| Software | Resource | Containers | Description | AI Tags | AI Research Discipline | AI Software Type | Documentation, Uses, and more |
|---|---|---|---|---|---|---|---|
| abricate | lcc | 1.0 | Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. | Antimicrobial Resistance, Genomic Analysis, Bacterial Genomics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| absence-aware-clustering | mcc | 1.0 | Documentation, Uses, and more | ||||
| abyss | lcc | N/A | ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Description Source: https://www.bcgsc.ca/resources/software/abyss |
Assembly, De Novo Assembly, Sequence Assembler, Large Genomes | Biological Sciences | Hpc Tool | Documentation, Uses, and more |
| adapterremoval | lcc | 1.0 | AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. | Bioinformatics, Hts Data Processing, Sequence Analysis | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| adios | lcc | N/A | The Adaptable IO System (ADIOS) | I/O, High Performance Computing, Data Management | High Performance Computing, Scientific Data Management | Library | Documentation, Uses, and more |
| adios2 | mcc, lcc | N/A | ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing Project. It is a framework for scientific data I/O to publish and subscribe to data when and where required. ADIOS2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes. ADIOS2 can be used on supercomputers, cloud systems, and personal computers. | I/O Middleware, High-Performance Computing, Data Management, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| admixture | mcc, lcc | 1.0 | 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. | genetics, population genetics, bioinformatics | Bioinformatics, Population Genetics | Statistical Software | Documentation, Uses, and more |
| advisor | mcc, ecc, lcc | N/A | Intel Advisor is a performance analysis tool designed to help developers optimize and parallelize their software on Intel architectures. It provides insights for efficient vectorization, threading, and offloading to accelerators, aiding in achieving maximum performance from applications. | Hpc, Performance Optimization, Parallel Computing | Engineering & Technology | Performance Optimization | Documentation, Uses, and more |
| aflow | mcc, lcc | 1.0 | AFLOW is a comprehensive software framework for autonomous density functional theory calculations and materials properties analysis. It offers diverse tools and modules for structure analysis, property prediction, and error correction, including thermodynamic stability analysis and modeling of chemically disordered materials, with public access through the AFLOW website and search API. | Computational Software, Materials Science, Density Functional Theory | Physics & Physical Sciences, Physical Sciences | Materials Modeling & Simulation | Documentation, Uses, and more |
| afterqc | lcc | 1.0 | Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. | Quality Control, High-Throughput Sequencing Data, Next-Generation Sequencing | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| agat | lcc | 1.0 | Agat is a suite of tools to handle gene annotations in any GTF/GFF format | Genome Assembly, Annotation, Evaluation, Genomic Analysis | Genomics, Biological Sciences | Pipeline | Documentation, Uses, and more |
| agptools | mcc | 1.0 | The AGP format is a tab-separated table format describing how components of a genome assembly fit together. NCBI accepts assemblies for submission in the format of a fasta file giving the sequences of components (usually contigs) along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. | Genome Assembly | Bioinformatics | Documentation, Uses, and more | |
| allmaps | lcc | N/A | With Allmaps, you can georeference any map from any institution that supports IIIF. Allmaps doesn’t require complicated GIS infrastructure and it doesn’t need to generate XYZ map tiles. All that’s needed is a IIIF server. | Genomics, chromosome reconstruction, bioinformatics | Genome Assembly, Bioinformatics | assembly scaffolding tool | Documentation, Uses, and more |
| alphafold3 | lcc | 1.0 | AlphaFold 3 is an AI model from Google DeepMind and Isomorphic Labs that can predict the structure and interactions of all life’s molecules, including proteins, DNA, RNA, and small molecules (ligands). For the interactions of proteins with other molecule types it has provided least a 50% improvement compared with existing prediction methods, and for some important categories of interaction it has doubled prediction accuracy.\r Description Source: https://blog.google/innovation-and-ai/products/google-deepmind-isomorphic-alphafold-3-ai-model/\r |
Protein-Structure, Deep-Learning, Bioinformatics | Bioinformatics, Biochemistry and Molecular Biology | Predictive Modeling | Documentation, Uses, and more |
| amas | mcc | 1.0 | Documentation, Uses, and more | ||||
| amber | mcc, lcc | 1.0 | Amber MD application | Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics | Documentation, Uses, and more |
| ambertools | mcc, lcc | 1.0 | Ambertools is a suite can of complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. | Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization | Biophysics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| amdblis | mcc | N/A | AMD Optimized BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | Computational Software, Data Analysis, Visualization | Biophysics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| amdfftw | mcc | N/A | An AMD optimized version of FFTW. FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. Description Source: https://www.fftw.org/ |
Mathematics | Library | Documentation, Uses, and more | |
| amdlibflame | mcc | N/A | libFLAME AMD Optimized version is a portable library for dense matrix computations, providing much of the functionality present in Linear Algebra Package LAPACK. It includes a compatibility layer, FLAPACK, which includes complete LAPACK implementation. | Linear Algebra, Numerical Computations, Performance Optimization | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| amdlibm | mcc | N/A | AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor-based machines. It provides many routines from the list of standard C99 math functions. Applications can link into AMD LibM library and invoke math functions instead of compilers math functions for better accuracy and performance. | Mathematics, Numerical Computation, Math Library | Mathematics, Engineering & Technology | Math Library | Documentation, Uses, and more |
| amdscalapack | mcc | N/A | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. | Mathematics | Library | Documentation, Uses, and more | |
| anaconda | lcc | N/A | Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. | Data Science, Scientific Computing, Package Management, Python, R | Computer and Information Sciences | Package Management | Documentation, Uses, and more |
| ancestry_hmm | lcc | 1.0 | ancestry_hmm is a hidden Markov model–based software tool for inferring local ancestry along the genome in admixed individuals using genotype or sequencing data. It identifies ancestry transitions and ancestry proportions by modeling recombination, allele frequencies, and admixture history. | Computational genomics, Population genetics | population-genetics | Documentation, Uses, and more | |
| angsd | mcc, lcc | 1.0 | Angsd is a software for analyzing next generation sequencing data. | Ngs Data Analysis, Genome-Wide Association Studies, Population Genomics, Genetic Variation | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| annoy | lcc | 1.0 | Annoy (Approximate Nearest Neighbors Oh Yeah) is a high-performance library for searching large, high-dimensional vector spaces using approximate nearest-neighbor queries. It is designed for extremely fast similarity search, making it ideal for recommendation engines, clustering, retrieval, and large-scale data mining or machine-learning applications. | Machine Learning, Data Science, Approximate Nearest Neighbors, High-Dimensional Data | Machine Learning, Data Mining | Library | Documentation, Uses, and more |
| ansysedt | lcc | N/A | Ansys Electronics Desktop Student offers free access to the industry gold-standard Ansys simulators for work with antenna, RF, microwave, PCB, IC and IC package designs, along with electromechanical devices such as electric motors and generators. Students will have access to Ansys HFSS, Ansys Maxwell, Ansys Q3D, Ansys Icepak, Ansys Twin Builder, and Ansys Circuit, allowing design work on a broad range of electrical and electromechanical systems. | Electrical Engineering, Computational Electromagnetics | Electromagnetic Simulation Software | Documentation, Uses, and more | |
| antismash | mcc | 1.0 | Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. | Bioinformatics, Genome Mining, Biosynthetic Gene Clusters, Secondary Metabolites | Bioinformatics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| anvio | mcc, lcc | 1.0 | Anvio is an analysis and visualization platform for 'omics data. | Omics Data Analysis, Microbiome, Metagenomics, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| aocc | mcc | N/A | AOCC a set of production compilers optimized for software performance when running on AMD host processors using the AMD “Zen” core architecture.The AOCC compiler environment simplifies and accelerates development and tuning for x86 applications built with C, C++, and Fortran languages. Description Source: https://www.amd.com/en/developer/aocc.html |
Compiler, C, C++, Fortran, Optimization | Software Engineering, Computer & Information Sciences | Service | Documentation, Uses, and more |
| aocl-sparse | mcc | N/A | AOCL-Sparse contains basic linear algebra subroutines for sparse matrices and vectors optimized for AMD processors. In addition, AOCL-Sparse includes iterative sparse solvers for solving linear system of equations. It is designed to be used with C and C++. | Sparse Matrix Operations, Fpga Optimization, Opencl Applications, High-Performance Computing | Mathematics, Engineering & Technology | Library | Documentation, Uses, and more |
| apptainer | ecc | N/A | Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments. Description Source: https://apptainer.org/ |
Containerization, Application Management, Devops, Software Development | Computer Science, Engineering & Technology | Development | Documentation, Uses, and more |
| argweaver | mcc | 1.0 | The ARGweaver software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs). An ARG is a rich data structure for representing the ancestry of DNA sequences undergoing coalescence and recombination. | bioinformatics, genetics, population genetics, software tool | Computational Evolutionary Biology, Bioinformatics | Command-line tool | Documentation, Uses, and more |
| arrayfire | lcc | N/A | Cell ranger tools . | Software Library, Parallel Computing, Gpu Acceleration, Linear Algebra, Signal Processing, Image Processing, Statistics | Parallel Computing, Computer & Information Sciences | Library | Documentation, Uses, and more |
| ase | lcc | N/A | ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. Description Source: https://wiki.fysik.dtu.dk/ase/index.html |
Computational Software, Python Library, Molecular Simulations | Chemistry, Other Natural Sciences | Tool | Documentation, Uses, and more |
| assembly-stats | mcc | 1.0 | Assembly-stats is a tool to get assembly statistics from FASTA and FASTQ files. | Genome Assembly, Bioinformatics | Biology, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| astra-toolbox | ecc | N/A | ASTRA Toolbox 2.3.0 installed via Conda environment. | tomography, image reconstruction, medical imaging, simulation | Image Reconstruction, Tomography | Library | Documentation, Uses, and more |
| astral | mcc | 1.0 | ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under the multi-species coalescent model (and thus is useful for handling incomplete lineage sorting, i.e., ILS). ASTRAL finds the species tree that has the maximum number of shared induced quartet trees with the set of gene trees, subject to the constraint that the set of bipartitions in the species tree comes from a predefined set of bipartitions. | Bioinformatics, Phylogenetics | Phylogenomics inference tool | Documentation, Uses, and more | |
| at-spi2-atk | mcc | N/A | Applications that provide accessibility through the ATK interfaces need a way to translate those interfaces to AT-SPI2 DBus calls. This module, at-spi2-atk, provides that translation bridge. Description Source: https://gitlab.gnome.org/Archive/at-spi2-atk |
Assistive Technology, Accessibility, User Interface | General, Computer & Information Sciences | Interface | Documentation, Uses, and more |
| at-spi2-core | mcc | N/A | AT-SPI2-Core is the central component of the Assistive Technology Service Provider Interface, providing APIs for assistive technologies to interact with Linux desktop applications, thereby enhancing accessibility for users with disabilities. | Accessibility, Assistive Technology, Gui Applications | General, Computer Science | Library | Documentation, Uses, and more |
| atacseqqc | mcc | 1.0 | Documentation, Uses, and more | ||||
| atk | mcc | N/A | ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. Description Source: https://hprc.tamu.edu/software/aces/ |
Computational Chemistry, Materials Science, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Simulation Software | Documentation, Uses, and more |
| atomsk | lcc | 1.0 | Atomsk is a command-line tool for creating, manipulating, and converting atomic structures. It is widely used in materials science for generating input files for various simulation software. | atomic structures, materials science, simulation, file conversion | Computational Materials Science, Atomic and Molecular Physics | Command-line tool | Documentation, Uses, and more |
| augustus | lcc | N/A | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. Description Source: https://bioinf.uni-greifswald.de/augustus/ |
Gene Prediction, Eukaryotes, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| augustus-braker | lcc | N/A | BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-ES/ET/EP/ETP R14, R15, R17, F1 and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction. | genome annotation, gene prediction, bioinformatics | Bioinformatics | Genome annotation software | Documentation, Uses, and more |
| autoconf | mcc, ecc, lcc | N/A | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. | Build Automation, Software Configuration, Makefiles | General, Engineering & Technology | Build Tools | Documentation, Uses, and more |
| autoconf-archive | mcc, ecc, lcc | N/A | The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. Description Source: https://github.com/autoconf-archive/autoconf-archive |
autoconf, macros, configuration, software development | General, Software Engineering | Service | Documentation, Uses, and more |
| autodock-vina | mcc | 1.0 | AutoDock Vina is an open-source program for doing molecular docking. AutoDock Vina is one of the docking engines of the AutoDock Suite. | Molecular Docking, Bioinformatics, Computational Chemistry, Drug Discovery | Biology, Molecular Docking | Application | Documentation, Uses, and more |
| automake | mcc, ecc, lcc | N/A | autoamke software. | Build Automation, Software Development, Compilers | General, Engineering & Technology | Compiler | Documentation, Uses, and more |
| autotools | mcc, ecc, lcc | N/A | Developer utilities | Programming, Software Development, Build Automation | Software Engineering, Systems & Development, Computer & Information Sciences | Build Automation | Documentation, Uses, and more |
| aws-cli | mcc | 1.0 | The AWS Command Line Interface (AWS CLI) is a unified tool to manage your AWS services. Description Source: https://aws.amazon.com/cli/ |
Aws, Command Line Interface, Cloud Management | General, Computer & Information Sciences, Engineering & Technology | Command Line Tool | Documentation, Uses, and more |
| aws-snowball | mcc | N/A | snowball software. | Data Transfer, Cloud Computing, AWS | Data Management, Computer Science | Data Transfer Service | Documentation, Uses, and more |
| azcopy | mcc | 1.0 | AzCopy is a command-line utility that you can use to copy data to, from, or between storage accounts. This article helps you download AzCopy, connect to your storage account, and then transfer data. | Data Transfer, Cloud Storage, Azure, Command Line Tool | Computer Science, Data Engineering | Command Line Utility | Documentation, Uses, and more |
| bacmet | mcc | 1.0 | Documentation, Uses, and more | ||||
| bader | mcc | 1.0 | Documentation, Uses, and more | ||||
| bakta | mcc, lcc | 1.0 | Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis. | bacterial genome annotation, prokaryotic genomes, bioinformatics, functional annotation, gene prediction, comparative genomics, sequence analysis | Microbial genomics, Bioinformatics | Genome annotation software | Documentation, Uses, and more |
| bam-readcount | lcc | 1.0 | Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bam-readcount/bam-readcount.html |
Bioinformatics, Genomics, Variant-Calling, Coverage-Assessment | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| bash | ecc | N/A | Bash is a Unix shell and command language that is widely used for scripting and automation in Unix-like operating systems. | scripting, automation, command-line, Unix, Linux | Computer Science, Software Engineering | Shell | Documentation, Uses, and more |
| bayescan | mcc, lcc | 1.0 | BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bayescan/bayescan.html |
Genetic Analysis, Natural Selection, Bayesian Model Comparison | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| bbmap | mcc | 1.0 | Bbmap is a short read aligner, as well as various other bioinformatic tools. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bbmap/bbmap.html |
Bioinformatics, DNA Sequencing, Sequence Alignment | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bc | ecc | N/A | bc is an arbitrary precision calculator language that supports complex mathematical operations. | Calculator, Mathematics, Command-line tool | Applied Mathematics, Other Mathematics | Command-line tool | Documentation, Uses, and more |
| bcftools | mcc, lcc | 1.0 | BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. Description Source: https://samtools.github.io/bcftools/howtos/index.html |
Variant Calling, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcftools-1.11-samtools | lcc | 1.0 | Bcftools is a set of utilities for variant calling and manipulating VCF and BCF files. It is designed to work with SAMtools and is widely used in bioinformatics for analyzing genomic data. | bioinformatics, genomics, variant analysis | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| bcl2fastq2 | mcc, lcc | 1.0 | Cell ranger tools . | bioinformatics, genomics, sequencing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| bdftopcf | mcc | N/A | Documentation, Uses, and more | ||||
| beagle | mcc | 1.0 | Beagle is is a software package for phasing genotypes and for imputing ungenotyped markers. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/beagle/beagle.html |
Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| beagle-lib | lcc | N/A | BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs. Description Source: https://github.com/beagle-dev/beagle-lib |
Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics | Biology | Library | Documentation, Uses, and more |
| beast | mcc, lcc | 1.0 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Description Source: https://www.beast2.org/ |
Bioinformatics, Computational Biology, Phylogenetics, Molecular Evolution, Bayesian Analysis | Systems Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| beast2 | mcc, lcc | 1.0 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Description Source: https://www.beast2.org/ |
Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference | Ecology, Biological Sciences | Tool | Documentation, Uses, and more |
| bedops | mcc, lcc | 1.0 | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Description Source: https://bedops.readthedocs.io/en/latest/ |
Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis | Bioinformatics, Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| bedtools | mcc, lcc | 1.0 | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. This is an older version of bedtools2. Description Source: https://bedtools.readthedocs.io/en/latest/ |
Bioinformatics, Genomics, Data Analysis, Tool | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| bedtools2 | mcc | N/A | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. Description Source: https://bedtools.readthedocs.io/en/latest/ |
Genomic Data Analysis, Bed Files, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| berkeley-db | mcc, ecc, lcc | N/A | Berkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications. Description Source: https://docs.oracle.com/database/bdb181/ |
Database, Embedded Systems, High Performance, Data Management | Storage, Hpc Applications, Computer Science | Library | Documentation, Uses, and more |
| bigsi | mcc | 1.0 | Documentation, Uses, and more | ||||
| bin | mcc | N/A | Container | Documentation, Uses, and more | |||
| binutils | mcc, lcc | N/A | binutils: GNU binary utilities | Binary Tools, Linker, Assembler, Object Files | General, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| bioawk | mcc | 1.0 | Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. \r Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bioawk/bioawk.html |
Bioinformatics, Data Processing, File Formats, Data Analysis | Bioinformatics, Biological Sciences | Scripting Tool | Documentation, Uses, and more |
| biobakery_workflows | lcc | 1.0 | bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. | bioinformatics, microbiome, data analysis, workflow | Computational Biology, Bioinformatics | Workflow Management | Documentation, Uses, and more |
| bioconductor | mcc | N/A | R | bioinformatics, genomics, R, data analysis | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| bioconductor-champ | lcc | N/A | The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations. | Bioinformatics, Genomics, R | Bioinformatics, Molecular Biology | R Package | Documentation, Uses, and more |
| bioconductor-deseq2 | lcc | N/A | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | RNA-Seq, Differential Expression, Bioconductor, Genomics, Statistics | Genomics, Molecular Biology | R Package | Documentation, Uses, and more |
| bioconductor-dss | lcc | 1.0 | DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | bioinformatics ,methylation, genomics, Bioconductor | Bioinformatics, Molecular Biology | R package | Documentation, Uses, and more |
| bioconductor-edger | lcc | N/A | Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage. | RNA-Seq, Differential Expression, Bioconductor, Statistics | Computational Biology, Bioinformatics | Statistical Analysis | Documentation, Uses, and more |
| bioconductor-lea | mcc | 1.0 | Documentation, Uses, and more | ||||
| bioconductor-maftools | mcc | 1.0 | Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort. | bioinformatics, cancer genomics, R package, data visualization | Cancer Research, Bioinformatics | R package | Documentation, Uses, and more |
| bionano | mcc | 1.0 | bionano OGM solutions provide the essential tools clinicians and researchers need to reveal actionable insights from all classes of genomic variations | structural variation, genome assembly, optical mapping | Molecular Biology, Life Sciences | Bioinformatics Software | Documentation, Uses, and more |
| biopython | mcc | 1.0 | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Description Source: https://biopython.org/ |
Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| bis-snp | mcc | 1.0 | BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. | bisulfite sequencing, DNA methylation, SNP calling, epigenomics, bioinformatics, NGS analysis | Epigenomics, Bioinformatics | Variant and DNA methylation analysis software | Documentation, Uses, and more |
| bismark | mcc, lcc | 1.0 | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Description Source: https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics | Genomics, Biological Sciences | Alignment & Methylation Analysis | Documentation, Uses, and more |
| bison | mcc, lcc | N/A | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. | Parser Generator, Programming Language Tool | General, Computer & Information Sciences | Parser Generator | Documentation, Uses, and more |
| blasr | mcc, lcc | 1.0 | Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blasr/blasr.html |
Alignment, Sequencing, Genomics | Biology, Biological Sciences | Mapping | Documentation, Uses, and more |
| blast | mcc, lcc | 1.0 | BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blast/blast.html |
Bioinformatics, Sequence Alignment, Homology Search | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| blat | lcc | N/A | BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. Description Source: https://genome.ucsc.edu/cgi-bin/hgBlat |
Sequence Analysis, DNA Alignment, Genomic Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| blobtoolkit | mcc | 1.0 | Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering. | genomics, bioinformatics, data visualization, software tools | Computational Biology, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| blobtools | mcc | 1.0 | Blobtools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blobtools/blobtools.html |
Genome Assembly, Data Visualization, Metagenomics | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| boltz | lcc | 1.0 | Documentation, Uses, and more | ||||
| bonito | lcc | N/A | Bonito is an open source research basecaller for Oxford Nanopore reads. | bioinformatics, nanopore sequencing, basecalling, deep learning | Molecular Biology, Bioinformatics | Basecalling Software | Documentation, Uses, and more |
| boost | mcc, lcc | N/A | Boost free peer-reviewed portable C++ source libraries | C++ Libraries, Programming Support, Efficiency Enhancement | Computer Science, Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| bowtie | mcc, lcc | 1.0 | Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. Description Source: https://bowtie-bio.sourceforge.net/manual.shtml |
Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| bowtie2 | mcc, lcc | 1.0 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning to relatively long (e.g. mammalian) genomes. Description Source: https://github.com/BenLangmead/bowtie3 |
Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Sequence Alignment | Documentation, Uses, and more |
| bpp | mcc, lcc | 1.0 | BPP is a Bayesian Markov chain Monte Carlo (MCMC) program for analyzing sequence alignments from multiple loci and multiple closely-related species under the multispecies coalescent (MSC) model. BPP takes into account episodic and continuous gene flow through its implementation of the multispecies coalescent with introgression (MSC-I) model for episodic events, and the multispecies coalescent with migration (MSC-M) model for continuous interactions. | phylogenetics, molecular evolution, comparative genomics | Evolutionary Biology, Life Sciences | Statistical Software | Documentation, Uses, and more |
| braker | lcc | 1.0 | BRAKER is a software tool for the automated gene prediction in eukaryotic genomes. It uses RNA-Seq data to improve the accuracy of gene models. | gene prediction, RNA-Seq, genomics, bioinformatics | Bioinformatics, Computational Biology | Bioinformatics Tool | Documentation, Uses, and more |
| braker3 | mcc | 1.0 | BRAKER3 is a software tool for automated gene prediction in eukaryotic genomes, leveraging RNA-Seq data and protein homology. | Gene Prediction, Genome Annotation, Bioinformatics, RNA-Seq, Eukaryotic Genomes | Bioinformatics, Computational Biology | Bioinformatics Tool | Documentation, Uses, and more |
| breakdancer | mcc, lcc | 1.0 | a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs. | genomics, bioinformatics, structural variants, next-generation sequencing | Genomic Analysis, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| bsbolt | lcc | 1.0 | a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. | bisulfite sequencing, DNA methylation, read alignment, variant calling, epigenomics, bioinformatics | Epigenomics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| burai | lcc | N/A | Burai is a graphical user interface (GUI) designed to simplify running and managing Quantum ESPRESSO calculations for materials science and computational physics. It allows users to set up input files, execute simulations, and visualize results without needing to work directly with complex command-line workflows. | quantum espresso, density functional theory, materials simulation | Computational Physics, Physical Sciences | Scientific Application | Documentation, Uses, and more |
| busco | mcc, lcc | 1.0 | Benchmarking Universal Single-Copy Orthologs (BUSCO) is used for assessing genome assembly and annotation completeness. Description Source: https://gitlab.com/ezlab/busco |
Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs | Bioinformatics, Biological Sciences | Tools | Documentation, Uses, and more |
| bvalcalc | mcc | 1.0 | Documentation, Uses, and more | ||||
| bwa | mcc, lcc | 1.0 | BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. Description Source: https://bio-bwa.sourceforge.net/ |
Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs) | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bwa-mem2 | mcc | 1.0 | bwa-mem2 is a fast and accurate alignment tool for mapping DNA sequences against a reference genome, designed to handle large datasets efficiently. | bioinformatics, genomics, alignment, DNA sequencing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| bwakit | mcc | 1.0 | bwakit is a bioinformatics tool designed for efficient and accurate processing of genomic data, particularly for handling large-scale sequencing data. | bioinformatics, genomics, sequencing, data processing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| bwameth | mcc | 1.0 | Bwameth is a tool for fast and accurante alignment of BS-Seq reads. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bwameth/bwameth.html |
DNA Methylation, Bisulfite Sequencing, Alignment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bzip2 | mcc, ecc, lcc | N/A | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. | File Compression, Data Compression, Utility Software | General, Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| c-blosc | mcc, lcc | N/A | c-blosc is a high-performance compressor optimized for binary data, designed to be used in conjunction with scientific computing applications. | compression, performance, binary data, scientific computing | Data Management, Data Compression | Library | Documentation, Uses, and more |
| ca-certificates-mozilla | ecc | N/A | Documentation, Uses, and more | ||||
| cactus | lcc | 1.0 | Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. Description Source = https://github.com/ComparativeGenomicsToolkit/cactus?tab=readme-ov-file | Computational Software, Hpc Tools | Gravitational Physics, Physical Sciences | Simulation Software | Documentation, Uses, and more |
| cairo | mcc | N/A | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Description Source: https://cairographics.org/ |
Graphics Library, 2D Graphics, Rendering Engine | Graphics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| calder | mcc | 1.0 | Documentation, Uses, and more | ||||
| canu | mcc, lcc | 1.0 | canu software. | Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics | Genomics, Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| canu-2.2 | mcc | 1.0 | Canu is a software package for assembling genomes from single-molecule sequencing reads. It is designed for high-throughput sequencing technologies and provides tools for error correction, trimming, and assembly. | genome assembly, bioinformatics, high-throughput sequencing, single-molecule sequencing | Computational Biology, Bioinformatics | Assembly Software | Documentation, Uses, and more |
