 5.63-95.0, 5.56-89.0	Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio
interproscan_data	-	5.64-96.0, 5.63-95.0	Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/
intervaltree	-	0.1	Description: 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. Homepage: https://github.com/ekg/intervaltree URL: https://github.com/ekg/intervaltree
ipopt	-	3.14.14	Description: IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. Homepage: https://projects.coin-or.org/Ipopt URL: https://projects.coin-or.org/Ipopt
ipp	tools	2020.1.217	Description: Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. Homepage: https://software.intel.com/en-us/articles/intel-ipp/ URL: https://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools
ipykernel	-	2020a, 2020b, 2021a, 2022a, 2023a, 2023b, 2024a	Description: Bundle which contains ipykernel 2024a and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: asttokens-2.4.1, comm-0.2.2, debugpy-1.8.1, decorator-5.1.1, executing-2.0.1, ipykernel-6.29.4, ipython-8.25.0, jedi-0.19.1, jupyter_client-8.6.2, jupyter_core-5.7.2, matplotlib_inline-0.1.7, nest_asyncio-1.6.0, packaging-24.1, parso-0.8.4, pexpect-4.9.0, platformdirs-3.9.1, prompt_toolkit-3.0.47, psutil-5.9.8, ptyprocess-0.7.0, pure_eval-0.2.2, pygments-2.18.0, python_dateutil-2.9.0.post0, pyzmq-26.0.3, six-1.16.0, stack_data-0.6.3, tornado-6.3.3, traitlets-5.14.3, wcwidth-0.2.13
ipython-kernel	-	2.7, 3.9, 3.10, 3.11, 3.12	Description: IPython kernelspec for Python 3.12 Homepage: https://ipython.org/ URL: https://ipython.org/
iq-tree	bio	2.0.7	Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio
ispc	-	1.10.0, 1.13.0, 1.18.0, 1.21.1	Description: Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. Homepage: https://ispc.github.io/ , https://github.com/ispc/ispc/ URL: https://ispc.github.io/ , https://github.com/ispc/ispc/
itac	tools	2021.5.0	Description: The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. Homepage: https://software.intel.com/en-us/intel-trace-analyzer/ URL: https://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools
itk	vis	5.3.0	Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.11, python/3.10 Keyword:vis
ivar	-	1.4.2	Description: iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Homepage: https://github.com/andersen-lab/ivar URL: https://github.com/andersen-lab/ivar
jags	math	4.3.2	Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation Homepage: http://mcmc-jags.sourceforge.net/ URL: http://mcmc-jags.sourceforge.net/ Keyword:math
jasper	vis	2.0.16, 4.0.0	Description: 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. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis
java	tools	1.8.0_192, 11.0.16_8, 1.8.0_292, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1	Documentation: Java Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools
jbigkit	-	2.1	Description: 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. Homepage: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ URL: https://www.cl.cam.ac.uk/~mgk25/jbigkit/
jemalloc	-	5.3.0	Description: jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. Homepage: http://jemalloc.net URL: http://jemalloc.net
jsoncpp	-	1.9.5	Description: 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. Homepage: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html URL: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html
judy	-	1.0.5	Description: A C library that implements a dynamic array. Homepage: http://judy.sourceforge.net/ URL: http://judy.sourceforge.net/
julia	tools	1.9.3, 1.10.0	Description: Julia is a high-level, high-performance dynamic programming language for numerical computing Homepage: https://julialang.org URL: https://julialang.org Keyword:tools
kahip	-	3.14, 3.16	Description: The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. Homepage: https://kahip.github.io/ URL: https://kahip.github.io/
kaiju	bio	1.10.1	Description: Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Homepage: http://kaiju.binf.ku.dk/ URL: http://kaiju.binf.ku.dk/ Keyword:bio
kalign	-	3.3.5	Description: Kalign is a fast multiple sequence alignment program for biological sequences. Homepage: https://github.com/TimoLassmann/kalign URL: https://github.com/TimoLassmann/kalign
kim-api	chem	2.3.0	Description: 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. Homepage: https://openkim.org/ URL: https://openkim.org/ Keyword:chem
kma	-	1.3.0, 1.4.14	Description: KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. Homepage: https://bitbucket.org/genomicepidemiology/kma URL: https://bitbucket.org/genomicepidemiology/kma
lammps-omp	chem	20230802	Documentation: LAMMPS Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Homepage: https://www.lammps.org URL: https://www.lammps.org Compatible modules: python/3.11, python/3.10 Keyword:chem
ldc	-	0.17.6	Description: The LLVM-based D Compiler Homepage: https://wiki.dlang.org/LDC URL: https://wiki.dlang.org/LDC
lerc	-	4.0.0	Description: 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). Homepage: https://github.com/Esri/lerc URL: https://github.com/Esri/lerc
libaec	-	1.0.6	Description: 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. Homepage: https://gitlab.dkrz.de/k202009/libaec URL: https://gitlab.dkrz.de/k202009/libaec
libbeef	-	0.1.2	Description: BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. Homepage: https://github.com/vossjo/libbeef URL: https://github.com/vossjo/libbeef
libcdms	-	3.1.2	Description: Climate Data Management System Library. Homepage: https://github.com/CDAT/libcdms/ URL: https://github.com/CDAT/libcdms/
libcerf	math	1.13, 2.4	Description: 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. Homepage: https://jugit.fz-juelich.de/mlz/libcerf URL: https://jugit.fz-juelich.de/mlz/libcerf Keyword:math
libdap	-	3.20.11	Description: A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. Homepage: https://www.opendap.org/software/libdap URL: https://www.opendap.org/software/libdap
libdrs	-	3.1.2	Description: PCMDI's old DRS format implementation Homepage: https://github.com/CDAT/libdrs/ URL: https://github.com/CDAT/libdrs/
libfabric	-	1.10.1, 1.18.0, 1.21.0	Description: 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. Homepage: https://ofiwg.github.io/libfabric/ URL: https://ofiwg.github.io/libfabric/
libfdf	-	0.2.2	Description: LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF). Homepage: https://launchpad.net/libfdf URL: https://launchpad.net/libfdf
libffi	-	3.3	Description: 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. Homepage: https://sourceware.org/libffi/ URL: https://sourceware.org/libffi/
libgd	vis	2.3.0	Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/ URL: https://libgd.github.io/ Keyword:vis
libgeotiff	-	1.7.1	Description: Library for reading and writing coordinate system information from/to GeoTIFF files Homepage: https://directory.fsf.org/wiki/Libgeotiff URL: https://directory.fsf.org/wiki/Libgeotiff
libpsml	-	1.1.12	Description: A library to handle pseudopotentials in PSML format Homepage: https://gitlab.com/siesta-project/libraries/libpsml URL: https://gitlab.com/siesta-project/libraries/libpsml
libraw	-	0.21.2	Description: The LibRaw library provides a simple and unified interface for extracting out of RAW files generated by digital photo cameras the following: - RAW data (pixel values) - Metadata necessary for processing RAW (geometry, CFA / Bayer pattern, black level, white balance, etc.) - Embedded preview / thumbnail. Homepage: https://www.libraw.org/ URL: https://www.libraw.org/
