Modules sse3: Difference between revisions

| align="center" | 2021

| Documentation: [[Abaqus]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://sourceforge.net/projects/actc actc]

| align="center" | 2020.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://annovar.openbioinformatics.org/en/latest/ annovar]

| align="center" | [https://ant.apache.org/ ant]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://apptainer.org apptainer]

| align="center" | 1.1.3, 1.1.5, 1.1.6, 1.1.8, 1.2.4

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://downloads.asperasoft.com/ ascp]

| align="center" | 1.1.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://sourceforge.net/projects/bbmap/ bbmap]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio<br /><br /><br /></div>

|-

| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://dx.doi.org/10.1103/PhysRevB.85.235149. beef]

| align="center" | 0.1.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://bioperl.org/ bioperl]

| align="center" | 1.7.7, 1.7.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast]

| align="center" | 2.2.26

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.blender.org/ blender]

| align="center" | vis

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/flame/blis/ blis]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://www.boost.org/ boost]

| align="center" | tools

|-

| align="center" | [https://www.boost.org/ boost-mpi]

| align="center" | tools

|-

| align="center" | [https://github.com/BUStools/bustools bustools]

| align="center" | [http://bio-bwa.sourceforge.net/ bwa]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://seq.cs.iastate.edu/ cap3]

| align="center" | 4_0_a02

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome cellranger]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | -

|-

| align="center" | [http://www.cesm.ucar.edu/models/cesm2/ cesm]

| align="center" | 2.1.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.cgal.org/ cgal]

| align="center" | 4.14.3, 5.5.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.cmake.org cmake]

| align="center" | [https://www.comsol.com comsol]

| align="center" | phys

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/Oshlack/Corset/wiki corset]

| align="center" | 4.7.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cppzmq is a C++ binding for libzmq Homepage: https://github.com/zeromq/cppzmq URL: https://github.com/zeromq/cppzmq<br /><br /><br /></div>

|-

| align="center" | [http://cromwell.readthedocs.io/ cromwell]

| align="center" | [https://docs.nvidia.com/cuda/cusparselt/index.html cusparselt]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/ComputeCanada/custom_ctypes/ custom-ctypes]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://developer.nvidia.com/cutensor cutensor]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cuTENSOR is a high-performance CUDA library for tensor primitives. Homepage: https://developer.nvidia.com/cutensor URL: https://developer.nvidia.com/cutensor<br /><br /><br /></div>

|-

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | tools

|-

| align="center" | tools

|-

| align="center" | -

|-

| align="center" | [https://github.com/nanoporetech/dorado dorado]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | math

|-

| align="center" | math

|-

| align="center" | [https://github.com/embree/embree embree]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | 9.3.0, 23.2.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://libexpat.github.io expat]

| align="center" | 2.2.9, 2.2.10

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | 2.6.0.3, 2.7.0.9

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/rrwick/Filtlong filtlong]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas]

| align="center" | -

|-

| align="center" | [https://fmriprep.org/ fmriprep]

| align="center" | 5.3.0, 6.2.1, 7.0.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/<br /><br /><br /></div>

|-

| align="center" | [http://freesurfer.net/ freesurfer]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | geo

|-

| align="center" | [http://www.broadinstitute.org/gatk/ gatk]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://gcc.gnu.org/ gcc]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://geant4.cern.ch/ geant4-data]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/<br /><br /><br /></div>

|-

| align="center" | [https://wiki.gentoo.org/wiki/Project:Prefix gentoo]

| align="center" | 2020, 2023

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix<br /><br /><br /></div>

|-

| align="center" | [http://git-annex.branchable.com/ git-annex]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://git-lfs.github.com git-lfs]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.glfw.org glfw]

| align="center" | -

|-

| align="center" | [https://github.com/g-truc/glm glm]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | vis

|-

| align="center" | [https://www.golang.org go]

| align="center" | 1.14.1, 1.18.3, 1.21.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.gnu.org/software/gsl/ gsl]

| align="center" | math

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/gsl-lite/gsl-lite gsl-lite]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.gurobi.com gurobi]

| align="center" | math

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | 4.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://portal.hdfgroup.org/display/support hdf5]

| align="center" | io

|-

| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]

| align="center" | io

|-

| align="center" | [https://support.hdfgroup.org/products/java/hdfview/ hdfview]

| align="center" | 2.14

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://github.com/soedinglab/hh-suite hh-suite]

| align="center" | 3.3.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.open-mpi.org/projects/hwloc/ hwloc]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | 1.17.0, 1.18.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.broadinstitute.org/software/igv/ igv]

| align="center" | 2.9.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html imkl]

| align="center" | math

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | 1.1.5

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html intel]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | 2021.2.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://intelxed.github.io/ intelxed]

| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://software.intel.com/en-us/articles/intel-ipp/ ipp]

| align="center" | [https://ipython.org/ ipykernel]

| align="center" | -

|-

| align="center" | [https://ipython.org/ ipython-kernel]

| align="center" | -

|-

| align="center" | [http://www.iqtree.org/ iq-tree]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio<br /><br /><br /></div>

|-

| align="center" | -

|-

| align="center" | [https://software.intel.com/en-us/intel-trace-analyzer/ itac]

| align="center" | 2021.5.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]

| align="center" | vis

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://openjdk.java.net java]

| align="center" | tools

| Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://bitbucket.org/genomicepidemiology/kma kma]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://wiki.dlang.org/LDC ldc]

| align="center" | 0.17.6

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM-based D Compiler Homepage: https://wiki.dlang.org/LDC URL: https://wiki.dlang.org/LDC<br /><br /><br /></div>

|-

| align="center" | [https://github.com/CDAT/libcdms/ libcdms]

| align="center" | [https://jugit.fz-juelich.de/mlz/libcerf libcerf]

| align="center" | math

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/CDAT/libdrs/ libdrs]

| align="center" | [https://ofiwg.github.io/libfabric/ libfabric]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [https://sourceware.org/libffi/ libffi]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | chem

|-

| align="center" | [https://lldb.llvm.org/ lldb]

| align="center" | [https://llvm.org/ llvm]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [http://www.lstc.com/products/ls-opt ls-opt]

| align="center" | 4.8.11, 4.9.9

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://downloads.mariadb.org/connector-c/ mariadb-connector-c]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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/<br /><br /><br /></div>

|-

| align="center" | [http://www.mathworks.com/products/matlab matlab]

| align="center" | tools

| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://maven.apache.org/index.html maven]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | tools

|-

| align="center" | [https://docs.computecanada.ca/wiki/META_package_for_serial_farming meta-farm]

| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]

| align="center" | bio

|-

| align="center" | [http://metagene.nig.ac.jp/ metageneannotator]

| align="center" | 5.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://github.com/codeandkey/mii mii]

| align="center" | 1.1.1, 1.1.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A smart search engine for module environments. Homepage: https://github.com/codeandkey/mii URL: https://github.com/codeandkey/mii<br /><br /><br /></div>

|-

| align="center" | [http://mixcr.readthedocs.io/en/latest/quickstart.html mixcr]

| align="center" | 4.1.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />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<br /><br /><br /></div>

|-

| align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py]

| align="center" | tools