| caper | mcc | N/A | Caper is a tool for managing and executing workflows on cloud platforms, particularly designed for bioinformatics applications. | bioinformatics, workflow management, cloud computing, WDL | Bioinformatics, Biochemistry and Molecular Biology | Workflow Management Tool | Documentation, Uses, and more |
| ccl | mcc, ecc, lcc | N/A | CCL (Cpp Command Line Library) is a C++ library targeting Unix platform that makes it easy to define and parse command line arguments. It provides a simple and intuitive way to define and parse command-line arguments for C++ programs. | Command Line Interface, C++ Library | Documentation, Uses, and more | ||
| cd-hit | mcc, lcc | 1.0 | Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences. | Sequence Analysis, Clustering, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| cd-hit-auxtools | lcc | 1.0 | cd-hit-auxtools is a set of auxiliary tools for the CD-HIT software, which is used for clustering and comparing biological sequences. | bioinformatics, sequence analysis, clustering | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| cdhit | lcc | 1.0 | CD-HIT is a program for clustering and comparing large sets of protein or nucleotide sequences. It is widely used in bioinformatics for reducing redundancy in sequence datasets. | bioinformatics, sequence clustering, data reduction | Computational Biology, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| cdna_cupcake | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| cellbender | mcc | 1.0 | Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. | Single-Cell RNA-Seq, Data Processing, Denoising, Batch Effects, Bioinformatics | Genetics, Biological Sciences | Python Library | Documentation, Uses, and more |
| cellranger | mcc, lcc | 1.0 | Cell ranger tools . | Bioinformatics, Single-Cell RNA-Seq, Data Analysis | Biology, Biological Sciences | Documentation, Uses, and more | |
| cellranger-arc | lcc | N/A | Cell ranger arc tools . | Single-Cell Analysis, Chromatin Accessibility, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cellranger-atac | lcc | N/A | Cell ranger arc tools . | bioinformatics, single-cell genomics, ATAC-seq, chromatin accessibility | Biology, Genomics | Application | Documentation, Uses, and more |
| centrifuger | mcc | 1.0 | Documentation, Uses, and more | ||||
| cfour | mcc | N/A | cfour software. | Quantum Chemistry, Ab Initio Methods, High-Performance Computing | Chemical Sciences, Physical Chemistry | Scientific Software | Documentation, Uses, and more |
| cgal | mcc, lcc | N/A | CGAL is an open source software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. Description Source: https://www.cgal.org/ |
Computational Geometry, Geometric Algorithms, Software Library | Computer Science, Computer & Information Sciences | Algorithm Library | Documentation, Uses, and more |
| cgmaptools | lcc | 1.0 | cgmaptools is a software package designed for the analysis of cytosine methylation data, particularly in the context of genomic studies. | bioinformatics, genomics, methylation analysis | Bioinformatics, Biochemistry and Molecular Biology | Analysis Tool | Documentation, Uses, and more |
| cgns | mcc, lcc | N/A | The CFD General Notation System (CGNS) provides a standard for recording and recovering computer data associated with the numerical solution of fluid dynamics equations. Description Source: https://github.com/conda-forge/cgns-feedstock/blob/main/recipe/meta.yaml | Computational Software | Fluid & Plasma Physics, Physical Sciences | File Format | Documentation, Uses, and more |
| charliecloud | lcc | N/A | Lightweight user-defined software stacks for high-performance computing | Containerization, Software Development, Research Tools | High-Performance Computing, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| charmm | lcc | N/A | CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a molecular simulation software package designed for the study of biomolecules, including proteins, nucleic acids, and lipids. | molecular dynamics, biomolecular simulations, computational chemistry, bioinformatics | Chemical Sciences, Physical Chemistry | Simulation Software | Documentation, Uses, and more |
| checkm-genome | mcc, lcc | 1.0 | Checkm-genome provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. | Metagenomics, Microbial Ecology, Genome Quality Assessment | Environmental Biology, Biological Sciences | Genome Quality Assessment Tool | Documentation, Uses, and more |
| checkm2 | mcc | 1.0 | CheckM2 is a software tool designed for assessing the completeness and contamination of microbial genomes, providing a comprehensive framework for quality control in metagenomic studies. | bioinformatics, genomics, metagenomics, quality control | Genomics, Microbiology | Command-line tool | Documentation, Uses, and more |
| checkv | mcc | 1.0 | CheckV is a tool designed to assess the quality of viral genomes assembled from metagenomic data, providing metrics on completeness and contamination. | bioinformatics, metagenomics, viral genomes, genome assembly | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| chemshell | lcc | N/A | canu software. | Computational Chemistry, Quantum Mechanics, Molecular Dynamics | Computational Chemistry, Quantum Chemistry | Scientific Software | Documentation, Uses, and more |
| chewbbaca | lcc | 1.0 | chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. | Whole-Genome Analysis, Microbial Genotyping, Bacterial Typing, Phylogenetic Inference, Bioinformatics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| chopper | mcc | 1.0 | Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python. | Bioinformatics, Ngs Data Analysis, Sequence Trimming, High-Throughput Sequencing | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ciao | lcc | N/A | Documentation, Uses, and more | ||||
| circos | lcc | N/A | Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Description Source: https://circos.ca/ |
Data Visualization, Genomics, Biological Sciences, Circular Layout | Bioinformatics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| citcoms | lcc | N/A | CitcomS is a parallel finite-element simulation software used to model mantle convection and other large-scale geodynamic processes within the Earth. It is designed for high-performance computing environments and allows researchers to study thermal and compositional evolution of the mantle in spherical or regional geometries. | mantle convection, finite-element modeling, high-performance computing | Geodynamics, Earth Sciences | Simulation Software | Documentation, Uses, and more |
| clair3 | mcc | 1.0 | Clair3 is a germline small variant caller for long-reads. | Variant Calling, Illumina, Sequencing Data | Bioinformatics, Biological Sciences | Variant Caller | Documentation, Uses, and more |
| clck | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| cli11 | lcc | N/A | CLI11 is a command line parser for C++11 and beyond, designed to be easy to use and flexible. | C++, Command Line Interface, Parsing, Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| clumpp | mcc | 1.0 | CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. | population structure, clustering alignment, genetic analysis | Life Sciences, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| clust | mcc | 1.0 | Clust is a fully automated method for identification of clusters (groups) of genes that are consistently co-expressed (well-correlated) in one or more heterogeneous datasets from one or multiple species. | Clustering, Time Series Data, Pattern Identification | Other Computer & Information Sciences | Data Analysis Tool | Documentation, Uses, and more |
| cmake | mcc, ecc, lcc | N/A | CMake is an open-source, cross-platform family of tools designed to build, test and package software. | Build System, Cross-Platform, Software Development | Software Engineering, Systems & Development, Engineering & Technology | Developer Tools | Documentation, Uses, and more |
| cmdstanr 0.5.2 and opencl | lcc | 1.0 | Documentation, Uses, and more | ||||
| code_aster | mcc | N/A | Code_Aster is an open-source software package for finite element analysis in structural mechanics, developed and maintained by EDF (Ãlectricité de France). It's widely used for simulating various engineering problems, including static and dynamic analyses, thermal behavior, and fluid-structure interactions. | Finite Element Analysis, Numerical Simulation, Open Source, Engineering | Engineering, Mechanical Engineering | Simulation Software | Documentation, Uses, and more |
| cogent | mcc | 1.0 | Cogent NGS Discovery Software (CogentDS) is bioinformatic software for user-friendly analysis of sequencing data generated with Takara Bio platforms. The Cogent NGS Analysis Pipeline (CogentAP) can be used to prepare files ready for import into CogentDS. | long-read sequencing, transcript reconstruction, isoform analysis | Life Sciences, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| colabfold | lcc | N/A | ColabFold is a web-based tool that leverages artificial intelligence to predict protein structures rapidly and accurately, making cutting-edge protein folding accessible to researchers without requiring extensive computational resources. It builds on the technology of AlphaFold by DeepMind, providing a user-friendly platform for scientific exploration and discovery in the field of bioinformatics and structural biology. | Protein Structure Prediction, Deep Learning, Biophysical Modeling | Bioinformatics, Biological Sciences | Protein Structure Prediction Tool | Documentation, Uses, and more |
| compiler | mcc, ecc, lcc | N/A | A compiler is a special program that processes statements written in a particular programming language and turns them into machine language or "code" that a computer's processor uses. It typically acts as a translator that converts high-level programming languages into machine language. | Compiler, Software Development, Programming | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| compiler-intel-llvm | ecc | N/A | LLVM is a free and open source compiler infrastructure originally built for C and C++. Although its name initially stood for low-level virtual machine, LLVM is now a technology that deals with much more than just virtual machines. The name is no longer officially an initialism. | llvm, high-performance computing, intel optimization | High Performance Computing, Software Engineering | Compiler | Documentation, Uses, and more |
| compiler-rt | mcc, ecc, lcc | N/A | builtins - low-level target-specific hooks required by code generation and other runtime components sanitizer runtimes - AddressSanitizer, ThreadSanitizer, UndefinedBehaviorSanitizer, MemorySanitizer, LeakSanitizer, DataFlowSanitizer profile - library which is used to collect coverage information BlocksRuntime - target-independent implementation of Apple "Blocks" runtime interfaces Description Source: https://github.com/conda-forge/compiler-rt-feedstock/blob/main/recipe/meta.yaml | Runtime Library, Compiler Support, Low-Level Support, Language Features | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| compiler-rt32 | mcc, lcc | N/A | The compiler-rt32 project is a runtime library that provides functionality for compilers in the 32-bit architecture. It includes various runtime components such as sanitizers, builtins, and support libraries for handling memory operations and error detection. | Compiler, Runtime Library, 32-Bit Architecture | Computer Science, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| compiler32 | mcc, lcc | N/A | compiler32 is a lightweight and efficient compiler software designed for compiling source code into executable programs. It supports various programming languages and optimization techniques to enhance the performance of the compiled code. | Compiler, Software Development, Programming | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| compleasm | mcc | 1.0 | Compleasm is a bioinformatics tool for assessing the completeness of genome assemblies using conserved single-copy orthologs. It provides a fast, lightweight alternative to BUSCO for evaluating genome quality, particularly in large-scale or high-throughput assembly workflows. | genome completeness, assembly evaluation, ortholog analysis | Computational genomics, Bioinformatics | Computational Biology Tool | Documentation, Uses, and more |
| comsol | lcc | N/A | COMSOL is an advanced simulation software that provides a finite element analysis, solver, and multiphysics simulation capabilities. It allows for the modeling of complex engineering and scientific problems involving coupled phenomena across fields like electromagnetics, mechanics, fluid dynamics, and chemical engineering, offering a versatile platform for both research and industrial applications. | Simulation, Modeling, Physics, Engineering, Optimization | Mechanical Engineering, Engineering & Technology | Simulation Software | Documentation, Uses, and more |
| conda | lcc | N/A | R | package management, environment management, cross-platform, open-source | Software Engineering, Computer Science | Package Manager | Documentation, Uses, and more |
| conda-bioconductor | mcc | N/A | R | bioinformatics, genomics, data analysis, conda | Bioinformatics, Biological Sciences | Package Manager | Documentation, Uses, and more |
| conmon | ecc | N/A | Conmon is a lightweight tool that provides a way to monitor and manage container processes. It is primarily used in conjunction with container runtimes to provide logging and lifecycle management for containers. | Containerization, Monitoring, Logging, Lightweight | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| coreutils | mcc | N/A | Coreutils is a package that provides the basic file, shell, and text manipulation utilities of the GNU operating system. | GNU, Command Line, Utilities, Open Source | Computer Science, Software Engineering | Command Line Tool | Documentation, Uses, and more |
| cortex_con | mcc | 1.0 | Documentation, Uses, and more | ||||
| cortex_var | mcc | N/A | cortex_var software. | Documentation, Uses, and more | |||
| cortexassembler | lcc | N/A | assembler software. | genome assembly, bioinformatics, next-generation sequencing, de novo assembly | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| coseg | mcc | 1.0 | This program is derived from three C programs and several perl scripts written by Alkes Price as part of an analysis of Alu elements in the human genome. The program was first adapted for use with other repeat families and then extended to support consideration of three co-segregating mutations using Alkes statistical model. In 2008 with the help of Andy Siegel an alternative statistical model was developed and the codebase repackaged into the single source file. | co-segregation analysis, genomics, genetic variation, population genetics, comparative genomics, bioinformatics | Population Genetics, Bioinformatics | Bioinformatics analysis tool | Documentation, Uses, and more |
| coverm | mcc | 1.0 | Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. | Metagenomics, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| cp2k | mcc, lcc | 1.0 | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. Description Source: https://www.cp2k.org/ |
Computational Chemistry, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Molecular Simulation | Documentation, Uses, and more |
| cpio | mcc | N/A | cpio is a general file archiver and compression utility that is used to manage archives of files. It can create, extract, and list the contents of archives in various formats. | file management, archiving, compression, Unix, Linux | Computer Science | Command-line utility | Documentation, Uses, and more |
| crackling | mcc, lcc, ecc | 1.0 | Documentation, Uses, and more | ||||
| crest | mcc | 1.0 | Documentation, Uses, and more | ||||
| crossmap | lcc | N/A | Crossmap is a program for genome coordinates conversion between different assemblies. | Genome Assembly, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cuda | mcc, lcc | N/A | Nvidia CUDA toolkit and samples | Parallel Computing, Gpu Programming, High Performance Computing, Software Development | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| cudnn | lcc | 1.0 | Nvidia cudNN library | Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks | Computer Science | Deep Learning Accelerator | Documentation, Uses, and more |
| cufflinks | mcc, lcc | 1.0 | Cufflinks software. | RNA-Seq, Transcriptomics, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| curl | mcc, ecc, lcc | N/A | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. | Networking, Data Transfer, Command-Line, Scripting | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Networking Tool | Documentation, Uses, and more |
| cutadapt | mcc, lcc | 1.0 | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads. Description Source: https://cutadapt.readthedocs.io/en/stable/ |
Bioinformatics, Ngs, Sequence Analysis, Genomics | Computational Biology, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| dakota | lcc | N/A | Dakota is a software toolkit for optimization, uncertainty quantification, and sensitivity analysis. It provides a flexible framework for integrating various analysis codes and facilitates the exploration of design spaces. | Optimization, Uncertainty Quantification, Sensitivity Analysis, Simulation | Engineering, Mechanical Engineering | Toolkit | Documentation, Uses, and more |
| dal | mcc, lcc | N/A | DAL is a library for collision avoidance in robotics applications. | Robotics, Collision Avoidance | Engineering & Technology | Collision Avoidance Software | Documentation, Uses, and more |
| damageproto | mcc | N/A | Documentation, Uses, and more | ||||
| dartrverse | mcc | 1.0 | Documentation, Uses, and more | ||||
| dask | lcc | 1.0 | Dask makes it easy to scale the Python libraries that you know and love like NumPy, pandas, and scikit-learn. It also allows you to Parallelize any Python code with Dask Futures, letting you scale any function and for loop, and giving you control and power in any situation. Description Source: https://www.dask.org/ |
Parallel Computing, Scalable Computing, Analytics, Data Science | Data Analytics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| dbus | mcc | N/A | D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. Description Source: https://www.freedesktop.org/wiki/Software/dbus/ |
Message Bus System, Interprocess Communication, Process Lifecycle Management | Software Engineering, Computer & Information Sciences | Middleware | Documentation, Uses, and more |
| debugger | mcc, ecc, lcc | N/A | Intel® oneAPI Application Debugger (gdb-oneapi) | Debugging, Software Development | Engineering & Technology | Debugger | Documentation, Uses, and more |
| deep-md-cpu | lcc | N/A | DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning-based models of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. | Deep Learning,Molecular Dynamics,Computational Chemistry | Chemistry, Computational Science | Library | Documentation, Uses, and more |
| deep-md-gpu | lcc | N/A | DeepMD is a deep learning-based molecular dynamics simulation package that leverages GPU acceleration for enhanced performance. | Deep Learning, Molecular Dynamics, GPU Computing, Scientific Computing | Molecular Modeling, Computational Chemistry | Simulation Software | Documentation, Uses, and more |
| deepchem | lcc | 1.0 | DeepChem is a Python library for machine learning and deep learning on molecular and quantum datasets. It is built on top of PyTorch, and other popular ML frameworks. It is designed to make it easy to apply ML to new domains, and to build and benchmark new models. It is also designed to make it easy to use ML in production, by providing easy-to-use model export and deployment APIs. | deep learning, cheminformatics, drug discovery | Chemoinformatics, Drug Discovery | Library | Documentation, Uses, and more |
| deepchem-2.5.0-gpu | lcc | 1.0 | DeepChem is a Python library that aims to democratize the use of deep learning in drug discovery, bioinformatics, and cheminformatics. | Deep Learning, Bioinformatics, Chemoinformatics, Machine Learning | Bioinformatics, Drug Discovery | Library | Documentation, Uses, and more |
| deeppolisher | mcc | 1.0 | DeepPolisher is a transformer-based sequencing correction method similar to DeepConsensus. DeepPolisher is designed to identify errors in genome assemblies. DeepPolisher takes haplotype-specific reads aligned to phased assemblies and produces a VCF file containing potential errors in the assembly. Currently, DeepPolisher can take PacBio HiFi-based assemblies and read alignments to identify potential errors. | genome polishing, long-read sequencing, deep learning, neural networks, genome assembly, error correction, bioinformatics | Genome Assembly, Bioinformatics | Analysis software | Documentation, Uses, and more |
| deeptools | mcc, lcc | 1.0 | deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Description Source: https://deeptools.readthedocs.io/en/latest/ |
Bioinformatics, Hpc Tools, Computational Software | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| deepvariant | mcc, lcc | 1.0 | DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. | Variant Calling, Genetic Variants, Deep Learning, DNA Sequencing | Genomics, Biological Sciences | Variant Caller | Documentation, Uses, and more |
| delly | lcc | 1.0 | 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. | Structural Variant Discovery, Sv Detection, Genomics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| detonate | lcc | 1.0 | Documentation, Uses, and more | ||||
| dev-utilities | mcc, ecc, lcc | N/A | Sample headers and CLI sample browser (oneapi-cli). | Development, Utilities | Computer & Information Sciences, Other Computer & Information Sciences | Tools | Documentation, Uses, and more |
| diamond | mcc, lcc | 1.0 | diamond software. | Sequence Alignment, Ngs Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| diffdock | lcc | 1.0 | DiffDock is a software tool designed for molecular docking simulations, enabling the prediction of protein-ligand interactions with high accuracy and efficiency. | Molecular Docking, Bioinformatics, Computational Chemistry | Bioinformatics, Molecular Docking | Application | Documentation, Uses, and more |
| diffutils | mcc, ecc, lcc | N/A | GNU Diffutils is a package of several programs related to finding differences between files. Description Source: https://github.com/conda-forge/diffutils-feedstock/blob/main/recipe/meta.yaml | Text Comparison, File Difference, Text Analysis, Version Control | Software Engineering, Engineering & Technology | Text Processing | Documentation, Uses, and more |
| dimemas | mcc, lcc | N/A | Dimemas tool | Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems | Computer Science, Engineering & Technology | Performance Prediction Tool | Documentation, Uses, and more |
| dispy | lcc | N/A | dispy is a generic, comprehensive, yet easy to use framework and tools for creating, using and managing compute clusters to execute computations in parallel across multiple processors in a single machine (SMP), among many machines in a cluster, grid or cloud. | distributed computing, parallel processing, Python, task scheduling, cluster computing, HPC | High Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| dnnl | mcc, ecc, lcc | N/A | Performance library of basic building blocks for deep learning applications | Deep Learning, Neural Networks, Machine Learning, Performance Optimization | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| dnnl-cpu-gomp | mcc, lcc | N/A | The dnnl-cpu-gomp is an open-source deep neural network library developed for CPU-based computations employing OpenMP (Open Multi-Processing) as a thread-processing technology. | Deep Learning, Neural Networks, Openmp, Cpu Computing | Machine Learning, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| dnnl-cpu-iomp | mcc, lcc | N/A | dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance. | Deep Learning, Optimization, Cpu Acceleration | Computer & Information Sciences | Documentation, Uses, and more | |
| dnnl-cpu-tbb | mcc, lcc | N/A | DNNL (Deep Neural Network Library) with TBB (Threading Building Blocks) support for optimized performance on CPU architectures. | Deep Learning, High-Performance Computing, Multi-threading, CPU Optimization | Artificial Intelligence, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| docbook-xml | mcc | N/A | DocBook XML is a semantic markup language for technical documentation, providing a framework for writing structured documents. | XML, Documentation, Technical Writing | Computer Science | Markup Language | Documentation, Uses, and more |
| docbook-xsl | mcc | N/A | DocBook XSL is a set of stylesheets for transforming DocBook XML documents into various output formats, such as HTML, PDF, and more. | XML, XSLT, Documentation, Publishing | Computer Science, Computer and Information Sciences | Documentation Tool | Documentation, Uses, and more |
| dock6 | lcc | N/A | DOCK 6 is written in C++ and is functionally separated into independent components, allowing a high degree of program flexibility. Accessory programs are written in C and Fortran 77. We provide source code for all programs. The DOCK suite of programs has modest disk space and memory requirements. | molecular docking, virtual screening, drug discovery, protein–ligand interactions, computational chemistry, structure-based design | Chemistry, Computational Chemistry | Scientific Software | Documentation, Uses, and more |
| dorado | mcc, lcc | 1.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Description Source: https://github.com/nanoporetech/dorado |
Performance Evaluation, Benchmarking, Hpc, Supercomputing | Biology, Engineering & Technology | Tool | Documentation, Uses, and more |
| dorodo | mcc | 1.0 | Documentation, Uses, and more | ||||
| double-conversion | lcc | N/A | Double-Conversion provides binary-decimal and decimal-binary routines for IEEE doubles. This library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine. Description Source: https://github.com/google/double-conversion |
Conversion, Performance, Precision | Numerical Analysis, Computer & Information Sciences | Library | Documentation, Uses, and more |
| doxygen | lcc | N/A | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. | Documentation Generator, Software Development, Programming | Software Development, Software Engineering, Systems & Development | Tool | Documentation, Uses, and more |
| dpct | mcc, ecc, lcc | N/A | Migrate existing CUDA* code to SYCL code. | Cuda Programming, Gpu Computing, Parallel Programming | Computer Science, Computer & Information Sciences | Development Compiler | Documentation, Uses, and more |
| dpl | mcc, ecc, lcc | N/A | Intel(R) oneAPI DPC++ Library provides an alternative for C++ developers who create heterogeneous applications and solutions. Its APIs are based on familiar standards - C++ STL, Parallel STL (PSTL), Boost.Compute, and SYCL* - to maximize productivity and performance across CPUs, GPUs, and FPGAs. | Programming Language Analysis, Syntax Analysis, Language Structure Analysis | Documentation, Uses, and more | ||
| dram | mcc | 1.0 | Documentation, Uses, and more | ||||
| drep | mcc | 1.0 | Drep is a python program for rapidly comparing large numbers of genomes. | Microbiome, Genome Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| dsuite | mcc, lcc | 1.0 | Dsuite provides a fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species. Description Source: https://github.com/millanek/Dsuite |
Python Library, Data Analysis, Data Visualization | Biostatistics, Statistics & Probability | Python Library | Documentation, Uses, and more |
| e2fsprogs | ecc | N/A | e2fsprogs is a set of utilities for creating, checking, and maintaining the ext2, ext3, and ext4 file systems in Linux. | Linux, File System, Utilities | Operating Systems, File Systems | Utility | Documentation, Uses, and more |
| eaglev | mcc | 1.0 | Documentation, Uses, and more | ||||
| earlgrey | mcc | 1.0 | With the EarlGrey framework, you have access to enhanced synchronization features. EarlGrey automatically synchronizes with the UI, network requests, and various queues; but still allows you to manually implement customized timings, if needed. | General Tags transposable elements, repeat annotation, genome annotation, de novo TE discovery, eukaryotic genomes, bioinformatics pipeline | Evolutionary Genomics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| easybuild | mcc, ecc, lcc | N/A | Software build and installation framework | Software Building, High-Performance Computing, Automation | Computer Science, Engineering & Technology | Build Automation | Documentation, Uses, and more |
| ecc/cuda | ecc | N/A | NVIDIA CUDA Toolkit 12.8.0 installed at /share/apps/cuda/12.8.0_570.86.10 | Documentation, Uses, and more | |||
| ecc/miniconda3 | ecc | N/A | Miniconda is a minimal installer for conda, a package manager and environment manager. | Documentation, Uses, and more | |||
| ecc/rclone | ecc | N/A | Rclone is a command-line tool for syncing files to and from cloud storage. | Documentation, Uses, and more | |||
| ecc/spack | ecc | N/A | Spack 0.23.1 is a flexible package manager for HPC environments. | Documentation, Uses, and more | |||
| ed | ecc | N/A | ed is a line-oriented text editor for Unix systems, designed for editing text files in a simple and efficient manner. | Text Editor, Unix, Command Line | Software Engineering, Other Computer and Information Sciences | Text Editing Tool | Documentation, Uses, and more |
| eggnog-mapper | mcc | 1.0 | Eggnog-mapper is a tool for fast functional annotation of novel sequences. | Functional Annotation, Orthology, Gene Function Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| eigen | mcc, lcc | N/A | eigen free peer-reviewed portable C++ source libraries | Linear Algebra, Numerical Computation, C++ Library | Applied Mathematics, Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| elfutils | ecc | N/A | elfutils is a collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux. Description Source: https://sourceware.org/elfutils/ |
Binary Tool, Elf Files, Debugging, Programming | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| elpa | mcc | N/A | The publicly available ELPA library provides highly efficient and highly scalable direct eigensolvers for symmetric (hermitian) matrices. Descripiton Source:https://elpa.mpcdf.mpg.de/ABOUT_ELPA.html | Linear Algebra, Eigenvalue Problems, High-Performance Computing, Scalable Algorithms | Numerical Linear Algebra, Computer & Information Sciences | Library | Documentation, Uses, and more |
| em | lcc | N/A | Documentation, Uses, and more | ||||
| emboss | lcc | N/A | R is a language and environment for statistical computing and graphics (S-Plus like). | Bioinformatics, Computational Biology, Sequence Analysis, Biological Data | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| ensembl-vep | mcc, lcc | 1.0 | VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Description Source: https://useast.ensembl.org/info/docs/tools/vep/index.html |
bioinformatics, genomics, variant analysis | Biology, Genetics | Command-line tool | Documentation, Uses, and more |
| ensembletr | mcc | 1.0 | EnsembleTR is a tool for ensemble Tandem Repeat (TR) calling. It takes one or more VCF files with TR genotypes for a panel of samples and outputs a consensus set of genotypes. | transcriptomics, RNA-seq, ensemble methods, gene expression, transcript reconstruction, bioinformatics | RNA Sequencing Analysis, Bioinformatics | Analysis software | Documentation, Uses, and more |
| entap | mcc | 1.0 | The Eukaryotic Non-Model Transcriptome Annotation Pipeline (EnTAP) is designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. | transcriptome annotation, non-model organisms, functional annotation, ortholog identification, RNA-seq, bioinformatics pipeline | Genome Automation, Bioinformatics | Analysis software | Documentation, Uses, and more |
| exabayes | mcc, lcc | N/A | ExaBayes is a software package used for Bayesian inference of phylogenetic trees and parameters. | Bayesian Inference, Phylogenetics, Parallel Computing, Mcmc, Hpc | Ecology, Biological Sciences | Phylogenetic Software | Documentation, Uses, and more |