librttopo	-	1.1.0	Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo
libspatialindex	phys	1.9.3	Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: https://libspatialindex.org URL: https://libspatialindex.org Keyword:phys
libspatialite	phys	5.1.0	Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home URL: https://www.gaia-gis.it/fossil/libspatialite/home Keyword:phys
libxc	chem	4.3.4, 6.2.2	Description: 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. Homepage: https://libxc.gitlab.io URL: https://libxc.gitlab.io Keyword:chem
libyaml	-	0.2.5	Description: LibYAML is a YAML parser and emitter written in C. Homepage: https://pyyaml.org/wiki/LibYAML URL: https://pyyaml.org/wiki/LibYAML
links	bio	2.0.1	Description: LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer). Homepage: http://www.bcgsc.ca/platform/bioinfo/software/links URL: http://www.bcgsc.ca/platform/bioinfo/software/links Keyword:bio
lldb	-	11.0.0	Description: The debugger component of the LLVM project Homepage: https://lldb.llvm.org/ URL: https://lldb.llvm.org/
llvm	tools	8.0.1, 9.0.1, 14.0.3, 16.0.6	Description: 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. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools
lmdb	-	0.9.31	Description: 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. Homepage: https://symas.com/lmdb URL: https://symas.com/lmdb
ls-opt	phys	7.0.0	Description: LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. Homepage: http://www.lstc.com/products/ls-opt URL: http://www.lstc.com/products/ls-opt Keyword:phys
ls-prepost	-	4.8.11, 4.9.9	Description: LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. Homepage: http://lstc.com/products/ls-prepost URL: http://lstc.com/products/ls-prepost
lsd2	-	2.4.1	Description: Least-squares methods to estimate rates and dates from phylogenies Homepage: https://github.com/tothuhien/lsd2 URL: https://github.com/tothuhien/lsd2
maeparser	chem	1.2.4	Description: maeparser is a parser for Schrodinger Maestro files. Homepage: https://github.com/schrodinger/maeparser URL: https://github.com/schrodinger/maeparser Keyword:chem
magma	math	2.7.2	Description: 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. Homepage: https://icl.cs.utk.edu/magma/ URL: https://icl.cs.utk.edu/magma/ Keyword:math
mariadb	tools	11.5.0	Description: MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. Homepage: https://mariadb.org/ URL: https://mariadb.org/ Compatible modules: Extensions: DBD::mysql-5.004, Devel::CheckLib-1.16, IO::CaptureOutput-1.1105, mysql-connector-python-8.2.0, PyMySQL-1.1.0 Keyword:tools
mariadb-connector-c	-	3.1.7, 3.3.7	Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/ URL: https://downloads.mariadb.org/connector-c/
matio	io	1.5.26	Description: matio is an C library for reading and writing Matlab MAT files. Homepage: https://sourceforge.net/projects/matio/ URL: https://sourceforge.net/projects/matio/ Keyword:io
matlab	tools	2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2	Documentation: MATLAB Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools
maven	tools	3.6.3, 3.9.6	Description: 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. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools
mcr	tools	R2022b, R2021b, R2020b	Documentation: MATLAB Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ URL: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools
mctc-lib	-	0.3.1	Description: Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats. Homepage: https://grimme-lab.github.io/mctc-lib URL: https://grimme-lab.github.io/mctc-lib
meta-farm	-	1.0.2	Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.computecanada.ca/wiki/META_package_for_serial_farming URL: https://docs.computecanada.ca/wiki/META_package_for_serial_farming
metabat	bio	2.12.1, 2.17	Description: An efficient tool for accurately reconstructing single genomes from complex microbial communities Homepage: https://bitbucket.org/berkeleylab/metabat URL: https://bitbucket.org/berkeleylab/metabat Keyword:bio
metageneannotator	-	20080819	Description: MetaGeneAnnotator is a gene-finding program for prokaryote and phage. Homepage: http://metagene.nig.ac.jp/ URL: http://metagene.nig.ac.jp/
metis	math	5.1.0	Description: 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. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math
metis-64idx	-	5.1.0	Description: 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. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
mii	-	1.1.1, 1.1.2	Description: A smart search engine for module environments. Homepage: https://github.com/codeandkey/mii URL: https://github.com/codeandkey/mii
minc-toolkit	bio	1.9.18.3	Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/ URL: http://bic-mni.github.io/ Keyword:bio
miniasm	bio	0.3-20191007	Description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio
minimap2	bio	2.26, 2.28	Description: 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. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio
mixcr	bio	4.1.2	Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html URL: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio
mmseqs2	-	15-6f452	Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com
modflow	-	6.5.0	Description: MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions. Homepage: https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs URL: https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs
mpi4py	tools	3.0.3, 3.1.3, 3.1.4, 3.1.6	Description: 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. Homepage: https://bitbucket.org/mpi4py/mpi4py URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:tools
mrbayes	bio	3.2.7	Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Homepage: https://nbisweden.github.io/MrBayes/ URL: https://nbisweden.github.io/MrBayes/ Keyword:bio
mrcc	-	20230828	Description: MRCC is a suite of ab initio and density functional quantum chemistry programs for high-accuracy electronic structure calculations developed and maintained by the quantum chemistry research group at the Department of Physical Chemistry and Materials Science, TU Budapest. Its special feature, the use of automated programming tools enabled the development of tensor manipulation routines which are independent of the number of indices of the corresponding tensors, thus significantly simplifying the general implementation of quantum chemical methods. Homepage: https://www.mrcc.hu/index.php URL: https://www.mrcc.hu/index.php
mstore	-	0.2.0	Description: Molecular structure store for testing Homepage: https://github.com/grimme-lab/mstore URL: https://github.com/grimme-lab/mstore
mujoco	-	3.0.1, 3.1.6	Description: 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. Homepage: https://mujoco.org/ URL: https://mujoco.org/ Compatible modules: python/3.10, python/3.11 Extensions: mujoco-3.1.6
multichoose	-	1.0.3	Description: generate multiset combinations (n multichoose k). Homepage: https://github.com/ekg/multichoose URL: https://github.com/ekg/multichoose
muparserx	-	4.0.12	Description: A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more. Homepage: beltoforion.de/en/muparserx URL: beltoforion.de/en/muparserx
mysql	tools	8.3.0	Description: MySQL is one of the world's most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ URL: http://www.mysql.com/ Keyword:tools
