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
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
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	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
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
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
bbmap	bio	38.86	Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio
beagle	-	5.4	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
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
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
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
blender	vis	3.6.0	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	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	Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools
boost-mpi	tools	1.72.0	Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools
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	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
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
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	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: http://uscilab.github.io/cereal/ URL: http://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
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
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, 6.0.0.405, 6.1, 6.1.0.357, 6.2	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
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
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	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	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	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
ddt-cpu	tools	20.2, 22.0.1	Documentation: ARM software Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com URL: http://www.allinea.com
ddt-gpu	tools	20.2, 22.0.1	Documentation: ARM software Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com URL: http://www.allinea.com
delly	-	0.8.5	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. Homepage: https://github.com/dellytools/delly URL: https://github.com/dellytools/delly
dorado	-	0.2.1, 0.2.2, 0.3.0	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
eigen	math	3.3.7	Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org/index.php?title=Main_Page URL: https://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math
elpa	math	2020.05.001	Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: https://elpa.rzg.mpg.de URL: https://elpa.rzg.mpg.de Keyword:math
embree	-	3.11.0	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
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
fastqc	bio	0.11.9, 0.12.0	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
filtlong	bio	0.2.0	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	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
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/
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
g2clib	geo	1.6.0	Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ URL: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo
gatk	bio	4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0	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	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
geant4-data	-	10.7.3, 11.1.0	Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/
gentoo	-	2020, 2023	Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix
git-annex	tools	8.20200810, 10.20221003	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	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
glfw	-	3.3.2	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
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
gnuplot	vis	5.2.8	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
gsl	math	2.6	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	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	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
hdf5	io	1.10.6	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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io
hdf5-mpi	io	1.10.6	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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 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/
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
hwloc	-	2.4.0, 2.7.1	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
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/
imkl	math	2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0	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
intel	tools	2020.1.217, 2021.2.0, 2022.1.0	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
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	5.56-89.0, 5.63-95.0, 5.52-86.0, 5.55-88.0, 5.50-84.0, 5.53-87.0, 5.64-96.0	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/