| excerpt | mcc | 1.0 | The extra-cellular RNA processing toolkit (exceRpt) was designed to handle the variable contamination and often poor quality data obtained from low input smallRNA-seq samples such as those obtained from extra-cellular preparations. | text processing, field extraction, command-line, Unix utilities, shell pipelines, data wrangling | Software Utilities, Computer Science | Command-line utility | Documentation, Uses, and more |
| exonerate | lcc | 1.0 | Genomic software . | Sequence Alignment, Homology Search, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| expat | mcc, ecc, lcc | N/A | 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) | Xml Parser, Library | Software Engineering, Computer & Information Sciences | Xml Parser | Documentation, Uses, and more |
| extrae | mcc, lcc | N/A | Extrae tool | Performance Analysis, Trace Data, Parallel Applications, Distributed Applications | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development, Engineering & Technology, Training, Infrastructure & Instrumentation | Tool | Documentation, Uses, and more |
| fast5 | lcc | 1.0 | Documentation, Uses, and more | ||||
| fastani | lcc | 1.0 | FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Description Source: https://github.com/ParBLiSS/FastANI |
Bioinformatics, Genome Comparison, Bacterial Genomes | Biology, Biological Sciences | Genome Analysis Tool | Documentation, Uses, and more |
| fastp | mcc, lcc | 1.0 | Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc). | Bioinformatics, Sequencing, Data Processing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| fastplong | mcc | 1.0 | Documentation, Uses, and more | ||||
| fastqc | lcc | 1.0 | FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. Whereas Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems which were generated by the sequencer itself. Description Source: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/1%20Introduction/1.1%20What%20is%20FastQC.html |
Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| fastsimcoal2 | mcc | 1.0 | fastsimcoal2 is a software package designed for simulating and estimating demographic models in population genetics. It allows users to perform coalescent simulations and estimate parameters from genetic data. | Population Genetics, Coalescent Theory, Simulation, Demographic Modeling | Population Genetics | Simulation Software | Documentation, Uses, and more |
| faststructure | mcc | 1.0 | fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. | Population Genetics, Structural Biology, Genomics | Genetics, Biological Sciences | Inference Tool | Documentation, Uses, and more |
| fastx_toolkit | mcc, lcc | 1.0 | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Description Source: http://hannonlab.cshl.edu/fastx_toolkit/ |
Bioinformatics, Short-Reads, Preprocessing | Biology, Biological Sciences | Pre-Processing Tool | Documentation, Uses, and more |
| feems | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| feh | mcc | N/A | feh is a lightweight and fast image viewer for the X Window System, designed for simplicity and speed. | Image Viewer, Lightweight, Fast, X11 | Software Engineering, Other Computer and Information Sciences | Application | Documentation, Uses, and more |
| fenics | lcc | N/A | FEniCS is a popular open-source computing platform for solving partial differential equations (PDEs) with the finite element method (FEM). FEniCS enables users to quickly translate scientific models into efficient finite element code. | partial differential equations, finite element method, numerical simulation, scientific computing, Python, C++ | Computational Mathematics, Computational Science | Scientific computing software | Documentation, Uses, and more |
| fenicsx | mcc | 1.0 | FEniCSx is a popular open-source computing platform for solving partial differential equations (PDEs) using finite element methods (FEM). It provides a high-level interface for defining and solving complex mathematical models. | Finite Element Method, Partial Differential Equations, Computational Science, Open Source | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| fenicsx-mpc | mcc | 1.0 | Documentation, Uses, and more | ||||
| ffmpeg | mcc | 1.0 | FFmpeg is a collection of libraries and tools to process multimedia content such as audio, video, subtitles and related metadata. \r Description Source: https://github.com/FFmpeg/FFmpeg |
Media Processing, Multimedia, Video, Audio | Computer Science | Tool | Documentation, Uses, and more |
| fftw | mcc, lcc | N/A | A Fast Fourier Transform library | Signal Processing, Data Compression, Partial Differential Equations | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| filtlong | mcc | 1.0 | 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. | Bioinformatics, Long Read Sequencing, Sequence Data Processing | Biological Sciences | Data Filtering Tool | Documentation, Uses, and more |
| finder | lcc | 1.0 | Finder software. | Documentation, Uses, and more | |||
| findutils | mcc, ecc, lcc | N/A | The GNU Find Utilities are the basic directory searching utilities of the GNU operating system. These programs are typically used in conjunction with other programs to provide modular and powerful directory search and file locating capabilities to other commands. | Unix, Linux, file searching, command-line tools, system utilities, shell scripting | Systems Programming, Computer Science | System utility software | Documentation, Uses, and more |
| finestructure | mcc | 1.0 | fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals. | population genetics, haplotype analysis, genetic clustering, ancestry inference, ChromoPainter, genomics | Statistical Genetics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| firefox | mcc | N/A | Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. | Web Browser, Internet, Privacy, Open-Source, Cross-Platform | Software Engineering, Computer & Information Sciences | Web Browser | Documentation, Uses, and more |
| fixchr | mcc | 1.0 | Documentation, Uses, and more | ||||
| fixesproto | mcc | N/A | Documentation, Uses, and more | ||||
| flash | mcc | 1.0 | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. Description Source: https://ccb.jhu.edu/software/FLASH/ |
Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis | Physical Sciences | Computational Physics | Documentation, Uses, and more |
| flex | mcc, lcc | N/A | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. | Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator | Software Engineering, Other Computer and Information Sciences | Compiler Tool | Documentation, Uses, and more |
| fltk | mcc, lcc | N/A | FLTK is a cross-platform C++ GUI toolkit for UNIX®/Linux® (X11), Microsoft® Windows®, and macOS®. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL® and its built-in GLUT emulation. Description Source: https://www.fltk.org/ |
Gui Toolkit, Cross-Platform Development, C++ Library | Computer Science, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| fluent | lcc | N/A | Fluent is a computational fluid dynamics (CFD) software tool developed by ANSYS for modeling fluid flow, heat transfer, and chemical reactions in complex geometries. | CFD, fluid dynamics, heat transfer, engineering, simulation | Engineering, Mechanical Engineering | Commercial | Documentation, Uses, and more |
| flye | mcc, lcc | 1.0 | Flye: Fast and accurate de novo assembler for single molecule sequencing reads | Genome Assembly, Long-Read Sequencing, Nanopore Sequencing | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| font-util | mcc | N/A | Documentation, Uses, and more | ||||
| fontconfig | mcc | N/A | Fontconfig is a library for configuring and customizing font access. Description Source: https://www.freedesktop.org/wiki/Software/fontconfig/ |
Fontconfig, Font Management, Font Configuration, Linux, Unix-Like Systems | Software Engineering, Engineering & Technology | System Tool | Documentation, Uses, and more |
| fontsproto | mcc | N/A | Documentation, Uses, and more | ||||
| foss | lcc | N/A | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | Free Software, Open Source Software, Software Development | Other Computer & Information Sciences | Software Library | Documentation, Uses, and more |
| fragpipe | mcc | 1.0 | FragPipe is a software tool designed for the analysis of mass spectrometry data, particularly for proteomics applications. It provides a user-friendly interface and integrates various tools for data processing, including peptide identification and quantification. | Proteomics, Mass Spectrometry, Data Analysis, Bioinformatics | Biochemistry and Molecular Biology, Proteomics | Data Analysis Tool | Documentation, Uses, and more |
| freebayes | mcc, lcc | 1.0 | Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. | Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| freeglut | mcc | N/A | freeglut is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library. GLUT (and hence freeglut) takes care of all the system-specific chores required for creating windows, initializing OpenGL contexts, and handling input events, to allow for trully portable OpenGL programs. Description Source: https://freeglut.sourceforge.net/ |
Graphics Programming, Opengl, Cross-Platform Development, Free Software | Computer Science, Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| freetype | mcc, lcc | N/A | FreeType is a freely available software library to render fonts. Description Source: https://freetype.org/ |
Font Engine, Text Rendering, Typography | Software Engineering, Computer & Information Sciences | Font Engine | Documentation, Uses, and more |
| fribidi | mcc | N/A | The Free Implementation of the Unicode Bidirectional Algorithm. Description Source: https://github.com/fribidi/fribidi?tab=readme-ov-file |
Unicode, Bidirectional Algorithm | Natural Language Processing, Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| funannotate | mcc | 1.0 | Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. Description Source: https://funannotate.readthedocs.io/en/latest/# |
Genome Prediction, Genome Annotation, Fungi, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| fuse-overlayfs | ecc | N/A | This project provides a convenient way to automatically perform a static build using a container. The result is a self-contained binary without dependencies, that can be copied across hosts. | FUSE,Overlay Filesystem,Userspace Filesystem,Linux | Systems Engineering, Computer Science | System utility software | Documentation, Uses, and more |
| galba | mcc | 1.0 | Documentation, Uses, and more | ||||
| gamess | mcc, lcc | 1.0 | General Atomic and Molecular Electronic Structure System | Quantum Chemistry, Electronic Structure Calculations, Ab Initio Calculations | Physical Sciences, Chemical Sciences | Quantum Chemistry | Documentation, Uses, and more |
| gangstr | mcc | 1.0 | GangSTR is a tool for genome-wide profiling tandem repeats from short reads. | Str, Genotyping, Short Tandem Repeats, Sequencing Data Analysis | Genomics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| gapless-0.4 | mcc | 1.0 | Documentation, Uses, and more | ||||
| gatk | mcc, lcc | 1.0 | GATK tools . | Variant Calling, Genotyping, Sequencing Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| gatk4 | mcc | 1.0 | GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discoverye. | Bioinformatics, Genomic Analysis, Variant Discovery, High-Throughput Sequencing | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| gaussian | mcc, lcc | N/A | Gaussian is a computational chemistry software for quantum mechanical simulations, widely used by researchers for studying molecular structures and reactions. It offers advanced capabilities in electronic structure prediction and various spectroscopic properties analysis. | Computational Chemistry, Quantum Chemistry, Molecular Modeling | Chemical Sciences, Natural Sciences | Simulation Software | Documentation, Uses, and more |
| gawk | mcc, ecc | N/A | GaussView aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output. Description Source: https://gaussian.com/gaussview6/ |
Text Processing, Data Manipulation, Pattern Scanning | Chemistry, Computer & Information Sciences | Text Processing Tool | Documentation, Uses, and more |
| gbs-snp-crop | lcc | 1.0 | The GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP) is executed via a sequence of seven Perl scripts that integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files. | genotyping-by-sequencing, SNP filtering, variant curation, linkage mapping, population genetics, plant genomics | Genetic Mapping, Bioinformatics | Analysis software | Documentation, Uses, and more |
| gcc | mcc, lcc | N/A | 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,...). | Compiler, Software Development, Programming | Computer Science | Development Tools | Documentation, Uses, and more |
| gcc-runtime | ecc | N/A | The GCC Runtime Library is a part of the GCC compiler collection that provides runtime support for programs compiled with GCC. It includes various runtime libraries and support files necessary for programs compiled with GCC to execute correctly. | Compiler, Runtime, Library | Software Engineering, Systems & Development, Engineering & Technology | Runtime Library | Documentation, Uses, and more |
| gcccore | lcc | N/A | 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,...). | Compiler, Programming, Software Development | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Core Component | Documentation, Uses, and more |
| gcta | lcc | 1.0 | GCTA (Genome-wide Complex Trait Analysis) is a software tool for estimating the proportion of phenotypic variance explained by all SNPs (Single Nucleotide Polymorphisms) in a genome-wide association study (GWAS). It is widely used in genetic epidemiology and quantitative genetics. | genetics, bioinformatics, GWAS, heritability, SNP analysis | Bioinformatics, Genetics | Analysis Tool | Documentation, Uses, and more |
| gdal | mcc, lcc | 1.0 | GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation. Description Source: https://gdal.org/ |
Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis | Geographic Information Systems, Earth & Environmental Sciences, Engineering & Technology | Library | Documentation, Uses, and more |
| gdb | mcc | N/A | GDB, the GNU Project debugger, allows you to see what is going on `inside' another program while it executes -- or what another program was doing at the moment it crashed. Description Source: https://sourceware.org/gdb |
Debugger, Programming, Software Development | Computer Science, Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| gdbm | mcc, ecc, lcc | N/A | A library of database functions that use extensible hashing and works similar to the standard UNIX dbm functions. Description Source: https://github.com/conda-forge/gdbm-feedstock/blob/main/recipe/meta.yaml | Database Management, Key-Value Store, Persistent Storage, Api | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gdk-pixbuf | mcc | N/A | The Gdk Pixbuf package is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. Description Source: https://www.linuxfromscratch.org/blfs/view/11.2/x/gdk-pixbuf.html |
Image Processing, Graphics, Library | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| geant4 | mcc, lcc | 1.0 | Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. | Software, Physics, Simulation, Particle Transport | Particle Physics, Physical Sciences | Toolkit | Documentation, Uses, and more |
| genmap | mcc | 1.0 | GenMap: Ultra-fast Computation of Genome Mappability. | Genetic Mapping, Linkage Analysis, Genetic Loci Mapping, Family-Based Studies | Biological Sciences | Genetic Mapping Software | Documentation, Uses, and more |
| genomad | mcc | 1.0 | Documentation, Uses, and more | ||||
| genomescope2 | mcc | 1.0 | Genomescope2: Reference-free profiling of polyploid genomes | Genome Analysis, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| genometools | mcc | 1.0 | GenomeTools is a versatile software package for the analysis and manipulation of genomic data. It provides a wide range of tools for tasks such as genome annotation, sequence analysis, and data visualization. | genomics, bioinformatics, sequence analysis, data visualization | Bioinformatics, Genomics | Open Source | Documentation, Uses, and more |
| getorganelle | lcc | 1.0 | Getorganelle is a fast and versatile toolkit for accurate de novo assembly of organelle genomes. | Bioinformatics, Genomics, Molecular Biology, Computational Biology | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| gettext | mcc, ecc, lcc | N/A | GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation | Internationalization, Localization, Software Development | Software Engineering, Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| gfacpp | mcc | 1.0 | Documentation, Uses, and more | ||||
| gff3toolkit | lcc | 1.0 | Documentation, Uses, and more | ||||
| gfortran | mcc | N/A | GNU Fortran is the Fortran compiler of the GNU Compiler Collection (GCC). It supports Fortran 77, Fortran 90, Fortran 95, Fortran 2003, Fortran 2008, and Fortran 2018 standards. | Fortran, Compiler, Open Source, GCC | Numerical Methods, Applied Mathematics | Compiler | Documentation, Uses, and more |
| ghostscript | mcc | N/A | Ghostscript is an interpreter for the PostScript® language and PDF files. It is available under either the GNU GPL Affero license or licensed for commercial use from Artifex Software, Inc. Ghostscript consists of a PostScript interpreter layer and a graphics library. Description Source: https://ghostscript.com/ |
Document-Processing, File-Conversion, Print-Management | Computer Science, Computer & Information Sciences, Engineering & Technology | Software Development | Documentation, Uses, and more |
| ghostscript-fonts | mcc | N/A | Ghostscript fonts are a collection of fonts used by Ghostscript, a suite of software that provides an interpreter for the PostScript language and for PDF. | fonts, Ghostscript, PostScript, PDF | Computer Science, Computer and Information Sciences | Font Library | Documentation, Uses, and more |
| giflib | mcc | N/A | Giflib is a software package designed for reading and writing GIF (Graphics Interchange Format) images. It provides a set of utilities for processing GIFs, including conversion to and from various formats, making it a valuable tool for developers working with GIF animations and image processing in applications or web services. | Library, Image Processing, Gif Images | Image Processing, Computer Science | Package | Documentation, Uses, and more |
| gist-pipeline | lcc | 1.0 | Documentation, Uses, and more | ||||
| git | mcc | N/A | Git is a distributed version control system, widely used for tracking changes in source code during software development. It allows multiple developers to work collaboratively on a project, providing tools for managing versions, resolving conflicts, and maintaining a history of changes made to the codebase. | Version Control, Software Development, Source Code Management | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Development Tools | Documentation, Uses, and more |
| git-lfs | lcc | N/A | git-lfs software. | Version Control, File Storage, Git Extension | Version Control, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| gizmo | lcc | N/A | Documentation, Uses, and more | ||||
| gklib | mcc | 1.0 | A library of various helper routines and frameworks used by Karypis Lab software such as METIS. | Geometric Kernels, Computational Geometry, Algorithms | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| gl2ps | mcc | N/A | GL2PS is a C library providing high quality vector output for any OpenGL application. The main difference between GL2PS and other similar libraries is the use of sorting algorithms capable of handling intersecting and stretched polygons, as well as non manifold objects. GL2PS provides advanced smooth shading and text rendering, culling of invisible primitives, mixed vector/bitmap output, and much more... Description Source: https://www.geuz.org/gl2ps/ |
Opengl, Postscript, Printing, Graphics, Vector Graphics | Visualization, Computer Science | Library | Documentation, Uses, and more |
| glib | mcc, ecc | N/A | GLib is a general-purpose, portable utility library, which provides many useful data types, macros, type conversions, string utilities, file utilities, a mainloop abstraction, and so on. It is one of the base libraries of GTK+. Description Source: https://docs.gtk.org/glib/ |
Utility Library, C Programming, Data Structures, Memory Management, Thread Support | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| glibc | ecc | N/A | glibc, the GNU C Library, is an essential part of most systems running the Linux kernel. It provides the necessary functionality for programs written in the C programming language to interact with the operating system and hardware. | C Library, Operating System, System Programming | Computer & Information Sciences | Library | Documentation, Uses, and more |
| glimpse | mcc | 1.0 | Documentation, Uses, and more | ||||
| glnexus | lcc | 1.0 | Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects. | Variant Calling, Genotyping, Haplotype-Aware, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| glnexus-1.4.1 | mcc | 1.0 | glnexus is a tool for genotyping and variant calling from genomic data, specifically designed to handle large-scale sequencing projects efficiently. | genomics, bioinformatics, variant calling, high-performance computing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| globus-cli | mcc, lcc | N/A | A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. | Command-Line Interface, File Transfer Service, Data Management, Data Transfer | Computer Science, Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| glpk | mcc | N/A | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. Description Source: https://www.gnu.org/software/glpk/ |
Linear Programming, Optimization, Open-Source | Applied Mathematics, Mathematics | Mathematical Optimization | Documentation, Uses, and more |
| glproto | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| gmake | mcc, ecc | N/A | GNU Make is a tool that controls the generation of executables and other non-source files from a program's source files. It is widely used for managing build processes in software development. | Build Automation, Makefile, Open Source, GNU | Computer Science, Software Engineering | Build System | Documentation, Uses, and more |
| gmap | lcc | 1.0 | Gmap is a genomic mapping and alignment program for mRNA and EST sequences. | Bioinformatics, Computational Biology, Genomics, Transcriptomics, RNA-Seq | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gmp | mcc, ecc, lcc | N/A | GNU MP is a portable library written in C for arbitrary precision arithmetic on integers, rational numbers, and floating-point numbers. It aims to provide the fastest possible arithmetic for all applications that need higher precision than is directly supported by the basic C types. Description Source: https://gmplib.org/manual/Introduction-to-GMP |
Computational Software, Library, Mathematics, Software Development | Pure Mathematics, Mathematics | Library | Documentation, Uses, and more |
| gmsh | lcc | N/A | Mesh software . | mesh generation, finite element analysis, CAD, post-processing | Engineering, Finite Element Analysis | Mesh Generator | Documentation, Uses, and more |
| gnu | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Open Source, Development Tools, Utilities | Software Engineering, Computer Science | Development Tools | Documentation, Uses, and more |
| gnu-parallel | mcc | 1.0 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel. Description Source: https://www.gnu.org/software/parallel/ |
parallel computing, job scheduling, command-line tools, GNU, open-source | Computer Science | Command-line tool | Documentation, Uses, and more |
| gnu12 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu12/12.1.0 | mcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu12/openmpi4 | mcc | N/A | A powerful implementation of MPI/SHMEM | Documentation, Uses, and more | |||
| gnu14 | ecc, lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu7 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu8 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu9 | mcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu_parallel | mcc | N/A | GNU parallel 20240922 | parallel computing, shell scripting, command line | Computer Science | Command-line tool | Documentation, Uses, and more |
| gnuplot | mcc | N/A | GNUPlot 5.4.10 in a Conda environment | Graphing, Visualization, Data Analysis | Computational Science, Physical Sciences | Plotting & Data Visualization | Documentation, Uses, and more |
| go | ecc | N/A | Go is expressive, concise, clean, and efficient. Its concurrency mechanisms make it easy to write programs that get the most out of multicore and networked machines, while its novel type system enables flexible and modular program construction. Go compiles quickly to machine code yet has the convenience of garbage collection and the power of run-time reflection. It's a fast, statically typed, compiled language that feels like a dynamically typed, interpreted language. Description Source: https://go.dev/doc/ |
Programming Language, Open Source, Concurrency, Systems Programming | Software Engineering, Computer Science | Programming Language | Documentation, Uses, and more |
| go-bootstrap | ecc | N/A | go-bootstrap is a Go programming language template project that provides a starting point for building Go applications with a predefined project structure, configuration, and best practices. | Go, Template, Project Structure, Best Practices | Engineering & Technology | Template Project | Documentation, Uses, and more |
| go-md2man | ecc | N/A | A tool for converting Markdown files to man pages. | Markdown, Documentation, Man Pages | Software Engineering, Other Computer and Information Sciences | Command Line Tool | Documentation, Uses, and more |
| gobject-introspection | mcc | N/A | GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate metadata files, in addition to the actual native C library. Then language bindings can read this metadata and automatically provide bindings to call into the C library. Description Source: https://gi.readthedocs.io/en/latest/ |
Middleware, Language Bindings, Automation, Compatibility | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gocryptfs | ecc | N/A | gocryptfs is a user-space encryption tool for filesystems, designed to provide secure encryption of files and directories. | encryption, filesystems, security, data protection | Cryptography, Computer Science | Encryption Tool | Documentation, Uses, and more |
| gompi | lcc | N/A | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | Hpc, Parallel Computing, Mpi, Distributed Computing | Engineering & Technology | Documentation, Uses, and more | |
| gperf | mcc, ecc | N/A | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. Description Source: https://www.gnu.org/software/gperf/ |
Perfect Hash Function, Hash Table, Optimization, Gnu | Computer Science, Computer & Information Sciences | Compiler/Generator | Documentation, Uses, and more |
| graphaligner | mcc | 1.0 | Documentation, Uses, and more | ||||
| graphviz | lcc | N/A | Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. | Graph Visualization, Diagramming, Open Source Software | Graph Theory, Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| grep | ecc | N/A | grep is a command-line utility for searching plain-text data sets for lines that match a regular expression. | Text Processing, Command Line Tool, Regular Expressions | Computer Science | Command Line Utility | Documentation, Uses, and more |
| gridss | lcc | 1.0 | Gridss is a module software suite containing tools useful for the detection of genomic rearrangements. | Structural Variant Calling, DNA Sequencing, Genomic Rearrangements | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| gromacs | mcc, lcc | 1.0 | GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. | Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems | Chemistry, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| gromacs-plumed2 | lcc | N/A | GROMACS with PLUMED integration for enhanced molecular dynamics simulations and analysis. | Molecular Dynamics, Simulation, Biophysics, Computational Chemistry | Biophysics, Biochemistry and Molecular Biology | Simulation Software | Documentation, Uses, and more |
| gromacs-plumed2-gpu | lcc | N/A | Documentation, Uses, and more | ||||
| gsalign | mcc | 1.0 | Documentation, Uses, and more | ||||
| gsl | mcc, lcc | N/A | GNU Scientific Library (GSL) | Numerical Library, Mathematical Functions, C Programming, C++ Programming | Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| gtdbtk | mcc | 1.0 | GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. | bioinformatics, genomics, taxonomy, data analysis | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| gtf2csv | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| gtk-doc | mcc | N/A | gtk-doc is a documentation generation tool for GTK and GNOME projects. It allows developers to create API documentation from comments in the source code. | Documentation, API, GTK, GNOME | Software Engineering, Computer Science | Documentation Generator | Documentation, Uses, and more |
| gtkplus | mcc | N/A | GTK+ is a multi-platform toolkit for creating graphical user interfaces. It is used by many applications to provide a consistent look and feel across different operating systems. | GUI, Toolkit, Cross-platform, Open Source | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| gubbins | lcc | 1.0 | Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. | Bacterial Recombination, Whole-Genome Sequencing, Population Genetics | Bioinformatics, Biological Sciences | Standalone | Documentation, Uses, and more |
| guidance | lcc | 1.0 | Documentation, Uses, and more | ||||
| guppy | mcc | 1.0 | Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' production basecalling algorithms and several bioinformatic post-processing features. It is run from the command line in Windows, Mac OS, and on multiple Linux platforms. Guppy is also integrated with our sequencing instrument software, MinKNOW, and a subset of Guppy features are available via the MinKNOW UI. A selection of configuration files allows basecalling of DNA and RNA libraries made with Oxford Nanopore Technologies’ current sequencing kits, in a range of flow cells. Description Source: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview |
Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing | Genomics, Biological Sciences | Basecaller | Documentation, Uses, and more |
| harfbuzz | mcc | N/A | HarfBuzz is a text shaping library. Using the HarfBuzz library allows programs to convert a sequence of Unicode input into properly formatted and positioned glyph output—for any writing system and language. Description Source: https://harfbuzz.github.io/ |
Text Shaping Engine, Unicode Text, Text Layout, Font Features Customization | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hdf5 | mcc, lcc | N/A | A general purpose library and file format for storing scientific data | File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing | Computer Science | Library/Tool | Documentation, Uses, and more |
| help2man | mcc, lcc | N/A | help2man produces simple manual pages from the '--help' and '--version' output of other commands. | Documentation, Man Pages, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| herro | lcc | 1.0 | Documentation, Uses, and more | ||||
| hic-pro | lcc | N/A | Hic-Pro | Bioinformatics, Genomics, Chromatin Structure, Hi-C Data, Data Visualization, Chromatin Interactions | Genomics, Biological Sciences | Data Analysis | Documentation, Uses, and more |
| hicpro | mcc | 1.0 | HiCPro is a software tool designed for the analysis of Hi-C data, which is used to study the three-dimensional architecture of genomes. | bioinformatics, genomics, data analysis | Computational Biology, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| hicup | lcc | N/A | Documentation, Uses, and more | ||||