namd-multicore	chem	2.14	Documentation: NAMD Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ URL: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem
nanoflann	-	1.3.2	Description: nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies Homepage: https://github.com/jlblancoc/nanoflann URL: https://github.com/jlblancoc/nanoflann
nccl	tools	2.7.8, 2.8.4, 2.11.4, 2.18.3	Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools
ncl	vis	6.6.2	Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: https://www.ncl.ucar.edu URL: https://www.ncl.ucar.edu Keyword:vis
nco	io	5.1.7	Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: https://nco.sourceforge.net URL: https://nco.sourceforge.net Keyword:io
ncview	vis	2.1.8	Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html URL: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis
netcdf	io	4.7.4, 4.9.2	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io
netcdf-c++4	io	4.3.1	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-c++4-mpi	io	4.3.1	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-fortran	io	4.6.1	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-fortran-mpi	io	4.6.1	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-mpi	io	4.7.4, 4.9.2	Description: 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. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io
nextflow	-	20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3, 23.10.0	Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/
nextgenmap	bio	0.5.5	Description: NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. Homepage: http://cibiv.github.io/NextGenMap/ URL: http://cibiv.github.io/NextGenMap/ Keyword:bio
nextstrain.cli	-	3.1.0	Description: This is the source code repository for a program called nextstrain, the Nextstrain command-line interface (CLI). It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch. Homepage: https://github.com/nextstrain/cli/tree/3.1.0 URL: https://github.com/nextstrain/cli/tree/3.1.0
nibabel	-	5.2.0	Description: 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. Homepage: https://nipy.github.io/nibabel URL: https://nipy.github.io/nibabel Compatible modules: python/3.10, python/3.11 Extensions: bz2file-0.98, nibabel-5.2.0, pydicom-2.4.4
ninja-phylogenetics	-	0.97-cluster_only	Description: Nearly Infinite Neighbor Joining Application Compute correct neighbor-joining phylogenies for inputs of more than 10,000 sequences. This is a C++/SSE port of the original Java code described in: Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin. (LNCS webpage,preprint) The Java version of NINJA was the fastest available tool computing neighbor-joining phylogenies ( 10x faster than the fastest implemenation of the canonical neighbor-joining algorithm - QuickTree ) at the time of it's release. In addition to generating phylogenies, Ninja can be used to output pairwise distances using several common sequence distance measures, and cluster sequences using a nearest-neighbor approach. Homepage: https://github.com/TravisWheelerLab/NINJA URL: https://github.com/TravisWheelerLab/NINJA
nlopt	math	2.7.1	Description: 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. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Keyword:math
nodejs	tools	18.17.1	Description: 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. Homepage: https://nodejs.org URL: https://nodejs.org Keyword:tools
nspr	-	4.25	Description: Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR
nss	-	3.51	Description: Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS
ntl	math	11.4.3	Description: 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. Homepage: http://www.shoup.net/ntl/ URL: http://www.shoup.net/ntl/ Keyword:math
nvhpc	tools	20.7, 22.1, 22.7, 23.7, 23.9	Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/
occt	-	7.7.1	Description: Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. Homepage: https://www.opencascade.com/ URL: https://www.opencascade.com/
octave	tools	7.2.0	Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: https://www.gnu.org/software/octave/ URL: https://www.gnu.org/software/octave/ Extensions: control-3.5.0, general-2.1.3, io-2.6.4, optim-1.6.2, signal-1.4.5, statistics-1.4.3, struct-1.0.18 Keyword:tools
openbabel	chem	3.1.1	Description: 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. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem
openbabel-omp	chem	3.1.1	Description: 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. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem
openblas	math	0.3.17, 0.3.24	Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://www.openblas.net/ URL: http://www.openblas.net/ Keyword:math
opencoarrays	-	2.9.2	Description: OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran. Homepage: https://github.com/sourceryinstitute/opencoarrays URL: https://github.com/sourceryinstitute/opencoarrays
opencolorio	vis	2.3.0	Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ URL: http://opencolorio.org/ Compatible modules: python/3.11, python/3.10 Keyword:vis
opencv	vis	4.8.1, 4.9.0, 4.10.0	Description: 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. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:vis
openexr	vis	2.5.2	Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: https://www.openexr.com/ URL: https://www.openexr.com/ Keyword:vis
openfoam	phys	8, 11, v2012, v2306, v2312	Documentation: OpenFOAM Description: 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. Homepage: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys
openimagedenoise	-	2.0.1, 2.1.0	Description: Intel Open Image Denoise is an open source library of high-performance, high-quality denoising filters for images rendered with ray tracing. Homepage: https://github.com/OpenImageDenoise/oidn URL: https://github.com/OpenImageDenoise/oidn
openimageio	vis	2.1.17.0, 2.4.14.0	Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: https://openimageio.org/ URL: https://openimageio.org/ Compatible modules: python/3.10, python/3.11 Keyword:vis
openmc	-	0.15.0	Description: OpenMC is a community-developed Monte Carlo neutron and photon transport simulation code. It is capable of performing fixed source, k-eigenvalue, and subcritical multiplication calculations on models built using either a constructive solid geometry or CAD representation. OpenMC supports both continuous-energy and multigroup transport. The continuous-energy particle interaction data is based on a native HDF5 format that can be generated from ACE files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP programming model. Homepage: https://docs.openmc.org/en/stable/ URL: https://docs.openmc.org/en/stable/ Compatible modules: python/3.10, python/3.11, python/3.12
openmm	chem	8.0.0, 8.1.1	Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.10, python/3.11 Extensions: pdbfixer-1.9 Keyword:chem
openmpi	mpi	4.0.3, 4.1.5, 5.0.3	Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi
openrefine	-	3.4.1	Description: OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. Homepage: https://github.com/OpenRefine/OpenRefine URL: https://github.com/OpenRefine/OpenRefine
openslide	vis	4.0.0	Description: C library for reading virtual slide images Homepage: https://github.com/openslide/openslide URL: https://github.com/openslide/openslide Keyword:vis
openvdb	-	7.0.0, 10.1.0	Description: OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. Homepage: https://github.com/AcademySoftwareFoundation/openvdb URL: https://github.com/AcademySoftwareFoundation/openvdb