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	Description: Bundle which contains ipykernel 2023b and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.4, debugpy-1.6.7.post1, decorator-5.1.1, executing-1.2.0, importlib_metadata-6.8.0, ipykernel-6.25.1, ipython-8.15.0, ipython_genutils-0.2.0, jedi-0.19.0, jupyter_client-8.3.1, jupyter_core-5.3.1, matplotlib_inline-0.1.6, nest_asyncio-1.5.7, packaging-23.1, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.6.2, prompt_toolkit-3.0.39, psutil-5.9.5, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.16.1, python-dateutil-2.8.2, pyzmq-25.1.1, six-1.16.0, stack_data-0.6.2, tornado-6.3.3, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.16.2
ipython-kernel	-	2.7, 3.9, 3.10, 3.11	Description: IPython kernelspec for Python 3.11 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	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: http://ispc.github.io/ , https://github.com/ispc/ispc/ URL: http://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
jasper	vis	2.0.16	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	11.0.16_8, 1.8.0_192, 11.0.2, 13.0.2, 14.0.2, 17.0.2	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
kma	-	1.3.0	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
ldc	-	0.17.6	Description: The LLVM-based D Compiler Homepage: https://wiki.dlang.org/LDC URL: https://wiki.dlang.org/LDC
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	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
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	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/
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
libxc	chem	4.3.4	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://www.tddft.org/programs/libxc URL: https://www.tddft.org/programs/libxc Keyword:chem
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	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
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
mariadb-connector-c	-	3.1.7	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/
matlab	tools	2020a, 2020b, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3	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	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	R2020b, R2022b, R2021b	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: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools
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	Description: MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data 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
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
minced	-	0.4.2	Description: Mining CRISPRs in Environmental Datasets Homepage: https://github.com/ctSkennerton/minced URL: https://github.com/ctSkennerton/minced
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
mpi4py	tools	3.0.3, 3.1.3	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/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools
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	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
netcdf	io	4.7.4	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	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
nextflow	-	20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3	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
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
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
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	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/
openblas	math	0.3.17	Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: https://xianyi.github.com/OpenBLAS/ URL: https://xianyi.github.com/OpenBLAS/ 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
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, v2012	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
openimageio	vis	2.1.17.0	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/ Keyword:vis
openmpi	mpi	4.0.3	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
openvdb	-	7.0.0	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	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	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
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	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
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
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/
paraview	vis	5.8.0	Documentation: Visualization Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis
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/