| hifiasm | mcc | 1.0 | Hifiasm is fast haplotype-resolved de novo assembler for PacBio HiFi reads. | Assembler, De Novo Assembly | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| hifiasm-0.25.0 | mcc | 1.0 | Hifiasm is a high-performance assembler for long reads, designed to produce high-quality assemblies from high-throughput sequencing data. | genome assembly, bioinformatics, long-read sequencing | Computational Biology, Bioinformatics | Assembly Tool | Documentation, Uses, and more |
| hisat | lcc | 1.0 | HISAT is a fast and sensitive alignment program for mapping next-generation sequencing reads to a reference genome. | alignment, genomics, bioinformatics | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| hisat2 | mcc, lcc | 1.0 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs (Sirén et al. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first implementation. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). Description Source: https://daehwankimlab.github.io/hisat2/ |
Alignment, Ngs, Genomics, Transcriptomics | Biology, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| hmmer | mcc, lcc | 1.0 | HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Description Source: http://hmmer.org/ |
Bioinformatics, Computational Biology, Proteomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| hmmer2go | lcc | 1.0 | Documentation, Uses, and more | ||||
| hocort | mcc | 1.0 | Documentation, Uses, and more | ||||
| homer | mcc, lcc | 1.0 | HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. Description Source: http://homer.ucsd.edu/homer/motif/ |
Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| htseq | lcc | 1.0 | HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. | Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| htslib | mcc | N/A | HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. Description Source: https://github.com/samtools/htslib |
Bioinformatics, Sequencing Data, File Format Processing, C Library | Genomics, Biological Sciences | Data Processing | Documentation, Uses, and more |
| humann | mcc, lcc | 1.0 | Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). | Metagenomics, Microbiome, Pathway Analysis, Bioinformatics | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| humann2 | lcc | 1.0 | The HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately determining the presence, absence, and abundance of metabolic pathways in a microbial community from metagenomic or metatranscriptomic sequencing data. | Genomics | Documentation, Uses, and more | ||
| hwloc | mcc, lcc | N/A | Portable Hardware Locality | Machine Topology, Hardware Architecture, System Software | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hyphy | lcc | 1.0 | Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. | Bioinformatics, Molecular Evolution, Phylogenetics, Epidemiology | Bioinformatics, Biological Sciences | Open-Source Software | Documentation, Uses, and more |
| hyphy-analysis | lcc | N/A | HyPhy is a software package for hypothesis testing and model selection in molecular evolution. | bioinformatics, phylogenetics, molecular evolution, statistical analysis | Computational Biology, Molecular Evolution | Analysis Tool | Documentation, Uses, and more |
| hypo | mcc | 1.0 | HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | Statistical Analysis, Hypothesis Testing, Data Analysis | Statistics & Probability | Scientific Software | Documentation, Uses, and more |
| hypre | mcc, lcc | N/A | Scalable algorithms for solving linear systems of equations | Preconditioners, Solvers, Linear Systems, Sparse Matrices | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| icc | lcc | N/A | Intel C and C++ compilers | compiler, C++, performance, parallel computing | Software Engineering, Computer Science | Compiler | Documentation, Uses, and more |
| icc32 | lcc | N/A | Documentation, Uses, and more | ||||
| iccifort | lcc | N/A | Intel C, C++ & Fortran compilers | Compiler, High-Performance Computing, Optimization | Engineering & Technology | Programming Tool | Documentation, Uses, and more |
| icu4c | mcc | N/A | ICU (International Components for Unicode) is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software. | Unicode, Globalization, Cross-Platform, Libraries | Software Engineering, Computer & Information Sciences | Development | Documentation, Uses, and more |
| idr | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| ifort | lcc | N/A | Intel® Fortran Compiler Classic for building optimized Intel® 64, and IA-32 CPUs | Fortran, Compiler, High Performance Computing, Scientific Computing | Computer Science, Software Engineering | Compiler | Documentation, Uses, and more |
| ifort32 | lcc | N/A | Intel® Fortran Compiler Classic for building optimized Intel® 64, and IA-32 CPUs | Documentation, Uses, and more | |||
| igv | mcc | N/A | IGV software. | Visualization, Genomics, Sequencing, Data Analysis | Bioinformatics, Biological Sciences | Genomics Software | Documentation, Uses, and more |
| iimpi | lcc | N/A | Intel C/C++ and Fortran compilers, alongside Intel MPI. | Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis | Bioinformatics, Biological Sciences | Analytical Tool | Documentation, Uses, and more |
| imagemagick | mcc, lcc | 1.0 | ImageMagick https://imagemagick.org/script/install-source.php | Image Processing, Graphics Editing, Conversion Tool | Image Processing, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| imb | mcc, lcc | N/A | Intel MPI Benchmarks (IMB) | Benchmarking, In-Memory Databases | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| imkl | lcc | N/A | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. | Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Open-Source | Documentation, Uses, and more |
| imlib2 | mcc | N/A | Imlib2 is an image loading and rendering library that provides a simple API for handling images in various formats. | Image Processing, Graphics, Library | Image Processing, Computer Science | Library | Documentation, Uses, and more |
| impi | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Message Passing Library, Parallel Computing, Asynchronous Messaging | High-Performance Computing, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| impi/2018.3.222 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| impi/2019.3.199 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| impi/2019.4.243 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| implicit-landuse | lcc | 1.0 | Documentation, Uses, and more | ||||
| init_opencl | mcc, lcc | N/A | init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications. | Software, Compiler, Library, Hpc | Computer & Information Sciences | Software Development | Documentation, Uses, and more |
| inotify-tools | mcc, lcc | 1.0 | A set of command-line programs for using inotify, a Linux kernel feature that monitors filesystem events. | Linux, File Monitoring, System Tools | Systems, Other Computer and Information Sciences | Command-line Tools | Documentation, Uses, and more |
| inputproto | mcc, lcc | N/A | A package that provides the headers used to compile Xlib clients. | Software Development, Headers, Xlib | Computer & Information Sciences | Library | Documentation, Uses, and more |
| inspector | mcc, lcc | 1.0 | Inspector is a software tool used for monitoring and analyzing various aspects of computer systems and networks to detect and prevent security breaches or performance issues. | Monitoring, Security, Network Analysis | Computer Science, Computer & Information Sciences | Security Software | Documentation, Uses, and more |
| intel | lcc | N/A | Intel Compiler Family (C/C++/Fortran for x86_64) | Compiler, Optimization, Performance, Debugging | Computer and Information Sciences | Development Tools | Documentation, Uses, and more |
| intel-oneapi-compilers | mcc, lcc | N/A | Intel oneAPI Compilers provide a unified programming model for high-performance computing, enabling developers to optimize applications across various architectures including CPUs and GPUs. | compilers, high-performance computing, Intel, oneAPI, C++, Fortran | Computer Science, Software Engineering | Compiler | Documentation, Uses, and more |
| intel-oneapi-mkl | mcc | N/A | Intel oneAPI Math Kernel Library (MKL) provides highly optimized mathematical functions for scientific computing, including linear algebra, fast Fourier transforms, and vector mathematics. | Mathematics, High-Performance Computing, Numerical Libraries | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| intel-oneapi-mpi | mcc, lcc | N/A | Intel oneAPI MPI is a high-performance message passing interface library designed to facilitate parallel programming in distributed computing environments. | MPI, Parallel Computing, High Performance Computing, Distributed Systems | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| intel-oneapi-tbb | mcc | N/A | Intel oneAPI Threading Building Blocks (TBB) is a C++ template library for parallel programming that abstracts low-level threading details, allowing developers to write scalable and high-performance applications. | Parallel Computing, C++, Performance, Multithreading | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| intel-parallel-studio-cluster.2019.5-gcc | mcc | N/A | Intel Parallel Studio Cluster is a suite of tools for optimizing and debugging high-performance applications, particularly for clusters and cloud environments. | HPC, Parallel Computing, Performance Optimization, Debugging Tools | Computer Science | Development Tools | Documentation, Uses, and more |
| intel-parallel-studio-cluster.2020.4-gcc | mcc | N/A | Intel Parallel Studio Cluster is a suite of tools for developing high-performance applications on clusters, providing advanced capabilities for parallel programming, performance analysis, and debugging. | HPC, Parallel Computing, Performance Analysis, Debugging, Cluster Computing | Computer Science | Development Tools | Documentation, Uses, and more |
| intel_ipp_ia32 | mcc, lcc | N/A | Intel Integrated Performance Primitives (IPP) for IA-32 architecture provides a set of highly optimized software functions for multimedia processing, data processing, and communications. | HPC, Performance Optimization, Multimedia Processing | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| intel_ipp_intel64 | mcc, ecc, lcc | N/A | A library of multimedia and data processing optimized for Single Instruction, Multiple Data (SIMD) instructions. | Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography | Software Engineering, Computer & Information Sciences, Systems & Development | Commercial | Documentation, Uses, and more |
| intel_ippcp_ia32 | mcc, lcc | N/A | Intel Integrated Performance Primitives - Cryptography (IPP-Crypto) is a library that provides highly optimized building blocks for a variety of encryption and decryption algorithms on Intel architecture processors. It aims to accelerate cryptographic operations to enhance performance in software applications. | Cryptographic Library, Performance Optimization, Intel Architecture | Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| intel_ippcp_intel64 | mcc, ecc, lcc | N/A | Intel Integrated Performance Primitives Cryptography (IPP Cryptography) is a collection of highly optimized cryptographic functions and algorithms developed by Intel for high-performance computing applications. It provides a set of cryptographic functions optimized for Intel processors to enhance the security and performance of cryptographic operations in software. | Cryptography, High-Performance Computing, Intel Processors, Security | Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| intelpython3_full | lcc | N/A | Intel Distribution for Python is a distribution of Python optimized for performance on Intel architecture, providing libraries and tools for high-performance computing and data analytics. | Python, Data Science, Machine Learning, High Performance Computing, Intel | Data Analysis, Machine Learning | Programming Language Distribution | Documentation, Uses, and more |
| interproscan | mcc, lcc | 1.0 | Interproscan is the software package that allows sequences to be scanned against InterPro's member database signatures. | Bioinformatics, Proteomics, Sequence Analysis, Functional Annotation | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| intltool | mcc | N/A | intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. Description Source: https://freedesktop.org/wiki/Software/intltool/ |
Localization, Translation, Internationalization | Computer Science, Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| iphop | mcc | 1.0 | Documentation, Uses, and more | ||||
| ipyrad | lcc | N/A | ipyrad is a software package for assembling and analyzing RADseq data. It provides tools for processing raw sequence data, assembling loci, and performing population genetic analyses. | RADseq, Genomics, Bioinformatics, Population Genetics | Bioinformatics, Population Genetics | Command Line Tool | Documentation, Uses, and more |
| iqtree | mcc | 1.0 | IQ-TREE is an efficient phylogenomic software by maximum likelihood. | Phylogenetics, Evolutionary Biology, Bioinformatics | Biochemistry and Molecular Biology, Phylogenetics | Standalone | Documentation, Uses, and more |
| iqtree-2.2.0_beta | mcc | 1.0 | IQ-TREE is a fast and effective software for phylogenomic analysis, providing maximum likelihood estimation of phylogenetic trees. | phylogenetics, bioinformatics, maximum likelihood, tree estimation | Computational Biology, Phylogenetics | Executable | Documentation, Uses, and more |
| isoseq | mcc | 1.0 | Iso-Seq is a method for full-length transcript sequencing that allows for the identification of isoforms and alternative splicing events in RNA sequencing data. | RNA-Seq, Transcriptomics, Bioinformatics | Bioinformatics, Molecular Biology | Command Line Tool | Documentation, Uses, and more |
| isoseq3 | mcc, lcc | 1.0 | IsoSeq3 is a software tool for analyzing full-length transcript sequences generated by Pacific Biosciences (PacBio) sequencing technology. It focuses on the identification and characterization of isoforms in RNA sequencing data. | RNA-Seq, Transcriptomics, PacBio, Isoform Analysis | Molecular Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| itac | mcc, lcc | N/A | The Intel® Trace Analyzer and Collector profiles and analyzes MPI applications to help focus your optimization efforts. Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/trace-analyzer.html#gs.4oj2fp |
Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jags | lcc | 1.0 | JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. Description Source: https://mcmc-jags.sourceforge.io/ |
Bayesian Statistics, Hierarchical Modeling, Mcmc Simulation | Statistics & Probability, Mathematics | Statistical Modeling | Documentation, Uses, and more |
| jasper | mcc, lcc | N/A | 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. | Image Processing, Open-Source, Jpeg-2000 | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| java | mcc, lcc | N/A | Java jdk-11.0.2 | Programming Language, Computing Platform | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jax | lcc | 1.0 | JAX is Autograd and XLA, brought together for high-performance numerical computing, including large-scale machine learning research. Description Source: https://github.com/google/jax |
Machine Learning, Numerical Computing, Scientific Computing | Artificial Intelligence, Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| jellyfish | mcc, lcc | 1.0 | Jellyfish is a fast and memory-efficient software for counting k-mers in DNA sequences, which are commonly used in genome analysis and sequence assembly. It provides algorithms for k-mer counting, storage, and querying to extract valuable insights from biological data. | K-Mer Counting, DNA Sequences, Sequence Analysis | Computational Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| jmodeltest | lcc | N/A | jmodeltest. | phylogenetics, model selection, bioinformatics, evolutionary biology | Phylogenetics, Evolutionary Biology | Standalone | Documentation, Uses, and more |
| json-c | mcc | N/A | JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. It aims to conform to RFC 7159. Description Source: https://github.com/json-c/json-c/wiki |
C Library, Json Encoding, Json Decoding, Data Manipulation | Computer Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| jsoncpp | lcc | N/A | JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Description Source: https://github.com/open-source-parsers/jsoncpp |
C++, Json, Library, Data Manipulation | Software Engineering, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| juicebox_env | mcc | 1.0 | Documentation, Uses, and more | ||||
| julia | mcc, lcc | N/A | Julia is a high-level, high-performance dynamic programming language for technical computing. | Programming Language, Technical Computing, High-Performance Computing, Scientific Computing, Numerical Analysis | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| kaiju | mcc | 1.0 | Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database. | Bioinformatics, Computational Biology, Genomics, Sequencing Data | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| kallisto | mcc, lcc | 1.0 | Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kat | mcc, lcc | 1.0 | kat (K-mer Analysis Tool) is a software package designed for analyzing k-mer frequencies in DNA sequences, providing insights into genomic data. | bioinformatics, genomics, sequence analysis | Bioinformatics, Genomics | Analysis Tool | Documentation, Uses, and more |
| kbproto | mcc, lcc | N/A | The kbproto package provides the core XKB protocol and extension definitions for usage with X11 protocol libraries. | X11 Protocol, Keyboard Properties | Computer Science, Computer & Information Sciences | Protocol | Documentation, Uses, and more |
| kmc | mcc | 1.0 | Kmc is a tool for efficient k-mer counting and filtering of reads based on k-mer content. | Sequence Analysis, Genome Assembly, Metagenomics | Computational Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| kneaddata | mcc, lcc | 1.0 | Kneaddata is a tool designed to perform quality control on metagenomic sequencing data. | Bioinformatics, Metagenomics, Data Quality Control | Biomolecular Sciences, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| kount | lcc | 1.0 | Documentation, Uses, and more | ||||
| kraken-biom | lcc | 1.0 | Documentation, Uses, and more | ||||
| kraken2 | mcc | 1.0 | Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Description Source: https://github.com/DerrickWood/kraken2/wiki/About-Kraken-3 |
bioinformatics, sequence classification, metagenomics, taxonomy | Bioinformatics, Metagenomics | Command-line tool | Documentation, Uses, and more |
| kraken2-2.1.3 | mcc | 1.0 | Kraken 2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. | bioinformatics, sequence classification, metagenomics | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| krakenuniq | mcc | 1.0 | KrakenUniq is a taxonomic sequence classifier that uses a unique k-mer approach to classify sequences from metagenomic data. | bioinformatics, metagenomics, sequence classification | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| krb5 | mcc | N/A | Kerberos is a network authentication protocol designed to provide strong authentication for client/server applications through secret-key cryptography. | Authentication, Security, Networking | Computer Science | Library | Documentation, Uses, and more |
| krona | mcc | 1.0 | Documentation, Uses, and more | ||||
| lammps | mcc, lcc | 1.0 | Large-scale Atomic/Molecular Massively Parallel Simulator | Molecular Dynamics, Simulation, Computational Chemistry | Physical Chemistry, Chemical Sciences | Code/Package | Documentation, Uses, and more |
| lammps-mace | lcc | 1.0 | Documentation, Uses, and more | ||||
| lammps-mace-mliap | lcc | 1.0 | Documentation, Uses, and more | ||||
| lammpss-deepmd-kit-module-cpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| lammpss-deepmd-kit-module-gpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| laser | mcc | 1.0 | Documentation, Uses, and more | ||||
| lastz | lcc | 1.0 | LASTZ - pairwise DNA sequence aligner | Bioinformatics, DNA Sequencing, Alignment, Comparative Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| latex | lcc | N/A | LaTeX is a typesetting system commonly used for scientific and technical documentation preparation. It is widely used for the communication and publication of scientific documents in fields such as mathematics, computer science, physics, engineering, and more. | Typesetting, Scientific Communication, Document Preparation | Typesetting and Formatting, Natural Sciences, Mathematics, Computer & Information Sciences, Engineering & Technology | Publishing | Documentation, Uses, and more |
| lcc-user | lcc | N/A | Documentation, Uses, and more | ||||
| lcc-users | lcc | N/A | Documentation, Uses, and more | ||||
| lcms | mcc | N/A | LCMS (Liquid Chromatography Mass Spectrometry) is a software package designed for the analysis of mass spectrometry data, particularly in the context of liquid chromatography. | Mass Spectrometry, Data Analysis, Chemistry, Bioinformatics | Chemistry, Chemical Sciences | Data Analysis | Documentation, Uses, and more |
| lefse | mcc | 1.0 | LEfSe (Linear discriminant analysis Effect Size) is a tool for high-dimensional biomarker discovery and explanation. It is particularly useful in bioinformatics for analyzing microbiome data. | bioinformatics, microbiome, statistical analysis, biomarker discovery | Computational Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| lftp | mcc | 1.0 | lftp is a file transfer program that allows sophisticated FTP, HTTP and other connections to other hosts. If site is specified then lftp will connect to that site otherwise a connection has to be established with the open command. | File Transfer | Networking, Computer Science | Command Line Tool | Documentation, Uses, and more |
| lhapdf | lcc | 1.0 | LHAPDF is a library for reading and interpolating parton distribution functions (PDFs) used in high-energy physics. | High-Energy Physics, Parton Distribution Functions, Computational Physics | High-Energy Physics, Particle and High-Energy Physics | Library | Documentation, Uses, and more |
| libbsd | mcc, ecc, lcc | N/A | libbsd is a library that provides a collection of functions from the FreeBSD operating system for enhancing compatibility and portability across different Unix-like systems. It includes various system-related functions that are widely used in Unix programming to access system services and perform low-level operations. | Library, Bsd, Operating System | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| libcroco | mcc | N/A | libcroco is a library for manipulating CSS (Cascading Style Sheets) in a flexible and efficient manner, primarily used in web development and rendering engines. | CSS, Web Development, Library, Rendering | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libdrm | mcc | N/A | This is libdrm, a userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other operating systems that support the ioctl interface. The library provides wrapper functions for the ioctls to avoid exposing the kernel interface directly, and for chipsets with drm memory manager, support for tracking relocations and buffers. Description Source: https://gitlab.freedesktop.org/mesa/drm |
Graphics, Linux, Kernel, Driver | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libedit | mcc, lcc | N/A | libedit is a library for reading and editing user input in a command-line interface. It provides tools for handling input editing, command history, and line parsing in a terminal environment. | Library, Command-Line, Line Editing, History, Open-Source | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| libepoxy | mcc | N/A | Epoxy is a library for handling OpenGL function pointer management for you. It hides the complexity of dlopen(), dlsym(), glXGetProcAddress(), eglGetProcAddress(), etc. from the app developer, with very little knowledge needed on their part. They get to read GL specs and write code using undecorated function names like glCompileShader(). Description Source: https://github.com/anholt/libepoxy |
Opengl, Library, Graphics | Computer Science, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libevent | mcc, lcc | N/A | Libevent is an event notification library for developing scalable network servers. The Libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, Libevent also support callbacks due to signals or regular timeouts. Description Source: https://libevent.org/doc/ |
Event Notification, Callback Functions, Scalable, Efficient | Software Engineering, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libexif | mcc | N/A | libexif is a library for reading and writing EXIF (Exchangeable Image File Format) data in image files. | Camera make, Camera model, Exposure time, F-number, ISO speed ratings, Date and time | Software Engineering, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libfabric | mcc, ecc, lcc | N/A | Development files for the libfabric library | Fabric Interfaces, High-Performance Computing, Communication Resources | Computer Science, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| libffi | mcc, ecc, lcc | N/A | 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. FFI stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface. Description Source: https://github.com/libffi/libffi |
Library, Portability, Calling Conventions | Software Engineering, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libfontenc | mcc | N/A | libfontenc is a library used for encoding font data in X Window System, allowing for the representation of various character sets. | Font Management, X Window System, Character Encoding | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libfuse | mcc, ecc | N/A | libfuse is a library that allows the creation of fully functional file systems in userspace. It provides a simple interface for implementing file systems without the need for kernel-level code. | File System, Userspace, Linux, Development | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libgcrypt | mcc | N/A | Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG | Cryptography, Security, Encryption | Computer Science, Computer & Information Sciences | Cryptographic Library | Documentation, Uses, and more |
| libgit2 | mcc | N/A | libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language that supports C bindings. Description Source: https://libgit2.org/ |
Version Control System, Git, Library | Software Engineering, Computer & Information Sciences | Version Control System | Documentation, Uses, and more |
| libgpg-error | mcc, ecc | N/A | libgpg is a library that provides an API for interacting with GnuPG (GNU Privacy Guard) for encryption, decryption, and key management tasks. It allows developers to integrate GnuPG functionality into their applications. | Error Handling, Library, Gnupg | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libice | mcc, lcc | N/A | libice is a library that provides support for Inter-Client Exchange (ICE) in the X Window System, allowing X clients to securely exchange data through the X server. | Library, Inter-Client Exchange, X Window System | Computer & Information Sciences | Communication | Documentation, Uses, and more |
| libiconv | mcc, ecc, lcc | N/A | libiconv provides an iconv() implementation, for use on systems which don't have one, or whose implementation cannot convert from/to Unicode. Description Source: https://www.gnu.org/software/libiconv/#TOCintroduction |
Character Set Conversion, Text Data, Encoding | Other Computer & Information Sciences, Computer & Information Sciences | Conversion Tool | Documentation, Uses, and more |
| libid3tag | mcc | N/A | Documentation, Uses, and more | ||||
| libidn2 | mcc | N/A | libidn2 is a library that implements internationalized domain name (IDN) encoding and decoding functions. It provides support for handling domain names with non-ASCII characters according to the IDNA2008 specification. | Domain Names, Idns, Stringprep, Punycode | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libint | mcc, lcc | N/A | libint is a library for the evaluation of molecular integrals of many-body operators over Gaussian functions. Description Source: https://github.com/evaleev/libint?tab=readme-ov-file |
Computational Chemistry, Molecular Integrals, Quantum Chemistry | Physical Chemistry, Chemical Sciences | Computational | Documentation, Uses, and more |
| libjpeg-turbo | mcc, lcc | N/A | libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, Neon, AltiVec) to accelerate baseline JPEG compression and decompression on x86, x86-64, Arm, and PowerPC systems, as well as progressive JPEG compression on x86, x86-64, and Arm systems. On such systems, libjpeg-turbo is generally 2-6x as fast as libjpeg, all else being equal. On other types of systems, libjpeg-turbo can still outperform libjpeg by a significant amount, by virtue of its highly-optimized Huffman coding routines. Description Source: https://libjpeg-turbo.org/ |
Image Compression, Jpeg Compression, Library, Open Source | Image Processing, Computer & Information Sciences | Compression Library | Documentation, Uses, and more |
| libmd | mcc, ecc, lcc | N/A | libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials. | Molecular Dynamics, Simulation, Library | Physical Sciences | Computational | Documentation, Uses, and more |
| libnl | mcc | N/A | libnl is a set of libraries providing a generic netlink communication protocol for Linux kernel networking subsystems. It simplifies the process of interacting with the kernel networking stack. | Networking, Linux, Netlink, Kernel | Computer Science | Library | Documentation, Uses, and more |
| libnsl | mcc | N/A | Public client interface library for NIS(YP) Description Source: https://github.com/conda-forge/libnsl-feedstock/blob/main/recipe/meta.yaml | Network Services, Communication, Protocols | Computer Science, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| libogg | lcc | N/A | libogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. As with all Xiph.org technology is it an open format free for anyone to use. Description Source: https://www.xiph.org/ogg/ |
Library, Bitstream, Audio | Computer Science, Computer & Information Sciences | Data Format | Documentation, Uses, and more |
| libpciaccess | mcc, lcc | N/A | Generic PCI access library. | Library, Pci Bus Access, User-Space Drivers | Software Engineering, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libpng | mcc, lcc | N/A | libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 28 years. Description Source: http://www.libpng.org/pub/png/libpng.html |
Image Processing, Graphics Library, Raster Images | Image Processing, Computer & Information Sciences | Data Handling | Documentation, Uses, and more |
| libpthread-stubs | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| libreadline | lcc | N/A | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | Command-Line Interface, Text Editing, Gnu Library, Interactive Programs | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| librsvg | mcc | N/A | librsvg is a library to render SVG images to Cairo surfaces. GNOME uses this to render SVG icons. Outside of GNOME, other desktop environments use it for similar purposes. Wikimedia uses it for Wikipedia's SVG diagrams. Description Source: https://gitlab.gnome.org/GNOME/librsvg |
Software Library, Free Software, Svg Rendering, File Conversion | Software Engineering, Computer & Information Sciences | Rendering & Conversion | Documentation, Uses, and more |
| libseccomp | ecc | N/A | libseccomp is a library for implementing secure computing mode (seccomp) filters in Linux systems. It enables developers to apply fine-grained filtering on system calls, restricting the actions that processes can perform for improved system security. | Syscall Filtering, Linux Kernel, Security | Systems Security, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libsigsegv | mcc, ecc, lcc | N/A | libsigsegv is a library for handling segmentation fault signals in Unix-like systems. It provides a mechanism for detecting, handling, and recovering from segment violation errors during program execution. | Library, Memory, Page Fault | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libsm | mcc, lcc | N/A | Libsm is a library that provides a set of common utilities for scientific computing in C++. | Library, Scientific Computing, C++ | Other Natural Sciences | Library | Documentation, Uses, and more |