openvkl	-	0.10.0, 1.3.2	Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKL's performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl
optix	-	6.5.0, 7.7.0, 8.0.0	Description: 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. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix
orad	-	2.6.1	Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html URL: https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html
orthomcl	bio	2.0.9	Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ URL: http://orthomcl.org/ Keyword:bio
ospray	-	1.8.5, 2.12.0	Description: Intel OSPRay is an open source, scalable, and portable ray tracing engine for high-performance, high-fidelity visualization on Intel Architecture CPUs. Homepage: https://github.com/ospray/ospray URL: https://github.com/ospray/ospray
osu-micro-benchmarks	tools	7.1-1, 7.2	Description: OSU Micro-Benchmarks Homepage: https://mvapich.cse.ohio-state.edu/benchmarks/ URL: https://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools
ovito	-	3.3.3	Description: OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes. The program is freely available for all major platforms under an open source license. It has served in a growing number of computational simulation studies as a powerful tool to analyze, understand and illustrate simulation results. Homepage: https://www.ovito.org URL: https://www.ovito.org
paml	bio	4.10.7	Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio
panther	-	14.1	Description: Panther is the database part of InterProScan software. It contains only data. Homepage: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/ URL: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/
parasail	-	2.6.2	Description: parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. Homepage: https://github.com/jeffdaily/parasail URL: https://github.com/jeffdaily/parasail Compatible modules: python/3.10, python/3.11 Extensions: parasail-1.3.4
paraview	vis	5.8.0, 5.11.2	Documentation: Visualization Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.10, python/3.11 Keyword:vis
parmetis	math	4.0.3	Description: 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. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math
pcre2	-	10.34	Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/
pdal	-	2.7.1	Description: PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications for translating and processing point cloud data. It is not limited to LiDAR data, although the focus and impetus for many of the tools in the library have their origins in LiDAR. Homepage: https://pdal.io/ URL: https://pdal.io/
perl	tools	5.30.2, 5.36.1	Documentation: Perl Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Carp-1.50, constant-1.33, Data::Dumper-2.183, Exporter-5.77, File::Path-2.18, File::Spec-3.75, Getopt::Long-2.54, IO::File-1.51, Text::ParseWords-3.31, Thread::Queue-3.13, threads-2.21 Keyword:tools
petsc	tools	3.20.0	Description: 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. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools
petsc-complex	tools	3.20.0	Description: 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. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools
pflotran	-	5.0.0	Description: PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. Homepage: https://www.pflotran.org/ URL: https://www.pflotran.org/
photospline	-	2.2.1	Description: Detector response to a high-energy physics process is often estimated by Monte Carlo simulation. For purposes of data analysis, the results of this simulation are typically stored in large multi-dimensional histograms, which can quickly become unwieldy in terms of size or numerically problematic due to unfilled bins or interpolation artifacts. Photospline is a library that uses the penalized spline technique to efficiently compute, store, and evaluate B-spline representations of such tables. Homepage: https://github.com/icecube/photospline URL: https://github.com/icecube/photospline
picard	bio	2.23.3, 2.26.3, 3.1.0	Description: A set of tools (in Java) for working with next generation sequencing data in the BAM format. Homepage: https://broadinstitute.github.io/picard/ URL: https://broadinstitute.github.io/picard/ Keyword:bio
pilercr	-	1.06	Description: PILERCR is public domain software for finding CRISPR repeats. It is part of the PILER family of repeat analysis tools. Homepage: https://www.drive5.com/pilercr/ URL: https://www.drive5.com/pilercr/
pilon	bio	1.23, 1.24	Description: Pilon is an automated genome assembly improvement and variant detection tool Homepage: https://github.com/broadinstitute/pilon URL: https://github.com/broadinstitute/pilon Keyword:bio
plink	bio	1.9b_6.21-x86_64, 2.00-20231024-avx2, 2.00a5.8, 2.00-10252019-avx2	Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio
plumed	chem	2.8.3, 2.9.0	Description: 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. Homepage: https://www.plumed.org URL: https://www.plumed.org Compatible modules: python/3.10, python/3.11 Extensions: plumed-2.9.0 Keyword:chem
pmix	-	4.2.4, 5.0.2	Description: 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. Homepage: https://pmix.org/ URL: https://pmix.org/
pnetcdf	io	1.12.3	Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf URL: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io
podman	-	4.1.1, 4.5.0, 4.9.5	Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io
postgresql	tools	16.0	Description: 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. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Compatible modules: python/3.10, python/3.11 Extensions: psycopg2-2.9.9 Keyword:tools
pov-ray	-	3.7.0.10	Description: 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. Homepage: https://www.povray.org/ URL: https://www.povray.org/
pplacer	bio	1.1.alpha19	Description: 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. Homepage: http://matsen.fhcrc.org/pplacer/ URL: http://matsen.fhcrc.org/pplacer/ Keyword:bio
primme	-	3.2	Description: PRIMME, pronounced as prime, is a high-performance library for computing a few eigenvalues/eigenvectors, and singular values/vectors. PRIMME is especially optimized for large, difficult problems. Real symmetric and complex Hermitian problems, standard A x = \lambda x and generalized A x = \lambda B x, are supported. Besides, standard eigenvalue problems with a normal matrix are supported. It can find largest, smallest, or interior singular/eigenvalues, and can use preconditioning to accelerate convergence. Homepage: http://www.cs.wm.edu/~andreas/software/ URL: http://www.cs.wm.edu/~andreas/software/
prinseq	bio	0.20.4	Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net URL: http://prinseq.sourceforge.net Extensions: Cairo-1.109, Contextual::Return-0.2.1, ExtUtils::Depends-0.8001, ExtUtils::PkgConfig-1.16, Math::Cephes::Matrix-0.5305, Math::MatrixReal-2.13, MIME::Base64-3.15, Pod::Usage-2.0, Statistics::PCA-0.0.1, Text::SimpleTable-2.07 Keyword:bio
prodigal	bio	2.6.3	Description: 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. Homepage: https://github.com/hyattpd/Prodigal/ URL: https://github.com/hyattpd/Prodigal/ Keyword:bio
proj	geo	9.2.0, 9.4.1	Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org URL: https://proj.org Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: pyproj-3.6.1 Keyword:geo
protobuf	tools	24.4	Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Keyword:tools