perl	tools	5.30.2	Documentation: Perl Description: Larry Wall's Practical Extraction and Report Language Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.111, Algorithm::Diff-1.1903, aliased-0.34, AnyEvent-7.17, App::Cmd-0.331, App::cpanminus-1.7044, AppConfig-1.71, Archive::Extract-0.86, Array::Utils-0.5, Authen::SASL-2.16, AutoLoader-5.74, B::Hooks::EndOfScope-0.24, B::Lint-1.20, boolean-0.46, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, Class::Accessor-0.51, Class::Data::Inheritable-0.08, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Singleton-1.5, Class::Trigger-0.14, Clone-0.43, Clone::Choose-0.010, Config::General-2.63, Config::INI-0.025, Config::MVP-2.200011, Config::Tiny-2.24, constant-1.33, CPANPLUS-0.9906, Crypt::DES-2.07, Crypt::Rijndael-1.14, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.23, Data::Dumper-2.173, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.110, Data::Section-0.200007, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.224, Date::Handler-1.2, Date::Language-2.32, DateTime-1.52, DateTime::Locale-1.25, DateTime::TimeZone-2.38, DateTime::Tiny-1.07, DBD::SQLite-1.64, DBI-1.643, DBIx::Admin::TableInfo-3.03, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.14, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.005, Devel::StackTrace-2.04, Digest::HMAC-1.03, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.014, Email::Date::Format-1.005, Encode-3.04, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.44, Expect-1.35, Exporter-5.74, Exporter::Declare-0.114, Exporter::Tiny-1.002001, ExtUtils::CBuilder-0.280234, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.21, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.44, ExtUtils::ParseXS-3.35, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.15, File::Grep-0.02, File::HomeDir-1.004, File::Listing-6.04, File::Next-1.18, File::Path-2.16, File::pushd-1.016, File::Remove-1.58, File::ShareDir-1.116, File::ShareDir::Install-0.13, File::Slurp-9999.30, File::Slurp::Tiny-0.004, File::Slurper-0.012, File::Spec-3.75, File::Temp-0.2309, File::Which-1.23, Font::TTF-1.06, Getopt::Long-2.51, Getopt::Long::Descriptive-0.105, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9704, Graph::ReadWrite-2.09, Hash::Merge-0.300, HTML::Entities::Interpolate-1.10, HTML::Form-6.07, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.07, HTTP::Cookies-6.08, HTTP::Daemon-6.06, HTTP::Date-6.05, HTTP::Negotiate-6.01, HTTP::Request-6.22, HTTP::Tiny-0.076, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, IO::File-1.42, IO::Handle-1.42, IO::HTML-1.001, IO::Seekable-1.42, IO::Select-1.42, IO::Socket-1.42, IO::Socket::SSL-2.067, IO::String-1.08, IO::Stringy-2.113, IO::Tty-1.14, IPC::Cmd-1.04, IPC::Run-20180523.0, IPC::Run3-0.048, JSON-4.02, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.16, List::MoreUtils-0.428, List::SomeUtils-0.58, List::Util-1.54, List::UtilsBy-0.11, Locale::Maketext::Simple-0.21, Log::Dispatch-2.69, Log::Dispatchouli-2.019, Log::Handler-0.88, Log::Log4perl-1.49, Log::Message-0.08, Log::Message::Simple-0.10, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.07, LWP::Simple-6.43, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::VecStat-0.08, MCE::Mutex-1.866, Meta::Builder-0.004, MIME::Base64-3.15, MIME::Lite-3.031, MIME::Types-2.17, Mixin::Linewise::Readers-0.108, Mock::Quick-1.111, Module::Build-0.4231, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.19, Module::CoreList-5.20200314, Module::Implementation-0.09, Module::Install-1.19, Module::Load-0.34, Module::Load::Conditional-0.70, Module::Metadata-1.000037, Module::Pluggable-5.2, Module::Runtime-0.016, Moo-2.003006, Moose-2.2012, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.005, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.200002, MooseX::Types-0.50, MooseX::Types::Perl-0.101343, Mouse-v2.5.9, Mozilla::CA-20180117, MRO::Compat-0.13, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.11, Net::HTTP-6.19, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.88, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.17, Package::Stash-0.38, Package::Stash::XS-0.29, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.07, Params::Validate-1.29, Params::ValidationCompiler-0.30, parent-0.238, Parse::RecDescent-1.967015, Path::Tiny-0.112, PDF::API2-2.037, Perl::OSType-1.010, PerlIO::utf8_strict-0.007, Pod::Elemental-0.103005, Pod::Escapes-1.07, Pod::Eventual-0.094001, Pod::LaTeX-0.61, Pod::Man-4.14, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.40, Pod::Weaver-4.015, Readonly-2.05, Regexp::Common-2017060201, Role::HasMessage-0.006, Role::Identifiable::HasIdent-0.007, Role::Tiny-2.001004, Scalar::List::Utils-1.54, Scalar::Util-1.54, Scalar::Util::Numeric-0.40, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, Socket-2.029, Software::License-0.103014, Specio-0.46, SQL::Abstract-1.86, SQL::Statement-1.412, Statistics::Basic-1.6611, Statistics::Descriptive-3.0702, Storable-3.15, strictures-2.000006, String::Flogger-1.101245, String::RewritePrefix-0.008, String::Truncate-1.100602, Sub::Exporter-0.987, Sub::Exporter::ForMethods-0.100052, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Install-0.928, Sub::Name-0.26, Sub::Quote-2.006006, Sub::Uplevel-0.2800, Sub::Uplevel-0.2800, SVG-2.84, Switch-2.17, Template-3.007, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.36, Term::UI-0.46, Test-1.26, Test::ClassAPI-1.07, Test::Deep-1.130, Test::Differences-0.67, Test