| libssh2 | mcc | N/A | libssh2 is a library implementing the SSH2 protocol, providing a way to securely connect to remote servers and execute commands or transfer files. | SSH, Networking, Security, Library | Computer Science | Library | Documentation, Uses, and more |
| libtheora | lcc | N/A | libtheora is a free and open-source software library for encoding and decoding video in the Theora format, which is a lossy video compression format. | video, codec, open-source, multimedia | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libtiff | mcc, lcc | N/A | The LibTIFF software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data. Description Source: http://www.simplesystems.org/libtiff/ |
Image Processing, File Format, Library, Tiff, Image Storage | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libtirpc | mcc | N/A | The libtirpc package contains libraries that support programs that use the Remote Procedure Call (RPC) API. It replaces the RPC, but not the NIS library entries that used to be in glibc. Description Source: https://www.linuxfromscratch.org/blfs/view/stable/basicnet/libtirpc.html |
Software Library | Computer Science, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libtool | mcc, ecc, lcc | N/A | autoamke software. | Library Management, Software Development, Compilation | Software Engineering, Engineering & Technology | Utility/Tool | Documentation, Uses, and more |
| libunistring | mcc | N/A | libunistring is a library that provides functions for manipulating Unicode strings and characters, offering support for various Unicode operations and text processing tasks. It enables developers to work with Unicode data in a portable and efficient manner. | Unicode, Encoding, String Manipulation, Localization | Software Engineering, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| libunwind | lcc | N/A | libunwind is a portable and efficient C API for determining the current call chain of ELF program threads of execution and for resuming execution at any point in that call chain. The API supports both local (same process) and remote (other process) operation. Description Source: https://github.com/libunwind/libunwind |
Debugging, Profiling, Runtime Instrumentation, Call Stack, C Programming | Software Engineering, Engineering & Technology | Development | Documentation, Uses, and more |
| libx11 | mcc, lcc | N/A | libx11 is the X11 protocol client library. Description Source: https://gitlab.freedesktop.org/xorg/lib/libx11 |
X Window System, Client Library, Window System Interface, Graphics | Software Engineering, Computer & Information Sciences, Computer Science | Software Development | Documentation, Uses, and more |
| libxau | mcc, lcc | N/A | libXau is a library that provides authentication data for Xlib-based client programs. | Library, Authentication, Xlib | Computer & Information Sciences | Documentation, Uses, and more | |
| libxc | mcc, lcc | N/A | libxc is a library of exchange-correlation and kinetic energy functionals for density-functional theory. The original aim was to provide a portable, well tested and reliable set of these functionals to be used by all the codes of the European Theoretical Spectroscopy Facility (ETSF), but the library has since grown to be used in several other types of codes as well; see below for a partial list. Description Source: https://www.tddft.org/programs/libxc/ |
Quantum Mechanics, Computational Chemistry | Theoretical Chemistry, Chemical Sciences | Density Functional Theory | Documentation, Uses, and more |
| libxcb | mcc, lcc | N/A | The X protocol C-language Binding (libXCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. Description Source: https://xcb.freedesktop.org/ |
X Window System, C Library, X Protocol | Computer Science, Computer & Information Sciences | Programming | Documentation, Uses, and more |
| libxcrypt | ecc | N/A | libxcrypt is a library for cryptographic hashing and password hashing, providing modern and secure algorithms for password storage and verification. | Cryptography, Security, Password Hashing, Libraries | Cryptography, Computer Science | Library | Documentation, Uses, and more |
| libxdamage | mcc | N/A | Documentation, Uses, and more | ||||
| libxdmcp | mcc, lcc | N/A | libxdmcp is the X Display Manager Control Protocol library. It provides an API for the X Display Manager Control Protocol (XDMCP) for both the client and server side. | X11, Display Manager, Network Protocol | Software Engineering, Computer & Information Sciences | Networking | Documentation, Uses, and more |
| libxext | mcc, lcc | N/A | libXext is an extension library for the X Window System that provides additional functionality to the core Xlib library. | X Window System, Graphics, Library | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxfixes | mcc | N/A | libxfixes is a library that provides an interface for the X Window System to manage and manipulate window properties and visual effects. | X Window System, Graphics, Window Management | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libxfont | mcc | N/A | libXfont is a library used for font management in the X Window System, providing functionalities to load and manage bitmap and scalable fonts. | X Window System, Font Management, Graphics | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| libxft | mcc | N/A | libXft is a library for rendering text in X Window System applications using the FreeType font rendering library. | X11, Font Rendering, Graphics, Open Source | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libxi | mcc | N/A | Documentation, Uses, and more | ||||
| libxinerama | mcc | N/A | libXinerama is a library that provides an interface for the X Window System to support multiple screens and display configurations. | X Window System, Multi-screen, Graphics | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libxkbcommon | mcc | N/A | libxkbcommon is a library that provides an interface to the X Keyboard Extension (XKB) for handling keyboard input in a platform-independent manner. It is designed to be used in applications that need to manage keyboard layouts, keymaps, and input events. | keyboard, input handling, X11, cross-platform | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxkbfile | mcc | N/A | libxkbfile is a library for reading and writing XKB (X Keyboard Extension) files. It provides a simple API for manipulating keyboard configuration files used in X Window System. | X Window System, Keyboard Configuration, Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxml2 | mcc, ecc, lcc | N/A | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | Xml, Html, Parsing, Validation, Manipulation | Software Engineering, Computer & Information Sciences | Parsing | Documentation, Uses, and more |
| libxmu | mcc | N/A | libXmu is a library that provides various utility functions for X Window System applications, particularly those using the X Toolkit. | X Window System, Graphics, Utilities, Libraries | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxrandr | mcc, lcc | N/A | libxrandr is a library that provides an interface to the X Resize and Rotate (RandR) extension of the X Window System, allowing applications to dynamically change the size, orientation, and reflection of the display. | X11, Graphics, Display Management | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libxrender | mcc, lcc | N/A | libXrender is a library that provides an interface to the X Rendering Extension, which allows for the rendering of images and shapes in a more efficient manner than traditional X11 methods. | Graphics, Rendering, X11 | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxslt | mcc | N/A | libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML. Libxslt is based on libxml2 the XML C library developed for the GNOME project. Description Source: http://xmlsoft.org/libxslt/index.html |
Xml, Xslt, C Library, Transformation | Software Engineering, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| libxsmm | mcc | N/A | libxsmm is a library for specialized dense and sparse matrix operations as well as for deep learning primitives such as small convolutions. The library is targeting Intel Architecture with Intel SSE, Intel AVX, Intel AVX2, Intel AVX‑512 (with VNNI and Bfloat16), and Intel AMX (Advanced Matrix Extensions) supported by future Intel processor code-named Sapphire Rapids. Description Source: https://github.com/libxsmm/libxsmm |
Library, Matrix Multiplication, Intel Cpus | Computer Science, Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| libxt | mcc, lcc | N/A | Libxt is a library offering extensions for automating compilation, dependency tracking, and execution of computational tasks within HPC environments. | Library, Hpc, Automation, Compilation, Dependency Tracking, Parallel Processing | Engineering & Technology | Library | Documentation, Uses, and more |
| libxtst | mcc | N/A | Documentation, Uses, and more | ||||
| libxxf86vm | mcc | N/A | libxxf86vm is a library that provides an interface to the XFree86 Video Mode Extension, allowing applications to query and set video modes. | X11, Graphics, Video | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| liftoff | mcc | 1.0 | Liftoff is an accurate GFF3/GTF lift over pipeline. | Build System, Ios Development, Macos Development, Software Development, Apple Platforms | Engineering & Technology | Build Automation | Documentation, Uses, and more |
| liftover | mcc | 1.0 | Liftover is a tool used to convert genomic coordinates between different assemblies or reference genomes. | genomics, bioinformatics, coordinate conversion, genome assembly | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| ligpargen | lcc | N/A | LigParGen is a software tool for generating ligand parameters for molecular simulations, particularly for use with the AMBER and CHARMM force fields. | ligand parameter generation, molecular dynamics, bioinformatics | Molecular Modeling, Computational Chemistry | Standalone | Documentation, Uses, and more |
| likwid | mcc, lcc | N/A | Performance tools for the Linux console | Performance Analysis, Hpc, Performance Counter Profiling, Hardware Performance Counters | Performance Evaluation & Benchmarking, Engineering & Technology | Tool | Documentation, Uses, and more |
| lima | mcc, lcc | 1.0 | Lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. | Single-Cell RNA-Seq, Data Analysis, Transcriptomics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| linux-perf | mcc | N/A | perf v6.3.10 -- perf is a powerful Linux tool for profiling and benchmarking system and application performance by monitoring hardware and software events. | performance, monitoring, profiling, Linux | Computer Science | Performance Analysis Tool | Documentation, Uses, and more |
| llama | ecc | 1.0 | Documentation, Uses, and more | ||||
| llm-research | lcc | 1.0 | Documentation, Uses, and more | ||||
| llvm | mcc, lcc | N/A | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines. Description Source: https://llvm.org/ |
Compiler, Toolchain | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| llvm5 | lcc | N/A | LLVM Compiler Infrastructure | Compiler, Programming Language, Optimization, Toolchain | Software Engineering, Computer Science | Compiler Infrastructure | Documentation, Uses, and more |
| lmod | ecc, lcc | N/A | Lmod: An Environment Module System | Module Management, Software Environment, Environment Module System | Infrastructure & Instrumentation, Engineering & Technology | Utility | Documentation, Uses, and more |
| longstitch | mcc | 1.0 | Documentation, Uses, and more | ||||
| ltr_retriever | mcc | 1.0 | LTR_retriever is a software tool designed for the identification and retrieval of long terminal repeats (LTRs) in genomic sequences. It is particularly useful in the field of bioinformatics for studying transposable elements and their evolutionary dynamics. | bioinformatics, genomics, LTR retrotransposons, sequence analysis | Computational Biology, Genomics | Bioinformatics Tool | Documentation, Uses, and more |
| lua | ecc | N/A | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. | Programming Language, Scripting Language, Embedded Systems | Software Engineering, Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| lua-luafilesystem | ecc | N/A | LuaFileSystem is a Lua library that provides a portable way to access the underlying filesystem. It allows users to perform operations such as file and directory manipulation, path manipulation, and more. | Lua, Filesystem, Library, Cross-platform | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| lua-luaposix | ecc | N/A | LuaPosix is a Lua binding for the POSIX API, providing access to operating system functionalities such as file manipulation, process control, and threading. | Lua, POSIX, Bindings, Operating System | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| lumerical | lcc | N/A | Lumerical software. | photonic design, electromagnetic simulation, optical analysis, engineering | Engineering, Electrical, Electronic, and Information Engineering | Commercial | Documentation, Uses, and more |
| lz4 | mcc, ecc, lcc | N/A | LZ4 is lossless compression algorithm, providing compression speed > 500 MB/s per core (>0.15 Bytes/cycle). It features an extremely fast decoder, with speed in multiple GB/s per core (~1 Byte/cycle). A high compression derivative, called LZ4_HC, is available, trading customizable CPU time for compression ratio. Description Source: https://lz4.org/ |
Compression, Data Compression, Lossless Compression | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| lzo | ecc | N/A | LZO offers pretty fast compression and extremely fast decompression. MiniLZO is a very lightweight subset of the LZO library. Description Source: https://github.com/conda-forge/lzo-feedstock/blob/main/recipe/meta.yaml | Data Compression, Algorithm, High-Speed | Computer Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| m4 | mcc, ecc, lcc | N/A | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. | Macro Processor, Text Processing, Software Development, Build Process | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| maaslin2 | lcc | 1.0 | Maaslin2 is a tool for multivariate association analysis of microbiome data, allowing users to explore the relationships between microbial communities and various metadata factors. | bioinformatics, microbiome, statistics, data analysis | Bioinformatics, Microbial Ecology | Statistical Analysis Tool | Documentation, Uses, and more |
| macs | lcc | 1.0 | MACS (Model-based Analysis of ChIP-Seq) is a software tool designed for analyzing ChIP-Seq data to identify transcription factor binding sites. | ChIP-Seq, Bioinformatics, Genomics, Peak Calling | Bioinformatics, Genomics | Analysis Tool | Documentation, Uses, and more |
| macs2 | mcc, lcc | 1.0 | MACS2 is Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites. | Chip-Seq Analysis, Transcription Factor Binding Sites, Histone Modification, Bioinformatics | Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| mafft | mcc, lcc | 1.0 | MAFFT is a multiple alignment program for amino acid or nucleotide sequences. | Bioinformatics, Sequence Alignment, Phylogenetics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| make | lcc | N/A | Make is an open-source, tool designed to build, test and package software. | Build Automation, Software Development, Programming | Computer Science, Engineering & Technology | Utility | Documentation, Uses, and more |
| make_tracks_file | mcc | 1.0 | Documentation, Uses, and more | ||||
| maker | mcc, lcc | 1.0 | Maker is a portable and easily configurable genome annotation pipeline. | Genome Annotation, Bioinformatics | Genomics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| maple | lcc | N/A | maple tool designed to package software. | Mathematics, Symbolic Computation, Numerical Analysis, Data Visualization | Computational Mathematics, Applied Mathematics | Commercial | Documentation, Uses, and more |
| mapsplice | lcc | N/A | MapSplice is a software tool designed for accurate and efficient mapping of RNA-Seq reads to a reference genome, particularly focusing on the detection of splice junctions. | RNA-Seq, Splice Junction Detection, Bioinformatics, Genomics | Bioinformatics, Genomics | Bioinformatics Tool | Documentation, Uses, and more |
| marty | lcc | 1.0 | Documentation, Uses, and more | ||||
| mashmap | mcc, lcc | 1.0 | Mashmap is a fast approximate aligner for long DNA sequences. | Mapping, Alignment, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| mashtree | lcc | 1.0 | Mashtree is a tool to create a tree using Mash distances. | Phylogenetic Trees, Genomic Similarity, Mash Distances | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| masurca | mcc, lcc | 1.0 | The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner. | Genome Assembly, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| matlab | mcc, lcc | N/A | Matlab | Programming Language, Technical Computing, Visualization, Mathematical Notation | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| matplotlib | lcc | N/A | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible. Description Source: https://matplotlib.org/ |
Python Library, Data Visualization, Plotting Library | Computer Science, Computer & Information Sciences | Plotting & Graphing Tool | Documentation, Uses, and more |
| mcclintock | mcc, ecc | 1.0 | Documentation, Uses, and more | ||||
| mcl | lcc | 1.0 | Mcl is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs | Clustering, Network Analysis, Graph Algorithms | Computational Biology, Computer & Information Sciences | Clustering Algorithm | Documentation, Uses, and more |
| mcscanx | mcc | 1.0 | MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. | Gene Synteny, Genomic Analysis, Syntenic Relationships | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| mdanalysis | lcc | 1.0 | MDAnalysis is a Python library for the analysis of molecular dynamics simulations. It allows users to read, manipulate, and analyze trajectory data from various simulation software. | Molecular Dynamics, Simulation Analysis, Python, Scientific Computing | Molecular Dynamics, Biochemistry and Molecular Biology | Library | Documentation, Uses, and more |
| mdtraj | lcc | 1.0 | MDTraj is a Python library that allows users to analyze molecular dynamics trajectories. It provides tools to read, write, and manipulate trajectory data from various simulation packages. | Molecular Dynamics, Trajectory Analysis, Python, Bioinformatics | Molecular Dynamics, Biochemistry and Molecular Biology | Library | Documentation, Uses, and more |
| med | lcc | N/A | Documentation, Uses, and more | ||||
| medaka | mcc | 1.0 | Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. | Bioinformatics, Ngs Data Analysis, Nanopore Sequencing, Consensus Sequence Calling | Bioinformatics, Biological Sciences | Ngs Data Analysis Tool | Documentation, Uses, and more |
| megahit | lcc | 1.0 | Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | Metagenome Assembly, Bioinformatics, Sequencing Data, Snp-Aware, Draft Assemblies | Bioinformatics, Biological Sciences | Assembly Software | Documentation, Uses, and more |
| megahit-1.2.9 | mcc | 1.0 | MEGAHIT is a fast and memory-efficient tool for de novo assembly of large and complex metagenomic datasets. | metagenomics, assembly, bioinformatics | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| megan | lcc | 1.0 | Megan is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample. | Metagenomics, Microbiome, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| megax | lcc | 1.0 | Documentation, Uses, and more | ||||
| merqury | mcc | 1.0 | Merqury is a tool to evaluate genome assemblies with k-mers and more. | Computational Tool, Genomics, Bioinformatics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| meryl | lcc | N/A | Meryl is a genomic k-mer counter (and sequence utility) with nice features. | Bioinformatics, Genomics, K-Mer Counting | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mesa | mcc, lcc | N/A | The Mesa project began as an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Over the years the project has grown to implement more graphics APIs, including OpenGL ES, OpenCL, OpenMAX, VDPAU, VA-API, Vulkan and EGL. Description Source: https://docs.mesa3d.org/index.html |
Agent-Based Modeling, Complex Systems, Simulation, Computational Modeling | Other Computer & Information Sciences, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| mesa-glu | mcc, lcc | N/A | mesa-gl is an open-source implementation of the OpenGL specification, a system for rendering interactive 3D graphics, and a widely used and versatile graphics library. mesa-glu is the OpenGL Utility Library (GLU) component of Mesa, providing useful functions for building OpenGL applications. | Graphics, 3D Graphics, Opengl, Graphics Library | Library | Documentation, Uses, and more | |
| meshio | lcc | N/A | meshio is a Python library for reading and writing mesh files in various formats, making it easier to work with finite element analysis (FEA) and computational fluid dynamics (CFD) data. | mesh, finite element analysis, computational fluid dynamics, Python | Engineering, Mechanical Engineering | Library | Documentation, Uses, and more |
| meshlab | mcc | 1.0 | MeshLab is an open-source system for processing and editing 3D triangular meshes. It provides a set of tools for editing, cleaning, healing, inspecting, rendering, and converting meshes. | 3D Modeling, Mesh Processing, Open Source | 3D Modeling and Visualization, Computer Science | Desktop Application | Documentation, Uses, and more |
| meson | mcc, ecc, lcc | N/A | Meson is an open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible. Description Source: https://mesonbuild.com/ |
Build System, Software Development, Automation | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| metabat2 | mcc | 1.0 | MetaBAT 2 is a software tool designed for the binning of metagenomic assemblies, which helps in identifying and grouping sequences from environmental samples into their respective genomes. | metagenomics, binning, bioinformatics, sequence analysis | Bioinformatics, Metagenomics | Command-line tool | Documentation, Uses, and more |
| metaphlan | mcc, lcc | 1.0 | Metaphlan is computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. | Metagenomics, Microbiome, Microbial Ecology, Bioinformatics | Environmental Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| methpipe | mcc | 1.0 | Documentation, Uses, and more | ||||
| methyldackel | mcc, lcc | 1.0 | Methyldackel is a (mostly) universal methylation extractor for BS-seq experiments. | DNA Methylation, Bisulfite Sequencing, Epigenetics | Genetics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| metis | mcc, lcc | N/A | Metis development files | Computational Software, Graph Partitioning, Mesh Partitioning, Hypergraph Partitioning | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mfem | lcc | N/A | Lightweight, general, scalable C++ library for finite element methods | Finite Element Method, C++ Library, Parallel Computing | Applied Mathematics, Engineering & Technology | Library | Documentation, Uses, and more |
| mhm2 | mcc | 1.0 | MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes. | Monte Carlo Simulation, Liquid Crystal Membranes, Bilayer Simulation | Physical Sciences | Computational Software | Documentation, Uses, and more |
| microbecensus | mcc | 1.0 | Documentation, Uses, and more | ||||
| microbecensus-sourceapp | mcc | 1.0 | Documentation, Uses, and more | ||||
| migrate-n | lcc | N/A | Documentation, Uses, and more | ||||
| miniconda3 | mcc, lcc | N/A | Miniconda is a free minimal installer for conda. It is a small bootstrap version of Anaconda that includes only conda, Python, the packages they both depend on, and a small number of other useful packages (like pip, zlib, and a few others). If you need more packages, use the conda install command to install from thousands of packages available by default in Anaconda’s public repo, or from other channels, like conda-forge or bioconda. Description Source: https://docs.anaconda.com/free/miniconda/index.html |
Package Management, Dependency Management, Software Installation | Computer Science, Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| miniforge3 | mcc, lcc | N/A | Miniforge is a community-driven minimal installer for Conda, designed to provide a lightweight and flexible environment for managing packages and environments in Python and other languages. | Conda, Package Management, Environment Management, Python | Bioinformatics, Biological Sciences | Package Manager | Documentation, Uses, and more |
| minigraph | lcc | 1.0 | Documentation, Uses, and more | ||||
| minimap | mcc | 1.0 | Minimap is a versatile sequence alignment program that is designed for aligning long DNA or RNA sequences against a reference genome. It is particularly useful for applications in genomics and bioinformatics. | alignment, genomics, bioinformatics, sequence analysis | Bioinformatics, Sequence Alignment | Command-line tool | Documentation, Uses, and more |
| minimap2 | mcc, lcc | 1.0 | minimap2 software. | Sequence Alignment, Bioinformatics, Genomics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| miranda | mcc | 1.0 | Documentation, Uses, and more | ||||
| mirdeep | lcc | 1.0 | miRDeep is a computational tool for the identification of microRNAs from deep sequencing data. | bioinformatics, microRNA, deep sequencing, RNA analysis | Molecular Biology, Biochemistry and Molecular Biology | Analysis Tool | Documentation, Uses, and more |
| mirdeep2 | mcc | 1.0 | miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). | Bioinformatics, Computational Biology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| mitobim | lcc | 1.0 | mitobim is a software tool designed for the assembly and analysis of mitochondrial genomes from next-generation sequencing data. | bioinformatics, genomics, mitochondrial DNA, next-generation sequencing | Bioinformatics, Mitochondrial Genomics | Open-source | Documentation, Uses, and more |
| mitofinder | lcc | 1.0 | Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. | Bioinformatics, Genomics, Mitochondrial Genomes, Next-Generation Sequencing, Annotation | Genomics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| mitohifi | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| mitoz | lcc | 1.0 | Mitoz is a software tool designed for the analysis of mitochondrial DNA sequences, particularly focusing on the identification and quantification of mitochondrial variants in genomic data. | bioinformatics, genomics, mitochondrial analysis | Bioinformatics, Genomics | Analysis Tool | Documentation, Uses, and more |
| mkfontdir | mcc | N/A | mkfontdir is a utility that generates an index of font files in a directory, creating a fonts.scale file that is used by the X Window System to manage fonts. | Font Management, X Window System, Utilities | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| mkfontscale | mcc | N/A | mkfontscale is a utility that generates an index of scalable fonts for the X Window System. | Font Management, X Window System, Utilities | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| mkl | mcc, ecc, lcc | N/A | Intel Compiler Family (C/C++/Fortran for x86_64) | Mathematical Library, Optimized Computations, Thread-Safe Functions | Computer Science | Computational Software | Documentation, Uses, and more |
| mkl32 | mcc, lcc | N/A | The Intel® oneAPI Math Kernel Library (oneMKL) helps you achieve maximum performance with a math computing library of highly optimized, extensively parallelized routines for CPU and GPU. The library has C and Fortran interfaces for most routines on CPU, and SYCL interfaces for some routines on both CPU and GPU. Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html#gs.4ofwv10 |
Mathematics, Computational Software, Hpc Tools | Other Mathematics | Library | Documentation, Uses, and more |
| mmg | mcc, lcc | N/A | MMG is a software package designed for the generation and adaptation of unstructured meshes in two and three dimensions. It is particularly useful for numerical simulations in scientific computing. | mesh generation, mesh adaptation, scientific computing, numerical simulations | Numerical Methods, Computational Science | Open Source | Documentation, Uses, and more |
| mmseqs2 | lcc | 1.0 | Mmseqs2 is a software suite to search and cluster huge protein and nucleotide sequence sets. | Sequence Searching, Sequence Clustering, Bioinformatics, Computational Biology | Biological Sciences | Sequence Search & Clustering Tool | Documentation, Uses, and more |
| molpro | lcc | N/A | Molpro software. | Quantum Chemistry, Computational Chemistry, High-Performance Computing | Chemical Sciences, Physical Chemistry | Commercial | Documentation, Uses, and more |
| momap | mcc, lcc | N/A | momap software. | Documentation, Uses, and more | |||
| mono | lcc | N/A | mono software. | cross-platform, open-source, development, framework | Computer Science, Software Engineering | Framework | Documentation, Uses, and more |
| moose | lcc | 1.0 | MOOSE (Multiphysics Object-Oriented Simulation Environment) is a finite element simulation framework designed for solving complex multiphysics and multiscale engineering problems. It provides a flexible and extensible platform for researchers and engineers to develop and deploy simulation tools for a wide range of applications. | Simulation, Multiphysics, Finite Element Method | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| mosdepth | mcc | 1.0 | mosdepth is a tool for calculating the depth of coverage from sequencing data, particularly useful in genomic studies. | genomics, bioinformatics, sequencing, coverage | Bioinformatics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| mothur | mcc, lcc | 1.0 | Mothur is an open source software package for bioinformatics data processing. | Bioinformatics, Microbial Communities, High-Throughput Sequencing | Microbial Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| mpc | mcc | N/A | Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. | Cryptographic Protocol, Secure Computation, Privacy-Preserving, Collaborative Computation | Computer & Information Sciences | Cryptographic Protocol | Documentation, Uses, and more |
| mpdaf-3.5-fitsio | lcc | 1.0 | Documentation, Uses, and more | ||||
| mpfr | mcc, ecc, lcc | N/A | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPFR has continuously been supported by the INRIA and the current main authors come from the Caramba and AriC project-teams at Loria (Nancy, France) and LIP (Lyon, France) respectively; see more on the credit page. MPFR is based on the GMP multiple-precision library. Description Source: https://www.mpfr.org/ |
Arbitrary-Precision Arithmetic, Floating-Point Computation, Mathematical Library | Numerical Analysis, Mathematics | Computational Software | Documentation, Uses, and more |
| mpi | mcc, ecc, lcc | N/A | Intel(R) MPI Library | Hpc, Parallel Computing, Message Passing, Scalable Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpi4py | lcc | N/A | Mpi4py provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI specification and exposes an API which grounds on the standard MPI-2 C++ bindings. Description Source: https://pypi.org/project/mpi4py/ |
Parallel Computing, Message Passing Interface, Python Library | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| mpich | mcc, ecc, lcc | N/A | MPICH MPI implementation (device=ch3:nemesis) | Mpi Implementation, Parallel Computing, High Performance Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpip | lcc | N/A | mpiP: a lightweight profiling library for MPI applications. | Software Utility, Hpc, Mpi Libraries, Cluster Management, Installation Tool | Engineering & Technology | Documentation, Uses, and more | |