prrte	-	3.0.5	Description: PRRTE is the PMIx Reference RunTime Environment Homepage: https://docs.prrte.org/ URL: https://docs.prrte.org/
psi4	chem	1.9	Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ URL: http://www.psicode.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem
pullseq	-	1.0.2	Description: Utility program for extracting sequences from a fasta/fastq file Homepage: https://github.com/bcthomas/pullseq URL: https://github.com/bcthomas/pullseq
pypy	tools	5.8.0, 7.3.3	Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html URL: https://pypy.org/index.html Keyword:tools
pytest	-	6.1.2, 6.2.5, 7.0.1, 7.4.0, 8.2.2	Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: iniconfig-2.0.0, packaging-24.1, pluggy-1.5.0, pytest-8.2.2
python	tools	2.7.18, 3.6.10, 3.7.7, 3.7.9, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.10.13, 3.11.2, 3.11.5, 3.12.4	Documentation: Python Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: https://python.org/ URL: https://python.org/ Extensions: distlib-0.3.8, filelock-3.13.4, flit_core-3.9.0, hatch_vcs-0.4.0, hatchling-1.24.2, packaging-24.0, pathspec-0.12.1, pip-24.0, platformdirs-4.2.0, pluggy-1.5.0, setuptools-70.0.0, setuptools-scm-8.0.4, tomli-2.0.1, trove-classifiers-2024.4.10, typing_extensions-4.12.1, virtualenv-20.26.2, wheel-0.43.0 Keyword:tools
python-build-bundle	-	2022a, 2023a, 2023b, 2024a	Description: Bundle which contains Python packages useful for building Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.12, python/3.11, python/3.10 Extensions: archspec-0.2.4, build-1.2.1, cachecontrol-0.14.0, cachy-0.3.0, certifi-2024.6.2, cffi-1.16.0, charset-normalizer-3.3.2, cleo-2.1.0, clikit-0.6.2, crashtest-0.4.1, cryptography-42.0.8, distlib-0.3.8, distro-1.9.0, editables-0.5, exceptiongroup-1.2.1, filelock-3.14.0, flit-core-3.9.0, flit-scm-1.7.0, hatch_fancy_pypi_readme-24.1.0, hatch_vcs-0.4.0, hatchling-1.24.2, idna-3.7, importlib_metadata-7.1.0, importlib_resources-6.4.0, jeepney-0.8.0, keyring-25.2.1, keyrings.alt-5.0.1, meson-1.4.1, meson_python-0.16.0, msgpack-1.0.8, ninja-1.11.1.1, packaging-24.1, pastel-0.2.1, pathspec-0.12.1, pbr-6.0.0, pexpect-4.9.0, pkginfo-1.11.1, platformdirs-4.2.2, poetry-1.8.3, poetry_core-1.9.0, ptyprocess-0.7.0, pybind11-2.12.0, pycparser-2.22, pylev-1.4.0, pyparsing-3.1.2, pyproject_hooks-1.1.0, pyproject_metadata-0.8.0, pytoml-0.1.21, requests-2.32.3, requests-toolbelt-1.0.0, scikit_build-0.17.6, scikit_build_core-0.9.5, SecretStorage-3.3.3, semantic_version-2.10.0, setuptools-70.0.0, setuptools-rust-1.9.0, setuptools_scm-8.1.0, shellingham-1.5.4, toml-0.10.2, tomli-2.0.1, tomlkit-0.12.5, trove_classifiers-2024.5.22, typing_extensions-4.12.2, urllib3-2.2.1, virtualenv-20.26.2, webencodings-0.5.1, wheel-0.43.0, zipp-3.19.2
q6	-	6.0	Description: Q is a set of Molecular Dynamics (MD) tools tailored to the following specific kinds of free energy calculations: Free Energy Perturbation (FEP) Empirical Valence Bond (EVB) Linear Interaction Energies (LIE) Quantum Classical Path (QCP) Homepage: https://github.com/qusers/Q6 URL: https://github.com/qusers/Q6
qca	geo	2.3.7	Description: 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. Homepage: https://userbase.kde.org/QCA URL: https://userbase.kde.org/QCA Keyword:geo
qcint	-	6.1.2	Description: libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. Homepage: http://wiki.sunqm.net/libcint URL: http://wiki.sunqm.net/libcint
qgis	geo	3.28.12	Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/ URL: http://www.qgis.org/ Compatible modules: python/3.11, python/3.10 Extensions: OWSLib-0.29.3, psycopg2-2.9.9, PyYAML-6.0.1 Keyword:geo
qhull	math	2020.2	Description: 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. Homepage: http://www.qhull.org URL: http://www.qhull.org Keyword:math
qiime2	-	2021.11, 2023.5, 2024.5	Description: QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Homepage: http://qiime2.org/ URL: http://qiime2.org/
qrupdate	math	1.1.2	Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ URL: https://sourceforge.net/projects/qrupdate/ Keyword:math
qscintilla	tools	2.14.1	Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla URL: https://www.riverbankcomputing.com/software/qscintilla Compatible modules: python/3.10, python/3.11 Keyword:tools
qt	tools	5.12.8, 5.15.11	Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/3.10, python/3.11 Extensions: ply-3.11, PyQt-builder-1.15.3, PyQt5-5.15.10, PyQt5_sip-12.13.0, PyQtWebEngine-5.15.6, SIP-6.7.12, toml-0.10.2 Keyword:tools
qtkeychain	-	0.14.1	Description: Platform-independent Qt API for storing passwords securely. Homepage: https://github.com/frankosterfeld/qtkeychain URL: https://github.com/frankosterfeld/qtkeychain
quantumatk	-	2019.12	Description: QuantumATK is a complete atomistic simulation toolkit. QuantumATK addresses key applications in the semiconductor industry and is a core component of the Synopsys Design-Technology Co-Optimization (DTCO) solution. Atomic-scale modeling tools in QuantumATK range from classical force fields for handling large and to some extent more realistic materials systems to ab initio tools that provide highly accurate results for smaller systems. Homepage: https://www.synopsys.com/silicon/quantumatk.html URL: https://www.synopsys.com/silicon/quantumatk.html
quantumespresso	chem	6.6, 7.3.1	Documentation: Quantum ESPRESSO Description: 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). Homepage: https://www.quantum-espresso.org URL: https://www.quantum-espresso.org Keyword:chem
qwt	tools	6.2.0	Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/ URL: http://qwt.sourceforge.net/ Keyword:tools
r	tools	4.1.0, 4.2.1, 4.3.1, 4.4.0	Documentation: R Description: R is a free software environment for statistical computing and graphics. Homepage: https://www.r-project.org/ URL: https://www.r-project.org/ Keyword:tools
r-bundle-bioconductor	bio	3.18	Description: Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. Homepage: https://bioconductor.org URL: https://bioconductor.org Extensions: abind-1.4-5, ade4-1.7-22, admisc-0.34, affxparser-1.74.0, affy-1.80.0, affycoretools-1.74.0, affyio-1.72.0, AgiMicroRna-2.52.0, agricolae-1.3-7, ALDEx2-1.34.0, AlgDesign-1.2.1, ALL-1.44.0, annaffy-1.74.0, annotate-1.80.0, AnnotationDbi-1.64.1, AnnotationFilter-1.26.0, AnnotationForge-1.44.0, AnnotationHub-3.10.0, anytime-0.3.9, aod-1.3.3, ape-5.7-1, aroma.affymetrix-3.2.1, aroma.apd-0.7.0, aroma.core-3.3.0, aroma.light-3.32.0, ash-1.0-15, askpass-1.2.0, assertthat-0.2.1, ATACseqQC-1.26.0, aws-2.5-3, aws.s3-0.3.21, aws.signature-0.6.0, awsMethods-1.1-1, backports-1.4.1, ballgown-2.34.0, base64-2.0.1, base64enc-0.1-3, basilisk-1.14.1, basilisk.utils-1.14.1, batchelor-1.18.1, baySeq-2.36.0, BBmisc-1.13, beachmat-2.18.0, beanplot-1.3.1, beeswarm-0.4.0, BH-1.81.0-1, BiasedUrn-2.0.11, Biobase-2.62.0, BiocBaseUtils-1.4.0, BiocFileCache-2.10.1, BiocGenerics-0.48.1, BiocIO-1.12.0, BiocManager-1.30.22, BiocNeighbors-1.20.2, BiocParallel-1.36.0, BiocSingular-1.18.0, BiocStyle-2.30.0, BiocVersion-3.18.1, biomaRt-2.58.0, biomformat-1.30.0, Biostrings-2.70.1, biovizBase-1.50.0, bit-4.0.5, bit64-4.0.5, bitops-1.0-7, blme-1.0-5, blob-1.2.4, bluster-1.12.0, bookdown-0.37, boot-1.3-28.1, brio-1.1.4, broom-1.0.5, broom.helpers-1.14.0, BSgenome-1.70.1, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bslib-0.6.1, bumphunter-1.44.0, ca-0.71.1, cachem-1.0.8, Cairo-1.6-2, calibrate-1.7.7, callr-3.7.3, CAMERA-1.58.0, car-3.1-2, carData-3.0-5, caret-6.0-94, Category-2.68.0, caTools-1.18.2, ccdata-1.28.0, ccmap-1.28.0, cellranger-1.1.0, CGHbase-1.62.0, checkmate-2.3.1, ChIPpeakAnno-3.36.0, circlize-0.4.15, class-7.3-22, classInt-0.4-10, cli-3.6.2, clipr-0.8.0, clock-0.7.0, clue-0.3-65, cluster-2.1.6, CNEr-1.38.0, coda-0.19-4, codetools-0.2-19, coloc-5.2.3, colorRamps-2.3.1, colorspace-2.1-0, 