::Exception-0.43, Test::Fatal-0.014, Test::Harness-3.42, Test::LeakTrace-0.16, Test::More-1.302172, Test::Most-0.35, Test::NoWarnings-1.04, Test::Output-1.031, Test::Pod-1.52, Test::Requires-0.10, Test::RequiresInternet-0.05, Test::Simple-1.302172, Test::Version-2.09, Test::Warn-0.36, Test::Warnings-0.029, Text::Aligner-0.13, Text::Balanced-2.03, Text::CSV-2.00, Text::Diff-1.45, Text::Format-0.61, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.30, Text::Soundex-3.05, Text::Table-1.133, Text::Template-1.58, Thread::Queue-3.13, Throwable-0.200013, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9760, Time::Local-1.30, Time::Piece-1.34, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.31, Try::Tiny-0.30, UNIVERSAL::moniker-0.08, URI-1.76, URI::Escape-3.31, version-0.9924, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::XPath-1.44, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.73 Keyword:tools
picard	bio	2.23.3, 2.26.3	Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio
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	2.00-10252019-avx2, 1.9b_6.21-x86_64	Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ URL: https://www.cog-genomics.org/plink/1.9/ Keyword:bio
podman	-	4.1.1, 4.5.0	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
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/
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	Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: iniconfig-2.0.0, packaging-23.1, pluggy-1.2.0, py-1.11.0, pytest-7.4.0, tomli-2.0.1
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, 3.11.2, 3.11.5	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-0.3.7, editables-0.5, filelock-3.12.2, flit_core-3.9.0, hatch_vcs-0.3.0, hatchling-1.18.0, packaging-23.1, pathspec-0.11.2, pip-23.2.1, platformdirs-3.10.0, pluggy-1.3.0, pyparsing-3.1.1, setuptools-68.1.2, setuptools_scm-7.1.0, six-1.16.0, tomli-2.0.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, virtualenv-20.24.3, wheel-0.41.2 Keyword:tools
python-build-bundle	-	2022a, 2023a, 2023b	Description: Bundle which contains Python packages useful for building Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.11, python/3.10, python/3.9, python/3.8 Extensions: archspec-0.2.1, cachecontrol-0.13.1, cachy-0.3.0, certifi-2023.7.22, cffi-1.15.1, charset-normalizer-3.2.0, cleo-2.0.1, clikit-0.6.2, crashtest-0.4.1, cryptography-41.0.3, distlib-0.3.7, distro-1.8.0, editables-0.5, exceptiongroup-1.1.3, filelock-3.12.2, flit-core-3.9.0, flit-scm-1.7.0, hatch_fancy_pypi_readme-23.1.0, hatch_vcs-0.3.0, hatchling-1.18.0, html5lib-1.1, idna-3.4, importlib_metadata-6.8.0, importlib_resources-6.0.1, jeepney-0.8.0, keyring-24.2.0, keyrings.alt-5.0.0, meson-1.2.1, meson_python-0.14.0, msgpack-1.0.5, ninja-1.11.1, packaging-23.1, pastel-0.2.1, pathspec-0.11.2, pbr-5.11.1, pexpect-4.8.0, pkginfo-1.9.6, platformdirs-3.10.0, poetry-1.6.1, poetry_core-1.7.0, ptyprocess-0.7.0, pybind11-2.11.1, pycparser-2.21, pylev-1.4.0, pyparsing-3.1.1, pyproject-metadata-0.7.1, pytoml-0.1.21, requests-2.31.0, requests-toolbelt-1.0.0, scikit_build-0.17.6, scikit_build_core-0.5.0, SecretStorage-3.3.3, semantic_version-2.10.0, setuptools-68.1.2, setuptools-rust-1.7.0, setuptools_scm-7.1.0, shellingham-1.5.3, toml-0.10.2, tomli-2.0.1, tomlkit-0.12.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, urllib3-2.0.4, virtualenv-20.24.3, webencodings-0.5.1, wheel-0.41.2, zipp-3.16.2
qiime2	-	2021.11, 2023.5	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/
qt	tools	5.12.8	Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Extensions: enum34-1.1.10, PyQt5-5.12.3, PyQtWebEngine-5.12.1, sip-4.19.18 Keyword:tools
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	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
r	tools	4.1.0, 4.2.1	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
racon	bio	1.4.13	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
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	Description: Intel RenderKit common library Homepage: https://github.com/ospray/rkcommon URL: https://github.com/ospray/rkcommon
ruby	tools	2.7.1	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-5.2.4.2, addressable-2.7.0, arr-pm-0.0.10, backports-3.17.0, bundler-2.1.4, cabin-0.9.0, childprocess-3.0.0, clamp-1.3.1, concurrent-ruby-1.1.6, connection_pool-2.2.2, diff-lcs-1.3, ethon-0.12.0, faraday-0.17.3, faraday_middleware-0.14.0, ffi-1.12.2, gh-0.16.0, highline-2.0.3, i18n-1.8.2, json-2.2.0, launchy-2.5.0, minitest-5.14.0, multi_json-1.14.1, multipart-post-1.2.0, mustermann-1.1.1, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-4.0.3, pusher-client-0.6.2, rack-2.2.2, rack-protection-2.0.8.1, rack-test-1.1.0, rspec-3.9.0, rspec-core-3.9.1, rspec-expectations-3.9.1, rspec-mocks-3.9.1, rspec-support-3.9.2, ruby2_keywords-0.0.2, sinatra-2.0.8.1, thread_safe-0.3.6, tilt-2.0.10, typhoeus-1.3.1, tzinfo-1.2.7, websocket-1.2.8 Keyword:tools