| mrbayes | mcc, lcc | 1.0 | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. | Bayesian Inference, Phylogenetics, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Software Tool | Documentation, Uses, and more |
| multiqc | mcc, lcc | 1.0 | Multiqc is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools. | Bioinformatics, Computational Biology, Data Analysis, Reporting Tool | Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| mumax3 | lcc | 1.0 | mumax3 is a GPU-accelerated micromagnetic simulation software designed for simulating the dynamics of magnetic materials. | micromagnetics, GPU computing, simulation, magnetic materials | Condensed Matter Physics | Simulation Software | Documentation, Uses, and more |
| mummer4 | lcc | 1.0 | Mummer4 is a versatile alignment tool for DNA and protein sequences. | Bioinformatics, Sequence Alignment, Genomics | Genomics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| mumps | lcc | N/A | A MUltifrontal Massively Parallel Sparse direct Solver | Linear Algebra, Sparse Matrices, Computational Science, Engineering | Applied Mathematics, Mathematics | Solver | Documentation, Uses, and more |
| munge | mcc | N/A | Documentation, Uses, and more | ||||
| muscle | mcc, lcc | 1.0 | Muscle is a modified progressive alignment algorithm which has comparable accuracy to MAFFT, but faster performance. | Sequence Alignment, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mvapich2 | mcc, lcc | N/A | OSU MVAPICH2 MPI implementation | Mpi Implementation, High Performance Computing, Infiniband, Open-Source | Computer Science, Physical Sciences | Library/Tool | Documentation, Uses, and more |
| mvp | mcc | 1.0 | Documentation, Uses, and more | ||||
| namd | lcc | 1.0 | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Molecular Dynamics, Biomolecular Systems, Parallel Computing, Cuda, Simulation | Biochemistry and Molecular Biology | Computational Software | Documentation, Uses, and more |
| nanocomp | mcc | 1.0 | Documentation, Uses, and more | ||||
| nanofilt | mcc | 1.0 | Nanofilt is a tool for filtering and trimming of Oxford Nanopore Sequencing data. | Bioinformatics, Sequence Analysis, Nanopore Sequencing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| nanoplot | mcc | 1.0 | Nanoplot is a plotting tool for long read sequencing data and alignments. | Bioinformatics, Genomics, Sequencing Data, Quality Control, Visualization | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| nanostat | mcc | 1.0 | Documentation, Uses, and more | ||||
| nasm | mcc, lcc | N/A | Netwide Assembler (NASM) is an asssembler for the x86 CPU architecture portable to nearly every modern platform with code generation for many platforms old and new. Description Source: https://www.nasm.us/ |
Assembler, Cross-Platform, X86, Programming | Computer Science, Computer & Information Sciences | Assembler | Documentation, Uses, and more |
| ncbi-rmblastn | mcc | N/A | RMBlast is a tool for aligning nucleotide sequences against a database of reference sequences, optimized for use with the NCBI BLAST algorithm. | bioinformatics, sequence alignment, NCBI, BLAST | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| ncl | lcc | 1.0 | NCL is an interpreted language designed specifically for scientific data analysis and visualization. | Scientific Data Analysis, Data Visualization, Atmospheric Sciences | Environmental Sciences, Earth & Environmental Sciences | Scripting Language | Documentation, Uses, and more |
| ncurses | mcc, ecc, lcc | N/A | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. | Programming Library, Text-Based User Interfaces, Terminal Applications | Computer Science, Computer & Information Sciences | Programming/Development | Documentation, Uses, and more |
| ncview | lcc | 1.0 | Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher. \r Description Source: https://cirrus.ucsd.edu/ncview/ |
Data Visualization, Netcdf, Earth System Data | Earth and Environmental Sciences | Data Analysis Tool | Documentation, Uses, and more |
| netcdf | lcc | N/A | C Libraries for the Unidata network Common Data Form | Scientific Data, Data Storage, Data Access, Data Formats, Data Manipulation, Data Visualization | Environmental Data, Other Natural Sciences | Library | Documentation, Uses, and more |
| netcdf-c | mcc | N/A | The Unidata network Common Data Form (netCDF) is an interface for scientific data access and a freely-distributed software library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. Description Source: https://docs.unidata.ucar.edu/netcdf-c/current/ |
Data Format, Scientific Data, Data Access, Data Sharing | Climate and Global Dynamics, Other Natural Sciences | Data Format | Documentation, Uses, and more |
| netcdf-cxx | lcc | N/A | C++ Libraries for the Unidata network Common Data Form | Netcdf, C++ | Earth & Environmental Sciences | Data Processing | Documentation, Uses, and more |
| netcdf-fortran | mcc, lcc | N/A | Fortran Libraries for the Unidata network Common Data Form | Scientific Data, Fortran Interface, Netcdf Library | Data Analysis, Other Natural Sciences | Programming Interface | Documentation, Uses, and more |
| netcdf-intel | lcc | N/A | NetCDF-Intel is a high-performance implementation of the NetCDF data format, optimized for Intel architectures. It provides tools for reading and writing array-oriented scientific data in a platform-independent manner. | Data Format, Scientific Computing, High Performance Computing, Data Management | Data Analysis, Computer and Information Sciences | Library | Documentation, Uses, and more |
| netlib-scalapack | mcc, lcc | N/A | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. Description Source: https://www.netlib.org/scalapack/ |
linear algebra, parallel computing, high-performance computing, distributed systems | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| netlogo | mcc | N/A | NetLogo software. | Modeling, Simulation, Agent-based, Education | Social Sciences, Other social sciences | Simulation Software | Documentation, Uses, and more |
| networkx | lcc | N/A | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Description Source: https://networkx.org/ |
Python Library, Graph Theory, Network Analysis, Data Visualization | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| nextflow | mcc, lcc | 1.0 | Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Description Source: https://www.nextflow.io/ |
Workflow Manager, Computational Biology, Data Science | Computational Biology, Biological Sciences | Open Source | Documentation, Uses, and more |
| nextpolish | mcc | 1.0 | NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. | Bioinformatics, Computational Biology, Long-Read Sequencing, Error Correction | Genetics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| nextpolish2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| ngenomesyn | mcc | 1.0 | Documentation, Uses, and more | ||||
| nghttp2 | ecc | N/A | This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API. | Http/2, Web Protocol, Networking | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| nginx | lcc | 1.0 | nginx is a high-performance HTTP server and reverse proxy, as well as an IMAP/POP3 proxy server. | Web Server, Reverse Proxy, Load Balancer, Open Source | Computer Science | Web Server | Documentation, Uses, and more |
| ngsdist | lcc | 1.0 | ngsDist is a program for estimating pairwise genetic distances while explicitly accounting for uncertainty in genotype assignment. Instead of relying on traditional genotype calling, it operates directly on genotype likelihoods or posterior probabilities. | Documentation, Uses, and more | |||
| ngsld | mcc | 1.0 | ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. | Ngs, Bioinformatics, Genomics, Sequencing | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ngstools | lcc | 1.0 | Documentation, Uses, and more | ||||
| ngsutils | lcc | 1.0 | Ngsutils is suite of software tools for working with next-generation sequencing datasets. | Ngs, Bioinformatics, Sequencing, Data Analysis | Bioinformatics, Biological Sciences | Research Tools | Documentation, Uses, and more |
| ninja | mcc, ecc, lcc | 1.0 | Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible. Description Source: https://github.com/ninja-build/ninja |
Build System, Software Development, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| node | lcc | N/A | Node.js JavaScript runtime (LTS, glibc-2.17 build) | Javascript, Server-Side Scripting, Cross-Platform | Computer Science, Computer & Information Sciences | Programming Platform | Documentation, Uses, and more |
| node-js | mcc | N/A | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine, enabling developers to build scalable network applications. | JavaScript, Runtime, Server-side, Event-driven, Network applications | Software Engineering, Computer Science | Open Source | Documentation, Uses, and more |
| nonpareil | mcc | 1.0 | Nonpareil is a software tool designed for the analysis of metagenomic data, specifically for estimating the completeness of metagenome assemblies. | metagenomics, assembly analysis, bioinformatics | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| notebook | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| notung | lcc | N/A | Notung is a software tool for the reconciliation of gene trees and species trees. It is designed to analyze phylogenetic relationships and to help in the study of evolutionary biology. | Phylogenetics, Evolutionary Biology, Bioinformatics | Computational Biology, Bioinformatics | Application | Documentation, Uses, and more |
| novoplasty | lcc | 1.0 | Novoplasty is a software tool designed for de novo assembly of genomes from next-generation sequencing data, particularly focusing on the assembly of mitochondrial genomes. | bioinformatics, genomics, assembly, next-generation sequencing | Bioinformatics, Genomics | Assembly Tool | Documentation, Uses, and more |
| npm | mcc | N/A | Documentation, Uses, and more | ||||
| nri-md | lcc | 1.0 | Documentation, Uses, and more | ||||
| ntlink | mcc | 1.0 | Documentation, Uses, and more | ||||
| numactl | mcc, lcc | N/A | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. | Numa, Memory Management, Performance Optimization | Other Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| numba | lcc | N/A | Numba is an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code. Description Source: https://numba.pydata.org/ |
Jit Compiler, Python Optimization, Numpy Optimization | Computer Science, Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| numpy | lcc | N/A | NumPy is the fundamental package for scientific computing in Python. It is a Python library that provides a multidimensional array object, various derived objects (such as masked arrays and matrices), and an assortment of routines for fast operations on arrays, including mathematical, logical, shape manipulation, sorting, selecting, I/O, discrete Fourier transforms, basic linear algebra, basic statistical operations, random simulation and much more. Description Source: https://numpy.org/doc/stable/user/whatisnumpy.html |
Scientific Computing, Numerical Computing, Data Analysis, Mathematics | Mathematics, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| nvhpc | lcc | N/A | The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. Description Source: https://developer.nvidia.com/hpc-sdk |
Hpc, Gpu Acceleration, Compilers, Libraries, Development Tools | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| nvidia-rapids | lcc | 1.0 | The RAPIDS data science framework is a collection of libraries for running end-to-end data science pipelines completely on the GPU. The interaction is designed to have a familiar look and feel to working in Python, but utilizes optimized NVIDIA CUDA primitives and high-bandwidth GPU memory under the hood. | GPU Computing,Data Science,Machine Learning,Open Source | Data Analytics, Computer Science | Library | Documentation, Uses, and more |
| nwchem | mcc, lcc | 1.0 | NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of forcefields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations. \r Description Source: https://raw.githubusercontent.com/wiki/nwchemgit/nwchem/Capabilities.md |
Computational Chemistry, High-Performance Computing, Open-Source Software | Chemical Sciences | Computational Chemistry Software | Documentation, Uses, and more |
| ocelot | lcc | N/A | Documentation, Uses, and more | ||||
| ocelot_api | lcc | N/A | Documentation, Uses, and more | ||||
| oclfpga | mcc, lcc | N/A | The Intel® oneAPI DPC++/C++ Compiler provides optimizations that help your applications run faster on Intel® 64 architectures on Windows* and Linux*, with support for the latest C, C++, and SYCL language standards. This compiler produces optimized code that can run significantly faster by taking advantage of the ever-increasing core count and vector register width in Intel® Xeon® processors and compatible processors. Description Source: https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/get-started-guide/2024-0/overview.html |
Opencl, Fpga, Acceleration | Engineering & Technology | Framework | Documentation, Uses, and more |
| ocr | lcc | N/A | Open Community Runtime (OCR) for shared memory | Documentation, Uses, and more | |||
| octopus | lcc | 1.0 | Octopus is a software package designed for the simulation of quantum systems, particularly in the field of condensed matter physics. It allows for the study of various physical phenomena using time-dependent density functional theory (TDDFT) and other quantum mechanical methods. | Quantum Mechanics, Condensed Matter Physics, Simulation Software | Physics, Physical Sciences | Simulation | Documentation, Uses, and more |
| ohpc | mcc, ecc, lcc | N/A | OpenHPC is a collaborative, community-driven effort to provide a comprehensive and cohesive open-source HPC stack to the community. Through close collaboration with key stakeholders across the industry, OpenHPC aims to provide a reference collection of open-source HPC software components and best practices to enable the development, testing, and deployment of HPC systems. Ultimately, building on the resecarch outputs from various related fields. | Hpc, High Performance Computing, Open-Source, Collaborative, Community-Driven | Computer Science, Engineering & Technology | Computational Software | Documentation, Uses, and more |
| omb | mcc, lcc | N/A | OSU Micro-benchmarks | Documentation, Uses, and more | |||
| openbabel | mcc, lcc | 1.0 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Description Source: https://openbabel.org/ |
Cheminformatics, Molecular Modeling, File Conversion, Open Source | Cheminformatics, Molecular Modeling | Library | Documentation, Uses, and more |
| openbabel311 | mcc | 1.0 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It facilitates the interconversion of various chemical file formats and provides a variety of tools for molecular manipulation. | Chemistry, File Conversion, Molecular Modeling, Open Source | Chemical Sciences, Chemical Informatics | Library | Documentation, Uses, and more |
| openblas | mcc, lcc | N/A | An optimized BLAS library based on GotoBLAS2 | Linear Algebra, Blas Library, Optimized Functions, Open Source | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| opencoarrays | lcc | N/A | ABI to leverage the parallel programming features of the Fortran 2018 DIS | Fortran, Parallel Computing, Coarrays, High Performance Computing | Computer Science | Library | Documentation, Uses, and more |
| openfoam | mcc, lcc | N/A | OpenFOAM is the free, open source CFD software developed primarily by OpenCFD Ltd since 2004. It has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. Description Source: https://www.openfoam.com/ |
Computational Fluid Dynamics, Open-Source Software, Finite Volume Method, Hpc | Fluid Dynamics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| openjdk | mcc, ecc | N/A | OpenJDK is a free, Open-Source version of the Java Development Kit for the Java Platform, Standard Edition (Java SE). Description Source: https://openjdk.org/ |
Open-Source, Java Development, Software Development, Programming | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| openmm | mcc, lcc | 1.0 | OpenMM is a high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. We include extensive language bindings for Python, C, C++, and even Fortran. Description Source: https://openmm.org/ |
Molecular Dynamics, Biomolecular Simulations, Computational Chemistry, Biophysics, Gpu Acceleration | Bioinformatics, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| openmpi | mcc, lcc | N/A | The Open MPI Project is an open source MPI-3 implementation. | Mpi Library, Parallel Computing, High Performance Computing, Distributed Memory System | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| openmpi3 | lcc | N/A | A powerful implementation of MPI | MPI, Parallel Computing, High Performance Computing, Cluster Computing | Computer Science | Library | Documentation, Uses, and more |
| openmpi4 | mcc, lcc | N/A | A powerful implementation of MPI/SHMEM | HPC, Parallel Computing, Message Passing, Distributed Systems | Computer Science | Library | Documentation, Uses, and more |
| openmpi5 | ecc | N/A | A powerful implementation of MPI/SHMEM | HPC, MPI, Parallel Computing, Open Source | Computer Science | Library | Documentation, Uses, and more |
| opensees | lcc | N/A | OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. A number of OpenSees applications are released on this website. Description Source: https://opensees.berkeley.edu/ |
Simulation, Finite Element Analysis, Earthquake Engineering, Structural Analysis, Geotechnical Engineering | Civil Engineering, Engineering & Technology | Finite Element Analysis (Fea) | Documentation, Uses, and more |
| openssh | mcc, lcc | N/A | OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options. Description Source: https://www.openssh.com/ |
Ssh, Secure Networking, Utilities | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| openssl | mcc, ecc, lcc | N/A | OpenSSL software is a robust, commercial-grade, full-featured toolkit for general-purpose cryptography and secure communication. Description Source: https://www.openssl.org/ |
Cryptography, Security, Encryption, Networking | Cryptography, Computer & Information Sciences, Other Computer & Information Sciences | Toolkit | Documentation, Uses, and more |
| opera-ms | mcc | N/A | Documentation, Uses, and more | ||||
| operams | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| optislang | lcc | N/A | optislang is a software platform for optimization, robustness analysis, and sensitivity analysis in engineering and scientific applications. | Optimization, Engineering, Simulation, Sensitivity Analysis | Mechanical Engineering, Optimization | Commercial | Documentation, Uses, and more |
| orca | mcc, lcc | N/A | orca software. | Quantum Chemistry, Computational Chemistry, Quantum Mechanics | Physical Chemistry, Chemical Sciences | Quantum Chemistry Software | Documentation, Uses, and more |
| orthofinder | mcc, lcc | 1.0 | Orthofinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. | Bioinformatics, Phylogenomics, Orthology, Gene Set Inference | Bioinformatics, Biological Sciences | Genome Analysis Software | Documentation, Uses, and more |
| orthologer | mcc | 1.0 | Documentation, Uses, and more | ||||
| os | mcc, ecc | N/A | The os module in Python provides a way of using operating system dependent functionality like reading or writing to the file system. | Python, Operating System, File Management | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| p4vasp | lcc | N/A | p4vasp | Documentation, Uses, and more | |||
| p7zip | ecc | N/A | p7zip is a port of 7za.exe for POSIX systems like Unix (Linux, Solaris, OpenBSD, FreeBSD, Cygwin, AIX, ...), MacOS X and also for BeOS and Amiga. Description Source: https://p7zip.sourceforge.net/ |
File Archiver, Compression Software, Command-Line Tool, Open-Source Software | Computer Science, Computer & Information Sciences | Command-line Tool | Documentation, Uses, and more |
| paml | lcc | 1.0 | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It may be used to estimate parameters and test hypotheses to study the evolutionary process. Description Source: http://abacus.gene.ucl.ac.uk/software/paml.html |
Phylogenetics, Evolutionary Analysis, Maximum Likelihood, Phylogenetic Inference | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| pango | mcc | N/A | pango is a library for layout and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed; however, most of the work on Pango so far has been done using the GTK widget toolkit as a test platform. Pango forms the core of text and font handling for GTK. Description Source: https://github.com/GNOME/pango |
Text Layout, Font Handling, Internationalization | Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| papi | mcc, lcc | N/A | Performance Application Programming Interface | Performance Monitoring, Api, Hardware Counter | Computer Science | Library | Documentation, Uses, and more |
| parallel | mcc, lcc | 1.0 | Parallel processing made simple and fast and runs any code in parallel processes(> use all CPUs), Threads(> speedup blocking operations), or Ractors(> use all CPUs). Description Source: https://github.com/grosser/parallel |
Parallel Computing, Command-Line Tool, Task Scheduling | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| parallel-netcdf | mcc | N/A | PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. Description Source: https://parallel-netcdf.github.io/ |
High-Performance I/O, Big Data, Parallel Computing | Earth & Environmental Sciences, Physical Sciences | I/O Library | Documentation, Uses, and more |
| paraview | mcc, lcc | 1.0 | ParaView 5.10.1 OSMesa build for server-side CPU/software rendering on any MCC compute node. | Visualization, Data Analysis, Open-Source, Multi-Platform | Data Visualization, Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences | Data Visualization | Documentation, Uses, and more |
| parmetis | mcc | N/A | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. Description Source: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview |
Graph Partitioning, Sparse Matrix Ordering, Scientific Computing, Parallel Computing | Computer Science, Computer & Information Sciences | Computational Tool | Documentation, Uses, and more |
| partitionfinder | lcc | 1.0 | PartitionFinder is a software tool for selecting the best partitioning schemes and models of molecular evolution for phylogenetic analyses. | phylogenetics, model selection, bioinformatics | Computational Biology, Bioinformatics | Desktop Application | Documentation, Uses, and more |
| patch | ecc | N/A | The `patch` utility is a tool used to apply changes to files based on a diff file, which contains the differences between two versions of a file or set of files. | version control, file management, diff, software development | Software Engineering, Other Computer and Information Sciences | Command-line tool | Documentation, Uses, and more |
| patchelf | mcc, lcc | N/A | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | Dependency Management, Executable Modification, Dynamic Linker Paths | Systems and Development, Computer & Information Sciences | Library Management | Documentation, Uses, and more |
| pathofact | lcc | N/A | Documentation, Uses, and more | ||||
| pb-assembly | lcc | 1.0 | Documentation, Uses, and more | ||||
| pbccs | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| pbjelly | mcc, lcc | 1.0 | bioinformatics, genomics, DNA assembly | Bioinformatics, Genomics | Assembly Tool | Documentation, Uses, and more | |
| pbmm2 | mcc, lcc | 1.0 | Pbmm2 is a minimap2 frontend for PacBio native data formats. | Long Read Aligner, Graph-Guided Mapping, Reference Genome Mapping, Bioinformatics | Bioinformatics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| pbtk | lcc | 1.0 | Documentation, Uses, and more | ||||
| pcangsd | mcc | 1.0 | PCAngsd is a program that estimates the covariance matrix and individual allele frequencies for low-depth next-generation sequencing (NGS) data in structured/heterogeneous populations using principal component analysis (PCA) to perform multiple population genetic analyses using genotype likelihoods. | Population Genetics, Genomic Data Analysis | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| pcre | mcc, lcc | 1.0 | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. NOTE:This version of PCRE is now at end of life, and is no longer being actively maintained. New Projects should use PCRE2 instead. Description Source: https://www.pcre.org/ |
Regular Expressions, Pattern Matching, Library | Biology, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| pcre2 | mcc, ecc | N/A | PCRE2 is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. NOTE: This is the current version of the PCRE library. Description Source: https://www.pcre.org/ |
Regular Expressions, Text Processing, Pattern Matching | Biology, Computer & Information Sciences | C Library | Documentation, Uses, and more |
| pdftotext | lcc | N/A | pdftotext is a command-line utility that converts PDF documents into plain text files, allowing for easier text extraction and manipulation. | PDF, Text Extraction, Command Line, Open Source | Information Retrieval, Computer Science | Utility | Documentation, Uses, and more |
| pdtoolkit | mcc, lcc | N/A | PDT is a framework for analyzing source code | Static Analysis, Source Code Parsing | Development library | Documentation, Uses, and more | |
| pegtl | lcc | N/A | PEGTL (Parsing Expression Grammar Template Library) is a C++ library designed for parsing expression grammars, providing a framework for implementing parsers in a straightforward manner. | C++, Parsing, Grammar, Template Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| perl | mcc, ecc, lcc | N/A | Larry Wall's Practical Extraction and Report Language | Programming Language, Text Processing, Scripting, Web Development, System Administration | Bioinformatics, Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| perl-bio-viennangs | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-bioperl | mcc, lcc | 1.0 | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. | bioinformatics, perl, sequence analysis, genomics, molecular biology | Computational Biology, Biological Sciences | Library | Documentation, Uses, and more |
| perl-data-dumper | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| perl-encode-locale | mcc | N/A | A Perl module that provides a way to determine the locale encoding of the environment and to set the encoding for input and output streams accordingly. | Perl, Encoding, Locale, Internationalization | Natural Language Processing, Computer Science | Library | Documentation, Uses, and more |
| perl-extutils-config | mcc | N/A | perl-extutils-config is a Perl module that provides a way to retrieve configuration information about Perl installations and modules. | Perl, Configuration, Build Tools | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| perl-extutils-helpers | mcc | N/A | Documentation, Uses, and more | ||||
| perl-extutils-installpaths | mcc | N/A | A Perl module that provides methods to determine installation paths for Perl modules and scripts. | Perl, Installation, Module Management | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| perl-file-listing | mcc | N/A | A Perl module that provides a way to create directory listings in a structured format, often used for generating HTML file listings. | Perl, File Management, Web Development | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| perl-html-parser | mcc | N/A | A Perl module for parsing HTML documents and extracting data from them. | HTML, Parsing, Perl, Web Scraping | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| perl-html-tagset | mcc | N/A | The HTML::Tagset module provides a set of constants for HTML tags and attributes, which can be used in conjunction with HTML::Parser and other modules to facilitate HTML parsing and manipulation. | a, div, span, p, img, table, tr, td | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| perl-http-cookies | mcc | N/A | A Perl module for managing HTTP cookies, allowing for easy handling of cookie storage and retrieval in web applications. | Perl, HTTP, Cookies, Web Development | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| perl-http-daemon | mcc | N/A | A simple HTTP server written in Perl that can be used for testing and development purposes. | Perl, HTTP, Web Server, Development | Computer Science, Software Engineering | Web Server | Documentation, Uses, and more |
| perl-http-date | mcc | N/A | perl-http-date is a Perl module that provides functions for parsing and formatting HTTP date strings. | Perl, HTTP, Date, Parsing, Formatting | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| perl-http-message | mcc | N/A | perl-http-message is a Perl module that provides classes for HTTP message handling, including HTTP requests and responses. | Perl, HTTP, Web Development, Networking | Computer Science | Library | Documentation, Uses, and more |
| perl-http-negotiate | mcc | N/A | A Perl module that provides content negotiation features for HTTP requests. | Perl, HTTP, Content Negotiation, Web Development | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| perl-io-html | mcc | N/A | The IO::HTML module provides an interface for reading HTML documents as if they were plain text files, allowing for easier parsing and manipulation of HTML content. | HTML, Perl, Parsing, Text Processing | Software Engineering, Informatics | Library | Documentation, Uses, and more |
| perl-libwww-perl | mcc | N/A | A collection of Perl modules that provide a simple and consistent interface for web programming. | Perl, Web Development, HTTP Client, Networking | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| perl-lwp-mediatypes | mcc | N/A | A Perl module that provides a way to handle media types (MIME types) in web applications. | Perl, Web Development, MIME Types, HTTP | Software Engineering, Applied Computer Science | Library | Documentation, Uses, and more |
| perl-module-build | mcc | N/A | Perl Module Build is a system for building and installing Perl modules. It provides a simple way to create a Makefile for your Perl module, allowing for easy installation and management of dependencies. | Perl, Build System, Module Management | Computer Science, Software Engineering | Build Tool | Documentation, Uses, and more |
| perl-module-build-tiny | mcc | N/A | A minimalistic Perl module for building and installing Perl modules. | Perl, Build Tools, Module Management | Software Engineering | Library | Documentation, Uses, and more |
| perl-net-http | mcc | N/A | perl-net-http is a Perl library that provides an interface for HTTP client functionality, allowing users to send HTTP requests and handle responses. | Perl, HTTP, Networking, Web Development | Computer Science | Library | Documentation, Uses, and more |
| perl-test-needs | mcc | N/A | Documentation, Uses, and more | ||||
| perl-text-soundex | mcc | N/A | A Perl module that implements the Soundex phonetic algorithm for indexing names by sound, as pronounced in English. | Phonetics, Text Processing, Perl | Computational Linguistics, Other Natural Sciences | Library | Documentation, Uses, and more |
| perl-try-tiny | mcc | N/A | Try::Tiny is a minimalistic module for exception handling in Perl, providing a simple way to catch exceptions without the overhead of traditional Perl eval blocks. | Perl, Exception Handling, Error Management, Lightweight, Programming | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| perl-uri | mcc | N/A | perl-uri is a Perl module for manipulating Uniform Resource Identifiers (URIs). It provides a simple way to create, parse, and manipulate URIs in a consistent manner. | Perl, URI, Web Development, Networking | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| perl-velvetoptimiser | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| perl-www-robotrules | mcc | N/A | Documentation, Uses, and more | ||||
| perl-xml-parser | mcc | N/A | A Perl module for parsing XML documents. | XML, Parsing, Perl, SAX, DOM | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| petsc | mcc, lcc | N/A | Portable Extensible Toolkit for Scientific Computation | Scientific Computing, Computational Science, Numerical Analysis | Applied Mathematics, Natural Sciences | Library | Documentation, Uses, and more |