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rrcov-1.7-4, Rsamtools-2.18.0, Rsolnp-1.16, RSpectra-0.16-1, RSQLite-2.3.4, rstatix-0.7.2, rstudioapi-0.15.0, Rsubread-2.16.0, rsvd-1.0.5, rtracklayer-1.62.0, Rtsne-0.17, ruv-0.9.7.1, S4Arrays-1.2.0, S4Vectors-0.40.2, sampling-2.10, samr-3.0, sandwich-3.1-0, sass-0.4.8, SC3-1.30.0, ScaledMatrix-1.10.0, scales-1.3.0, SCANVIS-1.16.0, scater-1.30.1, scattermore-1.2, scran-1.30.0, scrime-1.3.5, sctransform-0.4.1, scuttle-1.12.0, segmented-2.0-1, SeqArray-1.42.0, seqLogo-1.68.0, SeqVarTools-1.40.0, seriation-1.5.4, Seurat-5.0.1, SeuratObject-5.0.1, sfsmisc-1.1-16, shape-1.4.6, shiny-1.8.0, shinyBS-0.61.1, shinydashboard-0.7.2, shinydashboardPlus-2.0.3, shinyFiles-0.9.3, shinyhelper-0.3.2, shinyjs-2.1.0, shinypanel-0.1.5, shinyWidgets-0.8.1, ShortRead-1.60.0, siggenes-1.76.0, Signac-1.12.0, SingleCellExperiment-1.24.0, SingleR-2.4.1, sitmo-2.0.2, slam-0.1-50, SMVar-1.3.4, sn-2.1.1, snow-0.4-4, SnowballC-0.7.1, SNPRelate-1.36.0, snpStats-1.52.0, sourcetools-0.1.7-1, sp-2.1-2, spam-2.10-0, SparseArray-1.2.3, SparseM-1.81, sparseMatrixStats-1.14.0, sparsesvd-0.2-2, spatstat.data-3.0-3, spatstat.explore-3.2-5, spatstat.geom-3.2-7, spatstat.random-3.2-2, spatstat.sparse-3.0-3, spatstat.utils-3.0-4, Spectra-1.12.0, SPIA-2.54.0, splitstackshape-1.4.8, SQUAREM-2021.1, stageR-1.24.0, statmod-1.5.0, stringi-1.8.3, stringr-1.5.1, struct-1.14.0, structToolbox-1.14.0, styler-1.10.2, SummarizedExperiment-1.32.0, survival-3.5-7, susieR-0.12.35, sva-3.50.0, sys-3.4.2, systemfonts-1.0.5, tensor-1.5, testthat-3.2.1, textshaping-0.3.7, TFBSTools-1.40.0, TFisher-0.2.0, TFMPvalue-0.0.9, TH.data-1.1-2, threejs-0.3.3, tibble-3.2.1, tidyr-1.3.0, tidyselect-1.2.0, tiff-0.1-12, timechange-0.2.0, timeDate-4032.109, tinytex-0.49, tkWidgets-1.80.0, TMB-1.9.10, truncnorm-1.0-9, TSP-1.2-4, tweenr-2.0.2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0, tximport-1.30.0, tzdb-0.4.0, ucminf-1.2.1, utf8-1.2.4, uwot-0.1.16, V8-4.4.1, variancePartition-1.32.2, VariantAnnotation-1.48.1, vctrs-0.6.5, vegan-2.6-4, venn-1.12, VennDiagram-1.7.3, VGAM-1.1-9, vipor-0.4.7, viridis-0.6.4, viridisLite-0.4.2, vroom-1.6.5, vsn-3.70.0, waiter-0.2.5, waldo-0.5.2, wateRmelon-2.8.0, webshot-0.5.5, widgetTools-1.80.0, withr-2.5.2, Wrench-1.20.0, WriteXLS-6.5.0, xcms-4.0.1, xfun-0.41, xgboost-1.7.6.1, XML-3.99-0.16, xml2-1.3.6, xtable-1.8-4, XVector-0.42.0, yaml-2.3.8, zCompositions-1.5.0-1, zip-2.3.0, zlibbioc-1.48.0, zoo-1.8-12 Keyword:bio
racon	bio	1.4.13, 1.5.0	Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/lbcb-sci/racon URL: https://github.com/lbcb-sci/racon Keyword:bio
rapidjson	-	1.1.0	Description: A fast JSON parser/generator for C++ with both SAX/DOM style API Homepage: https://rapidjson.org URL: https://rapidjson.org
raqm	-	0.10.1	Description: Raqm is a small library that encapsulates the logic for complex text layout and provides a convenient API. Homepage: https://github.com/HOST-Oman/libraqm URL: https://github.com/HOST-Oman/libraqm
raxml-ng	-	1.2.0	Description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Homepage: https://github.com/amkozlov/raxml-ng URL: https://github.com/amkozlov/raxml-ng
rdkit	chem	2023.09.3	Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/ URL: http://www.rdkit.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem
re2c	-	1.3	Description: 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. Homepage: https://re2c.org/ URL: https://re2c.org/
reframe	-	3.12.0	Description: ReFrame is a framework for writing regression tests for HPC systems. Homepage: https://github.com/eth-cscs/reframe URL: https://github.com/eth-cscs/reframe Compatible modules: python/3.8.10, python/3.9.6, python/3.10.2 Extensions: attrs-21.4.0, certifi-2021.10.8, chardet-4.0.0, idna-3.3, importlib_resources-5.7.1, jsonschema-4.4.0, pyrsistent-0.18.1, reframe-3.12.0, requests-2.27.1, semver-2.13.0, urllib3-1.26.9, zipp-3.8.0
rkcommon	-	1.4.2, 1.11.0	Description: Intel RenderKit common library Homepage: https://github.com/ospray/rkcommon URL: https://github.com/ospray/rkcommon
root	tools	6.28.06	Description: 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. Homepage: https://root.cern.ch/drupal/ URL: https://root.cern.ch/drupal/ Keyword:tools
rsem	bio	1.3.3	Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ URL: http://deweylab.github.io/RSEM/ Keyword:bio
rstudio-server	tools	4.3	Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ URL: https://www.rstudio.com/ Keyword:tools
ruby	tools	2.7.1, 3.2.2	Description: 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. Homepage: https://www.ruby-lang.org URL: https://www.ruby-lang.org Extensions: activesupport-5.2.8.1, addressable-2.8.4, arr-pm-0.0.12, backports-3.24.1, bundler-2.4.14, cabin-0.9.0, childprocess-4.1.0, clamp-1.3.2, concurrent-ruby-1.2.2, connection_pool-2.4.1, diff-lcs-1.5.0, ethon-0.16.0, faraday-1.2.0, faraday-net_http-3.0.2, faraday_middleware-1.2.0, ffi-1.15.5, gh-0.18.0, highline-2.1.0, i18n-1.14.1, json-2.6.3, launchy-2.5.2, minitest-5.18.0, multi_json-1.15.0, multipart-post-2.3.0, mustermann-3.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-5.0.1, pusher-client-0.6.2, rack-2.2.4, rack-protection-3.0.6, rack-test-2.1.0, rspec-3.12.0, rspec-core-3.12.2, rspec-expectations-3.12.3, rspec-mocks-3.12.5, rspec-support-3.12.0, ruby2_keywords-0.0.5, sinatra-3.0.6, thread_safe-0.3.6, tilt-2.2.0, typhoeus-1.4.0, tzinfo-1.1.0, websocket-1.2.9, zeitwerk-2.6.8 Keyword:tools
rust	tools	1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0, 1.76.0	Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools
salmon	bio	1.10.2	Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon URL: https://github.com/COMBINE-lab/salmon Keyword:bio
salmonbeta	bio	0.6.0	Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Homepage: https://github.com/COMBINE-lab/salmon/ URL: https://github.com/COMBINE-lab/salmon/ Keyword:bio
sambamba	bio	0.8.0	Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Homepage: https://lomereiter.github.io/sambamba/ URL: https://lomereiter.github.io/sambamba/ Keyword:bio
samblaster	bio	0.1.26	Description: samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Homepage: https://github.com/GregoryFaust/samblaster URL: https://github.com/GregoryFaust/samblaster Keyword:bio
samstat	-	1.5.1	Description: Displaying sequence statistics for next generation sequencing Homepage: http://samstat.sourceforge.net/ URL: http://samstat.sourceforge.net/
samtools	bio	1.10, 1.18, 1.20	Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio
sbt	tools	1.3.13	Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ URL: http://www.scala-sbt.org/ Keyword:tools
scalapack	math	2.2.0	Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: https://www.netlib.org/scalapack/ URL: https://www.netlib.org/scalapack/ Keyword:math
scipoptsuite	-	9.0.0	Description: SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver. Homepage: https://scipopt.org/ URL: https://scipopt.org/ Compatible modules: python/3.10, python/3.11 Extensions: PySCIPOpt-5.0.0