rust	tools	1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0	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
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
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	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
scipy-stack	math	2020a, 2020b, 2021a, 2022a, 2023a, 2023b	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/3.9, python/3.10, python/3.11 Extensions: anyio-3.7.1, arff-0.9, argon2_cffi-23.1.0, argon2_cffi_bindings-21.2.0, async_generator-1.10, attrs-23.1.0, backports-abc-0.5, backports.shutil_get_terminal_size-1.0.0, bcrypt-4.0.1, beautifulsoup4-4.12.2, bitarray-2.8.1, bitstring-4.1.1, bleach-6.0.0, certifi-2023.7.22, cffi-1.15.1, chardet-5.2.0, charset_normalizer-3.2.0, contourpy-1.1.0, cryptography-39.0.1, cycler-0.11.0, Cython-0.29.36, deap-1.4.1, defusedxml-0.7.1, dnspython-2.4.2, ecdsa-0.18.0, entrypoints-0.4, fastjsonschema-2.18.0, fonttools-4.42.1, funcsigs-1.0.2, idna-3.4, importlib_resources-6.0.1, Jinja2-3.1.2, jsonschema-4.19.0, jsonschema_specifications-2023.7.1, kiwisolver-1.4.5, lockfile-0.12.2, MarkupSafe-2.1.3, matplotlib-3.7.2, mistune-3.0.1, mock-5.1.0, mpmath-1.3.0, netaddr-0.8.0, netifaces-0.11.0, nose-1.3.7, numpy-1.25.2, pandas-2.1.0, pandocfilters-1.5.0, paramiko-3.3.1, path-16.7.1, path.py-12.5.0, pathlib2-2.3.7.post1, paycheck-1.0.2, pbr-5.11.1, Pillow-10.0.0, pkgutil_resolve_name-1.3.10, prometheus_client-0.17.1, pycparser-2.21, PyNaCl-1.5.0, pyparsing-3.0.9, pyrsistent-0.19.3, python_json_logger-2.0.7, pytz-2023.3, PyYAML-6.0.1, referencing-0.30.2, requests-2.31.0, rfc3339_validator-0.1.4, rfc3986_validator-0.1.1, rpds_py-0.10.0, scipy-1.11.2, Send2Trash-1.8.2, simplegeneric-0.8.1, singledispatch-4.1.0, sniffio-1.3.0, soupsieve-2.4.1, sympy-1.12, terminado-0.17.1, testpath-0.6.0, tinycss2-1.2.1, typing_extensions-4.7.1, tzdata-2023.3, urllib3-2.0.4, webencodings-0.5.1, websocket_client-1.6.2 Keyword:math
scotch	math	6.0.9	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://gforge.inria.fr/projects/scotch/ URL: https://gforge.inria.fr/projects/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	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/
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
shrinkwrap	-	1.2.0	Description: A std::streambuf wrapper for compression formats. Homepage: https://github.com/jonathonl/shrinkwrap URL: https://github.com/jonathonl/shrinkwrap
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
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/
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/
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
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
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/
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	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	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
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
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	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/
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	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/
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
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
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
ucx	-	1.8.0	Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: http://www.openucx.org/ URL: http://www.openucx.org/
udunits	tools	2.2.26	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
varscan	-	2.4.2	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
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
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
wasp	-	3.1.4, 4.0.3	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
xml-libxml	-	2.0205	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-2.23, Alien::Libxml2-0.16, File::chdir-0.1010, XML::LibXML-2.0205
xmlf90	tools	1.5.4	Description: xmlf90 is a suite of libraries to handle XML in Fortran. It has two major components: - A XML parsing library. The parser was designed to be a useful tool in the extraction and analysis of data in the context of scientific computing, and thus the priorities were efficiency and the ability to deal with very large XML files while maintaining a small memory footprint. The most complete programming interface is based on the very successful SAX (Simple API for XML) model, although a partial DOM interface and a very experimental XPATH interface are also present. - A library (xmlf90-wxml) that facilitates the writing of well-formed XML, including such features as automatic start-tag completion, attribute pretty-printing, and element indentation. There are also helper routines to handle the output of numerical arrays. Homepage: https://launchpad.net/xmlf90/ URL: https://launchpad.net/xmlf90/ Keyword:tools
xtensor	-	0.24.2	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

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