| pggb | mcc | 1.0 | pggb builds pangenome variation graphs from a set of input sequences. | Performance Evaluation, Benchmarking, Computational Applications | Performance Evaluation & Benchmarking, Training | Documentation, Uses, and more | |
| pgi | mcc, lcc | N/A | The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. Description Source: https://developer.nvidia.com/hpc-sdk |
Hpc, Compilers, Parallel Programming | Computer Science, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| pgi-cuda | lcc | N/A | Documentation, Uses, and more | ||||
| phasebook | mcc | 1.0 | Documentation, Uses, and more | ||||
| phaser | lcc | N/A | PHASER is a software package for macromolecular crystallography that is used for solving crystal structures using molecular replacement and experimental phasing techniques. | Crystallography, Structural Biology, Computational Chemistry | Biochemistry, Molecular Biology | Application | Documentation, Uses, and more |
| phastest | mcc | 1.0 | Documentation, Uses, and more | ||||
| phdf5 | lcc | N/A | A general purpose library and file format for storing scientific data | Parallel I/O, Phdf5, Hdf5, Large Datasets | Computer & Information Sciences | File Format | Documentation, Uses, and more |
| phrynomics | mcc | 1.0 | Documentation, Uses, and more | ||||
| phylophlan | lcc | 1.0 | PhyloPhlAn is a software tool for phylogenetic analysis of metagenomic data, focusing on the reconstruction of phylogenetic trees from genomic data. | bioinformatics, phylogenetics, genomics, microbiology | Microbial phylogenetics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| phyluce | lcc | N/A | Phyluce is a software package designed for the analysis of phylogenomic data, particularly for handling and processing genomic data for phylogenetic studies. | phylogenetics, bioinformatics, genomics, sequence analysis | Genomics, Phylogenetics | Analysis | Documentation, Uses, and more |
| phyml | lcc | 1.0 | PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. PhyML was designed to process moderate to large data sets and can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements. | phylogenetics,bioinformatics,maximum likelihood,tree estimation | Bioinformatics, Phylogenetics | Standalone | Documentation, Uses, and more |
| picard | mcc, lcc | 1.0 | Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Description Source: https://broadinstitute.github.io/picard/ |
Bioinformatics, Ngs, Hts, Sequencing Data, Sam, Bam, Vcf | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| picrust2 | mcc | 1.0 | Picrust2 is a software for predicting functional abundances based only on marker gene sequences. | Bioinformatics, Metagenomics, Microbiome Analysis, Functional Gene Prediction | Biological Sciences | Metagenomics Tool | Documentation, Uses, and more |
| pigz | ecc, lcc | N/A | pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. Description Source: https://zlib.net/pigz/ |
Compression, Parallel Processing, Utility, Command-Line Tool | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| pilon | lcc | 1.0 | Pilon is an automated genome assembly improvement and variant detection tool. | Genome Assembly, Genomics, Bioinformatics, Computational Biology | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| pipeline | mcc | 1.0 | Documentation, Uses, and more | ||||
| pixman | mcc | N/A | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. Description Source: https://www.pixman.org/ |
Pixel Manipulation, Rendering, Software Library, Performance | Software Development, Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| pkg-config | lcc | N/A | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). | Compilation, Library Management, Build Process | Computer Science, Engineering & Technology | Utility | Documentation, Uses, and more |
| pkgconf | mcc, ecc, lcc | N/A | pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility. Description Source: http://pkgconf.org/ |
Package Configuration, Build Flags, Link Flags, System-Agnostic | Software Engineering, Computer & Information Sciences | Package Configuration | Documentation, Uses, and more |
| plascad | lcc | 1.0 | Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization. | Documentation, Uses, and more | |||
| plasma | lcc | N/A | Parallel Linear Algebra Software for Multicore Architectures | Documentation, Uses, and more | |||
| plink | mcc, lcc | 1.0 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Description Source: https://zzz.bwh.harvard.edu/plink/ |
Genetic Analysis, Genomic Data Analysis, Gwas, Genetic Epidemiology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| plink2 | mcc | 1.0 | Plink2 is a whole genome association analysis toolset. | Genomics, Association Analysis, Genotype-Phenotype Data | Genetics | Tool | Documentation, Uses, and more |
| plotsr | mcc | 1.0 | Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies. | Plotting, Data Visualization, Python Library | Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| plumed | lcc | N/A | PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. Description Source: https://www.plumed.org/ |
Molecular Dynamics, Enhanced Sampling, Free Energy Calculations, Collective Variables | Chemistry, Biological Sciences | Library | Documentation, Uses, and more |
| pmix | mcc, lcc | N/A | The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for inter-process communication. Two versions (PMI-1 and PMI-2) have been released as part of the MPICH effort, with PMI-2 demonstrating better scaling properties than its PMI-1 predecessor. Description Source: https://pmix.github.io/standard |
Process Management, Parallel Computing, High-Performance Computing, Data Exchange, Resource Management, Scalability | Computer Science, Engineering & Technology | Hpc Tool | Documentation, Uses, and more |
| pnetcdf | lcc | N/A | A Parallel NetCDF library (PnetCDF) | Parallel I/O, Netcdf Files, Scalability, Performance | High-Performance Computing, Physical Sciences | I/O Library | Documentation, Uses, and more |
| popoolation | mcc | 1.0 | Popoolation is a software tool designed for the analysis of pooled next-generation sequencing data. It allows researchers to estimate allele frequencies, detect variants, and perform population genetic analyses. | bioinformatics, population genetics, next-generation sequencing | Population Genetics, Genomics | Analysis Tool | Documentation, Uses, and more |
| popt | mcc | N/A | Popt is a command line option parsing library that provides a simple, yet powerful mechanism for parsing command-line options and arguments. It assists in simplifying the process of writing command-line interfaces for applications. | Command Line Options, C Library | Computer & Information Sciences | Command Line Option Parser | Documentation, Uses, and more |
| porechop | mcc | 1.0 | Porechop is a tool designed for the trimming of Illumina sequencing data, specifically focusing on the removal of adapter sequences and low-quality reads. | bioinformatics, sequence analysis, data processing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| prank | lcc | 1.0 | PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. | Sequence Alignment, Bioinformatics, Genomics, Phylogenetics | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| pretext-suite | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| prodigal-2.6.3 | mcc | 1.0 | Documentation, Uses, and more | ||||
| prokka | lcc | 1.0 | Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Description Source: https://github.com/tseemann/prokka |
Genome Annotation, Bioinformatics, Genomics | Genetics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| proovread | lcc | N/A | Proovread is a software tool designed for the correction of sequencing errors in high-throughput sequencing data, particularly in the context of genomic and transcriptomic analyses. | bioinformatics, genomics, sequence analysis, error correction | Computational Biology, Bioinformatics | Open Source | Documentation, Uses, and more |
| protobuf | lcc | N/A | Protocol Buffers are language-neutral, platform-neutral extensible mechanisms for serializing structured data. Description Source: https://protobuf.dev/ |
Serialization, Data Interchange, Code Generation | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| prun | mcc, ecc, lcc | N/A | job launch utility for multiple MPI families | Parallel Computing, High-Performance Computing, Distributed Computing, Data Analysis, Computation | Other Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| psi4 | mcc, lcc | 1.0 | Psi4 is an open-source quantum chemistry package that provides a variety of methods for electronic structure calculations, including Hartree-Fock, post-Hartree-Fock, and density functional theory (DFT). | Quantum Chemistry, Electronic Structure, Computational Chemistry, Open Source | Theoretical Chemistry, Quantum Chemistry | Scientific Software | Documentation, Uses, and more |
| ptscotch | lcc | N/A | Graph, mesh and hypergraph partitioning library using MPI | Graph Partitioning, Parallel Computing, High Performance Computing, Scientific Computing | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| pugixml | lcc | N/A | pugixml is a light-weight C++ XML processing library | Xml Processing, C++ Library, Xpath, Parsing | Software Engineering, Computer & Information Sciences | Xml Processing | Documentation, Uses, and more |
| purge_dups | mcc | 1.0 | purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth. | Bioinformatics, Genomics, DNA Sequences | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| py-cython | mcc, ecc | N/A | Py-Cython is a compiler for writing C extensions for the Python language. It allows for combining Python and C code seamlessly to improve performance and efficiency. | Compiler, Python Library, Performance Optimization | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| py-docutils | mcc | N/A | A Python package for processing reStructuredText documents, primarily used for generating documentation. | Documentation, Python, reStructuredText | Software Engineering | Library | Documentation, Uses, and more |
| py-h5py | mcc | N/A | py-h5py is a Python interface for the HDF5 binary data format, providing efficient input/output operations for working with large datasets. | Python Library, Data Format, Input/Output Operations, Large Datasets | Data Science, Computer & Information Sciences | Interface | Documentation, Uses, and more |
| py-mako | mcc, lcc | N/A | Mako is a fast and lightweight templating engine for Python, designed to be easy to use and integrate with existing applications. | templating, Python, web development | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| py-markupsafe | mcc, lcc | N/A | A library for safe string handling in Python, particularly for HTML and XML. | Python, String Handling, Web Development | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| py-mpi4py | mcc | N/A | py-mpi4py is a Python interface to the Message Passing Interface (MPI) standard for parallel computing, allowing users to utilize MPI functionality within Python scripts and applications. | Python, Mpi, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| py-numpy | mcc | N/A | NumPy is a fundamental package for scientific computing in Python. It provides support for arrays, matrices, and a variety of mathematical functions to operate on these data structures. | Python, Scientific Computing, Data Analysis, Numerical Computation | Applied Mathematics, Other Mathematics | Python Library | Documentation, Uses, and more |
| py-pip | ecc, lcc | N/A | py-pip is the official installer for Python packages from the Python Package Index (PyPI). It is used to install and manage software packages written in Python. | Package Management, Python, Software Installation | Software Engineering, Computer & Information Sciences, Systems & Development | Package Management | Documentation, Uses, and more |
| py-pkgconfig | mcc | N/A | A Python package that provides a way to use pkg-config from Python code, allowing for easy retrieval of compiler and linker flags for libraries. | Python, pkg-config, build tools | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| py-pygments | mcc | N/A | Pygments is a syntax highlighting library written in Python that supports a wide range of programming languages and markup formats. | syntax highlighting, programming languages, markup formats, Python | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| py-setuptools | mcc, ecc, lcc | N/A | Setuptools is a package development process library designed to facilitate development and distribution of Python projects. It provides a common approach for managing project dependencies, packaging, and installation processes. | Python, Package Development, Distribution, Dependency Management | Computer Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| py-wheel | mcc, ecc, lcc | N/A | Documentation, Uses, and more | ||||
| py2-mpi4py | lcc | N/A | Python bindings for the Message Passing Interface (MPI) standard. | Documentation, Uses, and more | |||
| py2-numpy | lcc | N/A | NumPy array processing for numbers, strings, records and objects | Documentation, Uses, and more | |||
| py2-scipy | lcc | N/A | Scientific Tools for Python | Documentation, Uses, and more | |||
| py2.7-samtools | lcc | N/A | Documentation, Uses, and more | ||||
| py3-mpi4py | lcc | N/A | Python bindings for the Message Passing Interface (MPI) standard. | MPI, Python, Parallel Computing, High Performance Computing | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| py3-numpy | lcc | N/A | NumPy array processing for numbers, strings, records and objects | Python, Scientific Computing, Numerical Analysis, Data Science | Mathematics, Applied Mathematics | Library | Documentation, Uses, and more |
| py3-scipy | lcc | N/A | Scientific Tools for Python | Python, Scientific Computing, Numerical Analysis, Data Science | Applied Mathematics, Computer Science | Library | Documentation, Uses, and more |
| py4vasp | mcc | 1.0 | py4vasp is a Python package designed to facilitate the analysis and visualization of VASP (Vienna Ab initio Simulation Package) output files. It provides tools for extracting relevant data from VASP calculations and generating plots and other visualizations to aid in the interpretation of results. | Python, VASP, Computational Chemistry, Data Analysis, Visualization | Computational Chemistry, Physical Chemistry | Library | Documentation, Uses, and more |
| pyani-0.2.13.1 | mcc | 1.0 | pyani is a Python package for calculating average nucleotide identity (ANI) between microbial genomes. | bioinformatics, genomics, sequence analysis | Microbiology, Bioinformatics | Library | Documentation, Uses, and more |
| pybind11 | lcc | 1.0 | pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection. Description Source: https://github.com/pybind/pybind11 |
Software Development, Python Library, C++ Integration, Header-Only Library | Software Engineering, Computer & Information Sciences | Interoperability | Documentation, Uses, and more |
| pygenometracks | mcc | 1.0 | pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. | Genomics, Data Visualization, Python, Genomic Data Analysis | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| pymatgen | mcc | 1.0 | Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis and manipulation, particularly for computational materials science. | materials science, computational chemistry, data analysis, python | Computational Materials Science, Materials Science | Library | Documentation, Uses, and more |
| pymeshlab | lcc | 1.0 | PyMeshLab is a Python binding for the MeshLab software, allowing users to manipulate and process 3D meshes programmatically. | 3D modeling, Mesh processing, Computer graphics, Scientific computing | 3D Mesh Processing, Computer Science | Library | Documentation, Uses, and more |
| pypy | lcc | N/A | PyPy is a fast, compliant alternative implementation of the Python programming language. It aims to provide a high-performance, flexible, and efficient interpreter for Python, while maintaining compatibility with the CPython reference implementation. | Python Interpreter, Alternative Implementation, Just-In-Time Compilation, High Performance | Software Engineering, Computer & Information Sciences | Programming Language Implementation | Documentation, Uses, and more |
| pysam | lcc | 1.0 | Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. Description Source: https://github.com/pysam-developers/pysam |
Bioinformatics, Sequence Analysis, Sam/Bam Files, Python Module | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| pyside6 | mcc | 1.0 | Documentation, Uses, and more | ||||
| python | mcc, ecc, lcc | N/A | Python 3.10 installed via Conda environment. | Programming Language, Interpreted Language, High-Level Language | Software Engineering, Computer & Information Sciences, Systems & Development | Language | Documentation, Uses, and more |
| python-venv | ecc | N/A | A tool for creating isolated Python environments, allowing users to manage dependencies for different projects independently. | Python, Virtual Environment, Dependency Management | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| python312_ml | mcc | 1.0 | Documentation, Uses, and more | ||||
| pytorch | lcc | 1.0 | PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Description Source: https://pytorch.org/docs/stable/index.html |
Machine Learning, Deep Learning, Numerical Computation, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| pytraj | mcc, lcc | 1.0 | PyTraj is a Python library for analyzing molecular dynamics trajectories. It is part of the AmberTools suite and provides tools for trajectory manipulation, analysis, and visualization. | Molecular Dynamics, Bioinformatics, Computational Chemistry, Python | Molecular Dynamics, Biochemistry and Molecular Biology | Library | Documentation, Uses, and more |
| pyvcf | mcc | 1.0 | pyvcf is a Python library for parsing and manipulating VCF (Variant Call Format) files, which are commonly used in bioinformatics to store gene sequence variations. | bioinformatics, genomics, data analysis, variant calling | Genomics, Genetic Variation | Library | Documentation, Uses, and more |
| qiime2 | mcc, lcc | 1.0 | QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. \r Description Source: https://qiime2.org/ |
Microbiome, Bioinformatics, Sequencing | Bioinformatics | Analysis Software | Documentation, Uses, and more |
| qiime2-amplicon | lcc | 1.0 | QIIME 2 is an open-source bioinformatics platform for performing microbiome analysis. The amplicon plugin provides tools for analyzing amplicon sequence data. | bioinformatics, microbiome, amplicon sequencing, data analysis | Bioinformatics, Biological Sciences | Open-source | Documentation, Uses, and more |
| qiime2-shotgun | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2-tiny | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2amplicon | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiskit | lcc | 1.0 | Qiskit is an open-source quantum computing software development framework that provides tools for creating, simulating, and executing quantum programs. | Quantum Computing, Open Source, Simulation, IBM | Quantum Computing, Quantum Algorithms | Library | Documentation, Uses, and more |
| quantum-espresso | mcc, lcc | 1.0 | Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Description Source: https://www.quantum-espresso.org/ |
Quantum Mechanics, Materials Science, Computational Physics | Chemistry, Condensed Matter Physics | Package | Documentation, Uses, and more |
| quantumespresso | lcc | 1.0 | Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Description Source: https://www.quantum-espresso.org/ |
Quantum Mechanics, Materials Science, Computational Physics | Chemistry, Condensed Matter Physics | Package | Documentation, Uses, and more |
| quast | lcc | 1.0 | Quast is Quality Assessment Tool for Genome Assemblies. | Genome Assembly, Bioinformatics, Quality Assessment | Genomics, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| quorum | lcc | 1.0 | Documentation, Uses, and more | ||||
| r | mcc, lcc | 1.0 | R | Statistical Computing, Data Analysis, Statistical Graphics | Computer Science | Statistical Software | Documentation, Uses, and more |
| r-base | lcc | N/A | R is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. | Statistics, Data Science, Visualization, Open Source | Statistics, Statistical Computing | Programming Language | Documentation, Uses, and more |
| r-colorspace | mcc | N/A | Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny GUI) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Description Source: https://github.com/conda-forge/r-colorspace-feedstock/blob/main/recipe/meta.yaml | Color Models, Color Conversion, Data Visualization, R Package | Statistics, Other Mathematics | Package | Documentation, Uses, and more |
| r-fastbaps | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-peer | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-plm-1.6_5 | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-satscan | lcc | N/A | Documentation, Uses, and more | ||||
| r-seurat | mcc | 1.0 | Seurat is an R package designed for single-cell RNA sequencing data analysis, providing tools for data normalization, clustering, and visualization. | bioinformatics, single-cell analysis, R package, data visualization | Bioinformatics, Biochemistry and Molecular Biology | Library | Documentation, Uses, and more |
| r-wgcna | lcc | 1.0 | R package for Weighted Gene Co-expression Network Analysis (WGCNA), which is used for constructing co-expression networks and identifying modules of highly correlated genes. | R, Bioinformatics, Gene Expression, Network Analysis | Bioinformatics, Biological Sciences | Statistical Software | Documentation, Uses, and more |
| racon | lcc | N/A | Racon is consensus module for raw de novo DNA assembly of long uncorrected reads. | Bioinformatics, Sequence Analysis, Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ragtag | mcc, lcc | 1.0 | Ragtag is a tool for fast reference-guided genome assembly scaffolding. | Assembly Improvement, Genome Alignment, Assembly Evaluation | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| raisd | mcc | 1.0 | Documentation, Uses, and more | ||||
| randrproto | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| rapidjson | mcc | N/A | RapidJSON is a fast JSON parser/generator for C++ with both SAX/DOM style API. Description Source: https://github.com/Tencent/rapidjson/ |
Json, C++, Parser, Generator, Sax, Dom, Memory Efficient | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| raxml | mcc, lcc | 1.0 | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Description Source: https://github.com/amkozlov/raxml-ng |
Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raxml-ng | lcc | 1.0 | Raxml-ng is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. | Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raxml-ng-mpi | mcc | N/A | raxml-ng software. | phylogenetics, maximum likelihood, bioinformatics, high-performance computing | Bioinformatics, Phylogenetics | Command-line tool | Documentation, Uses, and more |
| raxml-ng_v0.9.0 | lcc | N/A | RAxML-NG is a next generation implementation of RAxML for phylogenetic inference and the estimation of the associated uncertainty. | Phylogenetics, Bioinformatics, Evolutionary Biology | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| raxmlng | mcc | 1.0 | RAxML-NG is a software tool for maximum likelihood-based phylogenetic inference and ancestral state reconstruction. | phylogenetics, maximum likelihood, tree inference, bioinformatics | Bioinformatics, Biological Sciences | Executable | Documentation, Uses, and more |
| rclone | mcc | N/A | Rcone 1.56.0 | Cloud Storage, File Synchronization, Command-Line Tool | Computer Science | Data Management | Documentation, Uses, and more |
| rcorrector | mcc | 1.0 | rcorrector is a software tool designed for correcting errors in RNA-Seq data, particularly useful for improving the accuracy of transcriptome assembly and quantification. | RNA-Seq, Error Correction, Bioinformatics, Transcriptomics | Bioinformatics, Biochemistry and Molecular Biology | Command-line tool | Documentation, Uses, and more |
| rdkit | mcc | 1.0 | RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Description Source: https://github.com/rdkit/rdkit |
Cheminformatics, Molecular Modeling, Cheminformatics Toolkit | Chemical Sciences, Natural Sciences | Toolkit | Documentation, Uses, and more |
| rdma-core | mcc | N/A | rdma-core is a set of userspace libraries and tools for Remote Direct Memory Access (RDMA) and kernel-level support for RDMA networking. | RDMA, Networking, High Performance Computing, InfiniBand | Computer Science | Library | Documentation, Uses, and more |
| re2c | ecc | N/A | re2c is a free and open-source lexer generator for C/C++, Go and Rust with a focus on generating fast code. It compiles regular expression specifications to deterministic finite automata and encodes them in the form of conditional jumps in the target language. This approach is generally faster than table-based lexers, and the generated code is easier to debug and understand. Description Source: https://re2c.org/ |
Lexer, Scanner, Regular Expressions, Dfa | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| readline | mcc, ecc, lcc | N/A | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | Gnu, Command Line Interface, Interactive Programs, Line Editing, History Manipulation | Software Engineering, Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| recon | mcc | 1.0 | Documentation, Uses, and more | ||||
| recordproto | mcc | N/A | Documentation, Uses, and more | ||||
| reditools1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| reditools2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| reindeer | lcc | 1.0 | Documentation, Uses, and more | ||||
| renderproto | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| repeatafterme | mcc | 1.0 | Documentation, Uses, and more | ||||
| repeatmasker | mcc, lcc | 1.0 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | Genomics, Bioinformatics, Sequence Analysis, Repeat Detection | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| repeatmodeler | mcc | 1.0 | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | Genomics, Bioinformatics, Repeat Sequences, De Novo Identification | Bioinformatics, Biological Sciences | Research Tool | Documentation, Uses, and more |
| repeatscout | mcc | 1.0 | RepeatScout is a tool to discover repetitive substrings in DNA. | Genomics, Bioinformatics, Computational Biology | Biological Sciences | Genomic Sequence Analysis | Documentation, Uses, and more |
| revbayes | lcc | N/A | RevBayes -- Bayesian phylogenetic inference using probabilistic graphical models and an interactive language. | Phylogenetics, Bayesian Inference, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Probabilistic Programming Tool | Documentation, Uses, and more |
| reviewer | mcc | 1.0 | Documentation, Uses, and more | ||||
| rmblast | mcc | 1.0 | rmblast is a high-performance implementation of the BLAST (Basic Local Alignment Search Tool) algorithm, optimized for rapid sequence alignment in bioinformatics applications. | bioinformatics, sequence alignment, BLAST, high-performance computing | Computational Biology, Biochemistry and Molecular Biology | Command-line tool | Documentation, Uses, and more |
| rnabloom | mcc | 1.0 | Documentation, Uses, and more | ||||
| rnahybrid | mcc | 1.0 | RNAhybrid is a tool for predicting the hybridization of a single-stranded RNA to a target RNA or DNA sequence. It is particularly useful in the field of bioinformatics for studying RNA-RNA interactions. | bioinformatics, RNA, hybridization, computational biology | Bioinformatics, Molecular Biology | Command-line tool | Documentation, Uses, and more |
| rnammer | lcc | 1.0 | RNAmmer is a software tool for the annotation of ribosomal RNA genes in genomic sequences. | bioinformatics, genomics, RNA, annotation | Bioinformatics, Biological Sciences | Standalone | Documentation, Uses, and more |
| rnastructure | lcc | 1.0 | RNAstructure is a software package for RNA secondary structure prediction and analysis, providing tools for both thermodynamic and comparative methods. | RNA, Bioinformatics, Computational Biology, Molecular Biology | Bioinformatics, Biochemistry and Molecular Biology | Standalone | Documentation, Uses, and more |
| roary | lcc | 1.0 | Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. | Bioinformatics, Genomics, Pan-Genome Analysis, Prokaryotic Genomes | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| root | mcc, lcc | 1.0 | ROOT is a framework for data processing, born at CERN, at the heart of the research on high-energy physics. Every day, thousands of physicists use ROOT applications to analyze their data or to perform simulations. Description Source: https://root.cern/about/ |
Data Analysis, Visualization, High-Energy Physics, Data Manipulation, Statistical Analysis | Particle & High-Energy Physics, Physical Sciences | Library | Documentation, Uses, and more |
| rosetta | lcc | N/A | rosetta software. | bioinformatics, computational biology, structural biology, molecular modeling | Bioinformatics, Structural Biology | Application | Documentation, Uses, and more |
| rsem | mcc, lcc | 1.0 | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. Description Source: https://github.com/deweylab/RSEM |
RNA-Seq, Transcriptomics, Gene Expression, Bioinformatics | Genomics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| rstan | lcc | N/A | R | Bayesian Statistics, MCMC, Statistical Modeling, Probabilistic Programming | Statistical Inference, Bayesian Statistics | Statistical Software | Documentation, Uses, and more |
| rstudio | lcc | 1.0 | RStudio is an integrated development environment (IDE) for the R and Python. It includes a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management. Description Source: https://posit.co/products/open-source/rstudio/ |
Ide, Statistical Computing, Data Visualization, Programming | Statistics, Other Natural Sciences | Ide | Documentation, Uses, and more |
| rsync | mcc | N/A | rsync is a fast and versatile file copying tool that can synchronize files and directories between two locations over a network or locally. | file transfer, synchronization, backup, networking | Computer Science | Command-line tool | Documentation, Uses, and more |
| ruby | mcc | N/A | 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. \r Description Source: https://www.ruby-lang.org/en/ |
Programming Language, Scripting Language, Web Development | Computer Science | Programming | Documentation, Uses, and more |
| rust | mcc | N/A | Rust is a systems programming language that is designed to be fast, memory-efficient, and safe. It is often used for building high-performance applications, such as operating systems, web browsers, game engines, and embedded systems. | Programming Language, System Programming, Concurrency | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| rvtests | mcc | 1.0 | rvtests is a software package designed for the analysis of genetic association studies, particularly focusing on rare variants. It provides statistical methods to evaluate the association of rare variants with traits in a population. | genetics, bioinformatics, statistical analysis, rare variants | Bioinformatics, Genetics | Analysis Tool | Documentation, Uses, and more |
| sabre | lcc | 1.0 | Documentation, Uses, and more | ||||
| salmon | mcc, lcc | 1.0 | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. | RNA-Seq, Transcript Expression Quantification | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| salome | mcc, lcc | N/A | salome software. | Open Source, Simulation, Pre-processing, Post-processing, Mesh Generation | Numerical Simulation, Engineering and Technology | Framework | Documentation, Uses, and more |