scipy-stack	math	2020a, 2020b, 2021a, 2022a, 2023a, 2023b, 2024a	Documentation: Python Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: contourpy-1.2.1, cycler-0.12.1, fonttools-4.53.0, kiwisolver-1.4.5, matplotlib-3.9.0, mpmath-1.3.0, numpy-1.26.4, packaging-24.1, pandas-2.2.1, pillow-10.3.0, pyparsing-3.1.2, python_dateutil-2.9.0.post0, pytz-2024.1, scipy-1.13.1, six-1.16.0, sympy-1.12.1, tzdata-2024.1 Keyword:math
scotch	math	6.0.9, 7.0.3	Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: https://www.labri.fr/perso/pelegrin/scotch/ URL: https://www.labri.fr/perso/pelegrin/scotch/ Keyword:math
seqan-library	-	2.4.0	Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ URL: https://www.seqan.de/
seqkit	-	0.13.2, 0.15.0, 2.3.1, 2.5.1	Description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. Homepage: https://bioinf.shenwei.me/seqkit/ URL: https://bioinf.shenwei.me/seqkit/
seqlib	-	1.2.0	Description: C++ interface to HTSlib, BWA-MEM and Fermi. Homepage: https://github.com/walaj/SeqLib URL: https://github.com/walaj/SeqLib
shapeit	-	2.r904	Description: SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
shapeit5	-	5.1.1	Description: SHAPEIT5 estimates haplotypes in large datasets, with a special focus on rare variants. Homepage: https://odelaneau.github.io/shapeit5/ URL: https://odelaneau.github.io/shapeit5/
shrinkwrap	-	1.2.0	Description: A std::streambuf wrapper for compression formats. Homepage: https://github.com/jonathonl/shrinkwrap URL: https://github.com/jonathonl/shrinkwrap
siesta	chem	5.0	Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: https://gitlab.com/siesta-project URL: https://gitlab.com/siesta-project Keyword:chem
signalp	bio	4.1f	Description: SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Keyword:bio
simnibs	-	4.1.0	Description: SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation Homepage: https://simnibs.github.io/simnibs URL: https://simnibs.github.io/simnibs Compatible modules: python/3.11, python/3.10 Extensions: msgpack-1.0.7, PyOpenGL-3.1.7, PyOpenGL-accelerate-3.1.7, SimNIBS-4.1.0
simple-dftd3	-	0.7.0, 1.0.0	Description: reimplementation of the DFT-D3 program Homepage: https://github.com/dftd3/simple-dftd3 URL: https://github.com/dftd3/simple-dftd3
singular	-	4.2.1	Description: Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. Homepage: https://www.singular.uni-kl.de/ URL: https://www.singular.uni-kl.de/
slepc	-	3.20.1	Description: 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. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.11, python/3.10 Extensions: slepc4py-3.20.1
slepc-complex	-	3.20.1	Description: 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. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.11, python/3.10 Extensions: slepc4py-3.20.1
slicer	-	4.11.20210226	Description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Homepage: https://www.slicer.org/ URL: https://www.slicer.org/
smithwaterman	-	20160702	Description: smith-waterman-gotoh alignment algorithm. Homepage: https://github.com/ekg/smithwaterman URL: https://github.com/ekg/smithwaterman
smrtlink-sequel2	-	13.1.0.221970	Description: PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided Homepage: https://www.pacb.com/support/software-downloads/ URL: https://www.pacb.com/support/software-downloads/
snappy	tools	1.1.8	Description: 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. Homepage: https://github.com/google/snappy URL: https://github.com/google/snappy Keyword:tools
snpeff	bio	5.0	Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: https://pcingola.github.io/SnpEff/ URL: https://pcingola.github.io/SnpEff/ Keyword:bio
soci	-	4.0.3	Description: SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. Homepage: http://soci.sourceforge.net/ URL: http://soci.sourceforge.net/
spades	bio	3.15.4	Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ URL: http://cab.spbu.ru/software/spades/ Keyword:bio
spark	tools	3.0.0, 3.3.0	Documentation: Apache Spark Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools
sparsehash	-	2.0.4	Description: 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. Homepage: https://github.com/sparsehash/sparsehash URL: https://github.com/sparsehash/sparsehash
spdlog	-	1.11.0	Description: Very fast, header-only/compiled, C++ logging library. Homepage: https://github.com/gabime/spdlog URL: https://github.com/gabime/spdlog
spectra	-	0.9.0	Description: SpectrA stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. SpectrA is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence SpectrA can be easily embedded in C++ projects that require calculating eigenvalues of large matrices. Homepage: https://spectralib.org/index.html URL: https://spectralib.org/index.html
sqlite	-	3.43.1	Description: SQLite: SQL Database Engine in a C Library Homepage: https://www.sqlite.org/ URL: https://www.sqlite.org/
sra-toolkit	bio	3.0.9	Description: 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 Homepage: https://github.com/ncbi/sra-tools URL: https://github.com/ncbi/sra-tools Keyword:bio
ssw	-	1.1, 1.2.5	Description: 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. Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library URL: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
star	bio	2.7.11a, 2.7.11b	Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR URL: https://github.com/alexdobin/STAR Keyword:bio
starccm	phys	15.04.010-R8, 16.02.008-R8, 16.02.009-R8, 16.04.007-R8, 16.04.012-R8, 16.06.008-R8, 17.02.007-R8, 17.02.008-R8, 17.04.007-R8, 17.04.008-R8, 17.06.007-R8, 17.06.008-R8, 18.02.008-R8, 18.04.008-R8, 18.06.006-R8, 19.04.007-R8	Documentation: StarCCM Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys
starccm-mixed	phys	15.04.010, 16.02.008, 16.02.009, 16.04.007, 16.04.012, 16.06.008, 17.02.007, 17.02.008, 17.04.007, 17.04.008, 17.06.007, 17.06.008, 18.02.008, 18.04.008, 18.06.006, 19.04.007	Documentation: StarCCM Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys
subread	bio	2.0.6	Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ URL: http://subread.sourceforge.net/ Keyword:bio
suitesparse	math	5.13.0, 7.6.0	Description: SuiteSparse is a collection of libraries to manipulate sparse matrices. Homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html URL: https://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math
sundials	-	6.6.0	Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computing.llnl.gov/projects/sundials URL: https://computing.llnl.gov/projects/sundials
supernova	bio	2.1.1	Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio
swat+	-	60.5.1	Description: The Soil and Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed. Homepage: https://swatplus.gitbook.io URL: https://swatplus.gitbook.io
swi-prolog	-	9.0.3	Description: SWI-Prolog offers a comprehensive free Prolog environment. Homepage: https://www.swi-prolog.org/ URL: https://www.swi-prolog.org/
swig	-	4.0.1, 4.1.1	Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/ URL: http://www.swig.org/
symengine	-	0.11.1, 0.11.2	Description: SymEngine is a standalone fast C++ symbolic manipulation library. Homepage: https://github.com/symengine/symengine URL: https://github.com/symengine/symengine Compatible modules: python/3.10, python/3.11 Extensions: symengine-0.11.0
tabix	bio	0.2.6	Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net URL: http://samtools.sourceforge.net Keyword:bio
tabixpp	-	1.1.2	Description: C++ wrapper to tabix indexer Homepage: https://github.com/ekg/tabixpp URL: https://github.com/ekg/tabixpp
taudem	-	5.3.8	Description: TauDEM (Terrain Analysis Using Digital Elevation Models) is a suite of Digital Elevation Model (DEM) tools for the extraction and analysis of hydrologic information from topography as represented by a DEM. Homepage: https://github.com/dtarb/TauDEM/wiki URL: https://github.com/dtarb/TauDEM/wiki
taxonkit	-	0.6.2	Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/
tbb	tools	2020.2, 2021.10.0	Description: 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. Homepage: https://github.com/oneapi-src/oneTBB URL: https://github.com/oneapi-src/oneTBB Keyword:tools
tbl2asn	-	25.8	Description: Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank Homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ URL: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
tblite	-	0.3.0	Description: Light-weight tight-binding framework Homepage: https://github.com/tblite/tblite URL: https://github.com/tblite/tblite Compatible modules: python/3.10, python/3.11 Extensions: tblite-0.3.0
tensorrt	-	8.6.1.6	Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11
thrift	-	0.19.0	Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11
tmhmm	bio	2.0c	Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio
transrate	bio	1.0.3	Description: 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. Homepage: http://hibberdlab.com/transrate/ URL: http://hibberdlab.com/transrate/ Keyword:bio
travis-analyzer	-	220729	Description: TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. Homepage: http://www.travis-analyzer.de/ URL: http://www.travis-analyzer.de/
trilinos	tools	15.1.1	Description: 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. Homepage: https://trilinos.org URL: https://trilinos.org Compatible modules: python/3.11 Keyword:tools
trimmomatic	bio	0.39	Description: 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. Homepage: http://www.usadellab.org/cms/?page=trimmomatic URL: http://www.usadellab.org/cms/?page=trimmomatic Keyword:bio
trnascan-se	bio	2.0.12	Description: tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. Homepage: http://lowelab.ucsc.edu/ URL: http://lowelab.ucsc.edu/ Keyword:bio
ucc	-	1.2.0, 1.3.0	Description: 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. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/
ucc-cuda	-	1.2.0	Description: 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. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/
ucx	-	1.8.0, 1.14.1, 1.16.0	Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: https://www.openucx.org/ URL: https://www.openucx.org/
ucx-cuda	-	1.14.1	Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. Homepage: http://www.openucx.org/ URL: http://www.openucx.org/
udunits	tools	2.2.26, 2.2.28	Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: https://www.unidata.ucar.edu/software/udunits/ URL: https://www.unidata.ucar.edu/software/udunits/ Keyword:tools
unixodbc	-	2.3.9	Description: unixODBC provides a uniform interface between application and database driver Homepage: https://www.unixodbc.org URL: https://www.unixodbc.org
valgrind-mpi	tools	3.21.0	Description: Valgrind: Debugging and profiling tools Homepage: https://valgrind.org URL: https://valgrind.org Keyword:tools
varscan	-	2.4.2, 2.4.6	Description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data Homepage: https://github.com/dkoboldt/varscan URL: https://github.com/dkoboldt/varscan
vaspkit	-	1.5.1	Description: PLATform for Assembling NUcleotide Sequences Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/
vcflib	-	1.0.9	Description: 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. Homepage: https://github.com/vcflib/vcflib URL: https://github.com/vcflib/vcflib
vcftools	bio	0.1.16	Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. Homepage: https://vcftools.github.io URL: https://vcftools.github.io Keyword:bio
visit	vis	2.13.3	Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit URL: https://wci.llnl.gov/simulation/computer-codes/visit Keyword:vis
vmd	vis	1.9.4a57	Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: https://www.ks.uiuc.edu/Research/vmd URL: https://www.ks.uiuc.edu/Research/vmd Keyword:vis
voro++	math	0.4.6	Description: 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. Homepage: http://math.lbl.gov/voro++/ URL: http://math.lbl.gov/voro++/ Keyword:math
vtk	vis	9.3.0	Description: 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. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.11, python/3.10 Keyword:vis
vtune	tools	2020.1, 2022.2	Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: https://software.intel.com/en-us/vtune URL: https://software.intel.com/en-us/vtune Keyword:tools
w3emc	-	2.11.0	Description: This library contains Fortran decoder/encoder routines for GRIB edition 1. GRIdded Binary or General Regularly-distributed Information in Binary form (GRIB) is a World Meteorological Organization (WMO) standard for gridded data. This is part of the NCEPLIBS project. Homepage: hthttps://github.com/NOAA-EMC/NCEPLIBS-w3emc/ URL: hthttps://github.com/NOAA-EMC/NCEPLIBS-w3emc/
wannier90	chem	1.2, 3.1.0	Description: The Maximally-Localised Generalised Wannier Functions calculates the counterpart of localized molecular orbitals for crystalline systems from the wavefuction. Homepage: http://www.wannier.org/ URL: http://www.wannier.org/ Keyword:chem
wasp	-	3.1.4, 4.0.3, 4.2.0	Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp
wfa2	-	2.3.4	Description: 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. Homepage: https://github.com/smarco/WFA2-lib URL: https://github.com/smarco/WFA2-lib
xbraid	-	3.1.0	Description: XBraid is a parallel-in-time software package. It implements an optimal-scaling multigrid solver for the (non)linear systems that arise from the discretization of problems with evolutionary behavior. Homepage: https://github.com/XBraid/xbraid URL: https://github.com/XBraid/xbraid
xdrfile	tools	1.1.4	Description: library for reading and writing xtc, edr and trr files Homepage: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library URL: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library Keyword:tools
xml-libxml	-	2.0205, 2.0208	Description: Perl binding for libxml2 Homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod URL: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod Extensions: Alien::Base-2.80, Alien::Build::Plugin::Download::GitLab-0.01, Alien::Libxml2-0.19, File::chdir-0.1011, XML::LibXML-2.0208
xmlf90	tools	1.5.4, 1.6.2	Description: A fast XML parser and generator in Fortran Homepage: https://gitlab.com/siesta-project/libraries/xmlf90 URL: https://gitlab.com/siesta-project/libraries/xmlf90 Keyword:tools
xtb	chem	6.6.1	Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.10, python/3.11 Extensions: ase-3.22.1, Pint-0.22, pydantic-1.9.1, qcelemental-0.27.1, xtb-6.6.1 Keyword:chem
xtensor	-	0.24.2, 0.25.0	Description: xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. Homepage: https://github.com/xtensor-stack/xtensor URL: https://github.com/xtensor-stack/xtensor
yaxt	tools	0.10.0	Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools
zeo++	-	0.3	Description: Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. Homepage: https://www.zeoplusplus.org/ URL: https://www.zeoplusplus.org/

GNU Compiler Collection, an open source compiler collection

Message Passing Interface