| salsa2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| sambamba | mcc | 1.0 | Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. | Sam/Bam Files, High-Performance Tool, Parallel Processing, Genomics | Bioinformatics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| samblaster | mcc | 1.0 | Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files. | Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| samtools | mcc, lcc | 1.0 | SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Description Source: https://samtools.sourceforge.net/ |
Sequence Analysis, Genomics, Bioinformatics | Bioinformatics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| samtools-bcftools-htslib | mcc | 1.0 | A suite of programs for interacting with high-throughput sequencing data, including tools for manipulating SAM/BAM/CRAM files and variant calling. | bioinformatics, genomics, data analysis, sequence alignment | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| sas | mcc, lcc | N/A | SAS | Documentation, Uses, and more | |||
| sbert | lcc | 1.0 | Documentation, Uses, and more | ||||
| scalapack | lcc | N/A | A subset of LAPACK routines redesigned for heterogenous computing | Linear-Algebra, Numerical-Computing, Distributed-Computing, Parallel-Computing | Other, Physical Sciences | Library | Documentation, Uses, and more |
| scalasca | mcc, lcc | N/A | Toolset for performance analysis of large-scale parallel applications | Performance Analysis, Parallel Applications, Performance Optimization, Mpi Applications, Visualization | Software Engineering, Systems & Development, Computer & Information Sciences | Performance Analysis Tool | Documentation, Uses, and more |
| scflow | lcc | N/A | Documentation, Uses, and more | ||||
| scipy | lcc | N/A | SciPy is a collection of mathematical algorithms and convenience functions built on NumPy . It adds significant power to Python by providing the user with high-level commands and classes for manipulating and visualizing data. Description Source: https://docs.scipy.org/doc/scipy-1.8.0/tutorial/general.html |
Scientific Computing, Numerical Algorithms, Python Library, Data Analysis, Signal Processing | Applied Mathematics, Computer & Information Sciences, Other Computer & Information Sciences | Python | Documentation, Uses, and more |
| scons | mcc, lcc | 1.0 | SCons is an Open Source software construction tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software. Description Source: https://scons.org/ |
Build Tool, Software Construction, Automation, Python | Software Development, Engineering & Technology | Build Tool | Documentation, Uses, and more |
| scorep | mcc, lcc | N/A | Scalable Performance Measurement Infrastructure for Parallel Codes | Performance Analysis, Profiling, Tracing, HPC | Computer Science | Performance Analysis Tool | Documentation, Uses, and more |
| scotch | mcc, lcc | N/A | Graph, mesh and hypergraph partitioning library | Graph Partitioning, Mesh Partitioning, Parallel Computing, Distributed Memory | Software Engineering, Systems & Development, Computer & Information Sciences | Library | Documentation, Uses, and more |
| screen | mcc | N/A | Screen is a terminal multiplexer that allows users to use multiple terminal sessions within a single window. It is particularly useful for managing long-running processes and for remote sessions. | Terminal, Multiplexer, Remote Access, Unix | Systems, and Development, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| scte | mcc | 1.0 | Documentation, Uses, and more | ||||
| sda | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| sed | ecc | N/A | sed (Stream Editor) is a Unix utility that parses and transforms text from a data stream or file using a simple, compact programming language. | Text processing, Unix, Command line, Scripting | Software Engineering, Other Computer and Information Sciences | Command-line tool | Documentation, Uses, and more |
| seqkit | mcc | 1.0 | Seqkit is a rapid tool for manipulating fasta and fastq files. | Sequence Manipulation, Fasta, Fastq | Bioinformatics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| seqsero2 | lcc | 1.0 | Documentation, Uses, and more | ||||
| seqtk | mcc | 1.0 | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It is designed for handling large sequence data efficiently. | bioinformatics, sequence processing, FASTA, FASTQ, data manipulation | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| settarg | lcc | N/A | The settarg module works with Lmod to help developers manage their compiled software projects. It does so by making it easy to switch between optimized or debug builds; change compiler or other modules; and let the build system know about the changes. The secret of settarg is that it consolidates the state of a build into one environment variable called $TARG. \r Description Source: https://lmod.readthedocs.io/en/latest/310_settarg.html |
Compilers, Optimization, Performance Enhancement, Command-Line Tool | Command-Line Utility | Documentation, Uses, and more | |
| shapeit2 | mcc | 1.0 | shapeit2 is a software tool for phasing genotype data, which is essential for understanding the genetic architecture of traits and diseases. | Genetics, Bioinformatics, Phasing, Genotype | Bioinformatics, Genetics | Command-line tool | Documentation, Uses, and more |
| shapeit5 | mcc | 1.0 | SHAPEIT5 is a software package to estimate haplotypes in large genotype datasets (WGS and SNP array). | Genomics, Data Phasing, Haplotype Inference | Genetics, Biological Sciences | Phasing Tool | Documentation, Uses, and more |
| shared-mime-info | mcc | N/A | A database of shared MIME types used to identify file types based on their content and extensions. | MIME types, file identification, desktop environments, file extensions | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| shasta | lcc | N/A | shasta software. | Genome Assembly, Long-Read Sequencing, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| shtools | lcc | N/A | SHTOOLS is a software package for the analysis and synthesis of spherical harmonic functions, widely used in geophysics and geodesy. | spherical harmonics, geophysics, geodesy, data analysis | Geodesy, Geophysics | Library | Documentation, Uses, and more |
| sibeliaz | mcc | 1.0 | Sibelias is a software tool designed for the analysis of genomic sequences, particularly for detecting and visualizing genomic rearrangements and structural variations. | bioinformatics, genomics, structural variation, genomic analysis | Bioinformatics, Genomic Analysis | Analysis Tool | Documentation, Uses, and more |
| signalp | mcc, lcc | 1.0 | SignalP is a software tool for predicting the presence and location of signal peptide cleavage sites in amino acid sequences of proteins. | bioinformatics, protein prediction, signal peptides | Bioinformatics, Molecular Biology | Prediction Tool | Documentation, Uses, and more |
| sigprofilerextractor | lcc | 1.0 | SigProfilerExtractor is a software tool used for extracting mutational signatures from genomic data, particularly in the context of cancer genomics. | bioinformatics, cancer genomics, mutation analysis | Bioinformatics, Biochemistry and Molecular Biology | Command-line tool | Documentation, Uses, and more |
| singlem | mcc | 1.0 | SingleM is a tool for profiling shotgun metagenomes. | Microbial Genomics, Metagenomics, Genome Assembly, Variant Calling | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| singularity | lcc | N/A | Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments. Description Source: https://apptainer.org/ |
Containerization, Scientific Computing, Hpc, Research | High-Performance Computing, Computer & Information Sciences, Engineering & Technology | Platform | Documentation, Uses, and more |
| singularity-devel | lcc | N/A | Singularity is a container platform designed for high-performance computing (HPC) environments, allowing users to create and run containers that encapsulate applications and their dependencies. | Containerization, HPC, Virtualization, Bioinformatics, Computational Chemistry | Computer Science, Software Engineering | Containerization Tool | Documentation, Uses, and more |
| sionlib | mcc, lcc | N/A | Scalable I/O Library for Parallel Access to Task-Local Files | I/O Interface, Scientific Data, Hdf5 Files | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| slepc | lcc | N/A | A library for solving large scale sparse eigenvalue problems | Eigenvalue Problems, Sparse Matrices, Parallel Computing | Numerical Linear Algebra, Other Mathematics | Numerical Computing | Documentation, Uses, and more |
| slow5tools | mcc | 1.0 | slow5tools is a suite of tools for working with the slow5 file format, which is used for storing raw signal data from nanopore sequencing technologies. | bioinformatics, nanopore sequencing, data processing | Bioinformatics, Genomics | Command-line tools | Documentation, Uses, and more |
| slurm | mcc | N/A | Slurm is an open-source cluster resource management and job scheduling system that strives to be simple, scalable, portable, fault-tolerant, and interconnect agnostic. Slurm currently has been tested only under Linux. Description Source: https://github.com/SchedMD/slurm |
Workload Manager, Cluster Management, High-Performance Computing | Computer Science, Engineering & Technology | Workload Manager | Documentation, Uses, and more |
| slurm-monitoring | mcc | N/A | This module loads seff and reportseff to display SLURM usage stats. | Documentation, Uses, and more | |||
| snakemake | mcc | 1.0 | The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. Description Source: https://snakemake.readthedocs.io/en/stable/ |
Workflow Management, Reproducibility, Traceability, Bioinformatics, Computational Biology, Data Science | Bioinformatics, Other Computer & Information Sciences | Software | Documentation, Uses, and more |
| snap | lcc | 1.0 | Snap is a semi-HMM-based Nucleic Acid Parser -- gene prediction tool. | Network Analysis, Large Networks, Graph Algorithms | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| snappy | mcc, lcc | N/A | 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. Description Source: https://github.com/google/snappy |
Compression, Big Data, Data Processing | Computer & Information Sciences | Data Processing Tool | Documentation, Uses, and more |
| sniffles | mcc | 1.0 | Sniffles is a tool for detecting and genotyping structural variants from long-read sequencing data. | genomics, bioinformatics, structural variants, long-read sequencing | Bioinformatics, Biochemistry and Molecular Biology | Command-line tool | Documentation, Uses, and more |
| sniffles-2.5.3 | lcc | 1.0 | Sniffles is a tool for detecting structural variants in genomic data, specifically designed for analyzing long-read sequencing data. | Genomics, Bioinformatics, Structural Variants | Bioinformatics, Genomics | Command-line Tool | Documentation, Uses, and more |
| snippy | lcc | 1.0 | Snippy is a tool for rapid haploid variant calling and core genome alignment. | Haploid Variant Calling, Core Genome Alignments, Bacterial Isolates | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| snp-dists | lcc | 1.0 | Snp-dists is a tool to convert a FASTA alignment to SNP distance matrix. | Genomics, Bioinformatics, Sequence Analysis, Phylogenetics | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| snp-sites | lcc | 1.0 | Snp-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment. | Bioinformatics, Computational Biology, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| soapdenovo | lcc | 1.0 | SOAPdenovo is a software package for de novo genome assembly from short reads, particularly designed for high-throughput sequencing data. | genome assembly, bioinformatics, high-throughput sequencing | Bioinformatics, Genomics | Open-source | Documentation, Uses, and more |
| solote | mcc | 1.0 | Documentation, Uses, and more | ||||
| sortmerna | lcc | N/A | SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. | Bioinformatics, Hpc Tools, Computational Software | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| sourmash | mcc | 1.0 | Sourmash is a tool for quickly search, compare, and analyze genomic and metagenomic data sets. | Bioinformatics, Genomics, Nucleotide Signatures, Minhash Sketches | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spaceranger | mcc, lcc | 1.0 | Cell ranger tools . | Bioinformatics, Hpc Tools | Molecular Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spack | mcc, ecc, lcc | N/A | Build and installation framework | Package Management, Software Installation, Dependency Management, Hpc, Scientific Computing | High Performance Computing, Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| spades | mcc, lcc | 1.0 | SPAdes is a genome assembly software that is specifically designed for single-cell and multi-cell bacterial sequencing data. It uses a combination of de Bruijn graph algorithms and error correction methods to construct accurate genome sequences. | Genome Assembly, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| splicev | lcc | N/A | Documentation, Uses, and more | ||||
| splishsplash | lcc | 1.0 | SPlisHSPlasH is an open-source library for the physically-based simulation of fluids and solids. The simulation in this library is based on the Smoothed Particle Hydrodynamics (SPH) method which is a popular meshless Lagrangian approach to simulate complex fluid effects. The SPH formalism allows an efficient computation of a certain quantity of a fluid particle by considering only a finite set of neighboring particles. One of the most important research topics in the field of SPH methods is the simulation of incompressible fluids. SPlisHSPlasH implements current state-of-the-art pressure solvers (WCSPH, PCISPH, PBF, IISPH, DFSPH, PF) to simulate incompressibility. Moreover, the library provides different methods to simulate viscosity, surface tension, vorticity, elasticity, and drag forces. | Documentation, Uses, and more | |||
| sqanti3 | mcc, lcc | 1.0 | SQANTI3 is a tool designed for the comprehensive assessment of transcriptome assemblies, particularly focusing on the quality and completeness of assembled transcripts. | bioinformatics, transcriptomics, RNA-seq, genomics | Bioinformatics, Transcriptomics | Analysis Tool | Documentation, Uses, and more |
| sqlite | mcc, ecc, lcc | N/A | SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. Description Source: https://www.sqlite.org/ |
Relational Database, Sql, Database Management | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| squashfs | ecc | N/A | SquashFS is a compressed read-only filesystem with built-in compression providing space-efficient storage. It is commonly used in embedded systems, live CDs, and Linux distributions to compress filesystem images and reduce storage space requirements while maintaining efficient access to files. | Filesystem, Compression, Read-Only | Computer Science, Computer & Information Sciences | Filesystem | Documentation, Uses, and more |
| squashfuse | ecc | N/A | Documentation, Uses, and more | ||||
| squigualiser | mcc | 1.0 | Documentation, Uses, and more | ||||
| sra-tools | mcc, lcc | 1.0 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Description Source: https://github.com/ncbi/sra-tools |
Bioinformatics, Hpc Tools, Sequence Analysis, Data Processing, High-Throughput Sequencing | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| sratoolkit | mcc, lcc | N/A | sratoolkit software. | bioinformatics, genomics, data processing | Biology, Genomics | Command-line tool | Documentation, Uses, and more |
| sshfs | mcc, ecc | N/A | SSHFS (SSH File System) is a filesystem client based on SSH (Secure Shell) that allows you to mount remote directories over a secure connection. | File System, SSH, Remote Access, Linux | Applied Computer Science, Computer Science | File System Client | Documentation, Uses, and more |
| stacks | mcc, lcc | 1.0 | Stacks is a software pipeline for building loci from RAD-seq | Software, Computational Biology, Bioinformatics | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| star | mcc, lcc | 1.0 | STAR (Spliced Transcripts Alignment to a Reference) is a fast and highly accurate RNA sequencing read mapper. It aligns RNA-Seq reads to a reference genome or transcriptome, enabling comprehensive analysis of gene expression and alternative splicing. | Software, RNA-Seq, Read Aligner, Splice Junctions, Alternative Splicing | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| starfish | mcc | 1.0 | Documentation, Uses, and more | ||||
| stitch | mcc | 1.0 | Documentation, Uses, and more | ||||
| stringtie | mcc, lcc | 1.0 | Stringtie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | RNA-Seq, Transcript Assembly, Transcript Quantification | Biological Sciences | Transcriptomics Tool | Documentation, Uses, and more |
| structure | mcc, lcc | 1.0 | Structure is a software package for using multi-locus genotype data to investigate population structure. | Population Genetics, Population Structure, Genotype Analysis, Data Analysis | Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| structure_threader | mcc | 1.0 | Documentation, Uses, and more | ||||
| structures | lcc | N/A | Documentation, Uses, and more | ||||
| subread | lcc | N/A | Subread carries out high-performance read alignment, quantification and mutation discovery. It is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and DNA-seq reads. It uses a new mapping paradigm called seed-and-vote to achieve fast, accurate and scalable read mapping. Subread automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports INDEL detection and can map reads with both fixed and variable lengths. | Ngs, Bioinformatics, Sequencing, Alignment | Bioinformatics, Biological Sciences | Ngs Analysis | Documentation, Uses, and more |
| superlu | lcc | N/A | A general purpose library for the direct solution of linear equations | Linear Algebra, Sparse Matrix, Direct Solver, Computational Science | Applied Mathematics, Mathematics | Solver Library | Documentation, Uses, and more |
| superlu-dist | mcc | N/A | SuperLU is a set of routines for solving large, sparse, nonsymmetric systems of linear equations. The 'dist' version is designed for distributed memory systems. | linear algebra, sparse matrices, parallel computing, HPC | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| superlu_dist | lcc | N/A | A general purpose library for the direct solution of linear equations | Linear Solver, Sparse Systems, Parallel Computing | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| svim-asm | lcc | 1.0 | Documentation, Uses, and more | ||||
| sweepfinder2 | mcc | 1.0 | SweepFinder2 is a software tool designed to detect and analyze selective sweeps in genomic data, particularly in populations. It is an improvement over the original SweepFinder, providing enhanced performance and accuracy. | genomics, population genetics, bioinformatics, selective sweeps | Bioinformatics, Genomics | Analysis Tool | Documentation, Uses, and more |
| swig | mcc, lcc | N/A | SWIG (Simplified Wrapper and Interface Generator) is a software development tool for building scripting language interfaces to C and C++ programs. SWIG simplifies development by largely automating the task of scripting language integration--allowing developers and users to focus on more important problems. \r Description Source: https://www.swig.org/Doc4.2/SWIGDocumentation.html |
Software Development, Programming Tool, Scripting Languages, Interface Generator | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Interface Generator | Documentation, Uses, and more |
| syny | mcc | 1.0 | Documentation, Uses, and more | ||||
| syri | mcc | 1.0 | Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements. | Network Analysis, Visualization, Complex Networks | Computer & Information Sciences | Network Analysis Tool | Documentation, Uses, and more |
| sz | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| szip | lcc | N/A | Szip compression software, providing lossless compression of scientific data | Compression Tool, Scientific Data Sets, Hdf5 File Format | Computer Science | Utility | Documentation, Uses, and more |
| talon | mcc | 1.0 | Talon is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. | Long-Read RNA Sequencing, Transcript Isoform Analysis, Gene Expression Quantification | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| tama | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| tar | mcc, ecc, lcc | N/A | tar is a command-line utility used for archiving files and directories on Unix-based systems. It allows bundling multiple files and directories into a single archive file, often compressed using utilities like gzip or bzip2. tar is commonly used for backup, data transfer, and file compression tasks. | File Archiving, Compression, Terminal | Other, Computer & Information Sciences | File Management | Documentation, Uses, and more |
| tassel | lcc | 1.0 | canu software. | Bioinformatics, Genetic Analysis, Plant Biology | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| tau | mcc, lcc | N/A | Tuning and Analysis Utilities Profiling Package | Software, Compiler, Hpc Tools | High-Performance Computing, Physical Sciences | Commercial | Documentation, Uses, and more |
| tbb | mcc, ecc, lcc | N/A | The Intel Threading Building Blocks (TBB) is a C++ library for parallel programming that enables developers to create multi-threaded applications efficiently. It offers high-level constructs for parallelism, task-based programming, and workload distribution, simplifying the development of scalable and performance-oriented applications. | Multicore Programming, Parallel Computing, C++ Library, High Performance Computing | Software Engineering, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| tbb32 | mcc, lcc | N/A | Intel Threading Building Blocks (TBB) is a widely used C++ template library developed by Intel for parallel programming on multi-core processors. TBB provides higher-level abstractions for parallelism, making it easier to write code that can take advantage of multicore processors. | Parallel Programming, Multi-Core Processors, C++ Template Library, Intel | Computer & Information Sciences | Library | Documentation, Uses, and more |
| tcl | ecc | N/A | Tcl (Tool Command Language) is a powerful dynamic programming language suitable for a wide range of uses, including web and desktop applications, networking, administration, and testing. Description Source: https://www.tcl.tk/ |
Scripting Language, Dynamic Programming Language, Cross-Platform, Scripting | Software Engineering, Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tcsh | mcc, lcc | N/A | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. | Command-Line Interpreter, Shell Scripting, Unix-Like Operating Systems | Operating Systems, Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| telseq | lcc | N/A | telseq is a tool for analyzing and processing telomere sequence data, particularly in the context of genomic studies. | bioinformatics, genomics, telomere analysis | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| tess3r | mcc | 1.0 | Documentation, Uses, and more | ||||
| tetools | mcc, lcc | 1.0 | Documentation, Uses, and more | ||||
| texinfo | mcc, ecc, lcc | N/A | Texinfo is the official documentation format of the GNU project. It is used to create both online information and printed output from a single source. | Documentation, Markup Language, GNU, Open Source | Software Engineering, Other Computer and Information Sciences | Documentation Tool | Documentation, Uses, and more |
| texlive | mcc | N/A | Comprehensive TeX document production system | Typesetting, Document Preparation, LaTeX, Open Source | Computer and Information Sciences, Computer Science | Typesetting System | Documentation, Uses, and more |
| time | mcc, lcc | N/A | The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. | Time, Measurement, Events, Synchronization | Other | Measurement & Timekeeping | Documentation, Uses, and more |
| tk | mcc, lcc | 1.0 | Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. | Gui, Python, Toolkit, Desktop Applications | Software Engineering, Computer & Information Sciences, Computer Science, Systems & Development | Library | Documentation, Uses, and more |
| tmhmm | lcc | 1.0 | TMHMM is a software tool for predicting transmembrane helices in proteins based on their amino acid sequences. | bioinformatics, protein structure, transmembrane prediction | Bioinformatics, Protein Structure Prediction | Prediction Tool | Documentation, Uses, and more |
| tophat | lcc | 1.0 | TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. | RNA-Seq, Splice Junction Mapper, Genomics | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| totalview | lcc | N/A | TotalView is a scalable and interactive debugger for parallel and high-performance computing (HPC) applications. It provides advanced debugging features to help developers analyze and optimize the performance of parallel programs running on clusters or supercomputers. | Debugging, Performance Analysis, Hpc, Big Data, Machine Learning | Computer Science | Development & Optimization Tools | Documentation, Uses, and more |
| tpmcalculator | mcc, lcc | 1.0 | TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. | Bioinformatics, Computational Biology, RNA-Seq, Transcriptomics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| transdecoder | lcc | 1.0 | Transdecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | Bioinformatics, Computational Biology, Transcriptomics, Protein Prediction | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| transrate | lcc | 1.0 | Transrate is software for de-novo transcriptome assembly quality analysis. | Transcriptome Assembly, Quality Assessment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| transrate-tools | lcc | 1.0 | Documentation, Uses, and more | ||||
| travis | lcc | 1.0 | Documentation, Uses, and more | ||||
| trf | mcc | 1.0 | Documentation, Uses, and more | ||||
| trilinos | lcc | N/A | A collection of libraries of numerical algorithms | Scientific Computing, Numerical Analysis, Parallel Computing, Computational Physics | Biology, Engineering & Technology | Library | Documentation, Uses, and more |
| trim-galore | mcc, lcc | 1.0 | Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files. | Ngs Data Processing, Quality Control, Adapter Trimming | Bioinformatics, Biological Sciences | Data Processing Tool | Documentation, Uses, and more |
| trimmomatic | mcc, lcc | 1.0 | Trimmomatic is a widely-used tool in bioinformatics for the preprocessing and quality control of high-throughput sequencing data, such as those from next-generation sequencing platforms. It offers various functions to remove adapters, trim low-quality reads, and filter sequences based on user-defined parameters. | Ngs Data Processing, Quality Control, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| trinity | mcc, lcc | 1.0 | Trinity is a software tool used for de novo transcriptome assembly from RNA-Seq data. It is designed to reconstruct full-length transcripts and address the challenges of assembling transcriptomes without a reference genome, contributing to gene expression and functional analysis. | Bioinformatics, Computational Biology, Transcriptomics, RNA-Seq, De Novo Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trinityrnaseq | lcc | 1.0 | Trinity is a software package for de novo transcriptome assembly from RNA-Seq data. It is designed to reconstruct full-length transcripts from short reads, allowing for the analysis of gene expression and alternative splicing. | RNA-Seq, Transcriptome, Assembly, Bioinformatics | Bioinformatics, Biological Sciences | Assembly Tool | Documentation, Uses, and more |
| trinotate | lcc | N/A | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Bioinformatics, Computational Biology, Transcriptomics, Functional Annotation | Bioinformatics, Biological Sciences | Functional Annotation Tool | Documentation, Uses, and more |
| trnascan-se | lcc | 1.0 | tRNAscan-SE is a widely used software tool for the identification of transfer RNA (tRNA) genes in genomic sequences. It utilizes covariance models to predict tRNA structures and gene locations, providing valuable insights into tRNA biology and facilitating genomic annotation. | Bioinformatics, Genomics, Computational Biology, Sequence Analysis | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trtools | mcc | 1.0 | TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing. | Python Library, Data Transformation, Tabular Data, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| ttt | mcc | 1.0 | Documentation, Uses, and more | ||||
| ucsc-bedgraphtobigwig | mcc | 1.0 | A tool for converting BEDGraph files to BigWig format, which is used for efficient visualization of genomic data. | genomics, bioinformatics, data visualization | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| ucsc-fatotwobit | lcc | N/A | Documentation, Uses, and more | ||||
| ucsc_utils | mcc | 1.0 | Documentation, Uses, and more | ||||
| ucx | mcc, ecc, lcc | N/A | UCX is a communication library implementing high-performance messaging | Communication Library, High-Performance Computing, Distributed Computing | Computer Science | Communication Library | Documentation, Uses, and more |
| ukyaro427 | lcc | 1.0 | Documentation, Uses, and more | ||||
| ultra | mcc | 1.0 | Documentation, Uses, and more | ||||
| umf | ecc | N/A | Documentation, Uses, and more | ||||
| uncalled4 | mcc | 1.0 | Documentation, Uses, and more | ||||
| unzip | mcc, ecc | N/A | UnZip is a utility tool used for extracting and viewing files compressed in the ZIP format. It allows users to decompress ZIP archives, extract individual files, and preserve the directory structure of the compressed content. | File Extraction, Compression, Utility | Computer Science, Computer & Information Sciences | File Extraction | Documentation, Uses, and more |
| util-linux-uuid | mcc, ecc, lcc | N/A | util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique. | Uuid Generator, Command-Line Utility, Unique Identifier, Data Management | Computer Science, Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| util-macros | mcc, lcc | N/A | util-macros is a collection of utility macros for C programmers to aid in simplifying common tasks and improving code readability. These macros are designed to enhance the efficiency and maintainability of C code by providing useful functions and utilities. | Programming, Development, C Programming, Utility Macros | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| valgrind | mcc, lcc | N/A | Memory debugging utilities | Debugging, Profiling, Development Tool | Computer Science, Computer & Information Sciences | Programming Tool | Documentation, Uses, and more |
| vamb | mcc | 1.0 | VAMB (Variational Autoencoder for Metagenomic Bins) is a software tool designed for the binning of metagenomic contigs using variational autoencoders. It leverages deep learning techniques to improve the accuracy of binning in metagenomic studies. | bioinformatics, metagenomics, machine learning, deep learning, data analysis | Computational Biology, Bioinformatics | Open-source | Documentation, Uses, and more |
| variantbam | lcc | 1.0 | Documentation, Uses, and more | ||||
| vasp | mcc, lcc | N/A | vasp software. | Materials Modelling, Electronic Structure Calculations, Quantum-Mechanical Simulations, Dft Calculations, Molecular Dynamics | Chemistry, Physical Sciences, Engineering & Technology | Package | Documentation, Uses, and more |
| vaspkit | mcc, lcc | N/A | VASPKIT post-processing tool for VASP. | VASP, post-processing, visualization, density of states, band structure | Materials Science, Condensed Matter Physics | Post-processing tool | Documentation, Uses, and more |
| vcf2arlequindiploid | mcc | 1.0 | Documentation, Uses, and more | ||||
| vcflib | mcc, lcc | 1.0 | vcflib is a C++ library for parsing and manipulating Variant Call Format (VCF) files, which are commonly used in bioinformatics for storing gene sequence variations. | bioinformatics, genomics, VCF, C++ | Bioinformatics, Genomics | Library | Documentation, Uses, and more |
| vcftools | mcc, lcc | 1.0 | VCFtools is a versatile set of tools for working with Variant Call Format (VCF) files commonly used in genetics and genomics research. It allows researchers to perform various operations on genetic variation data, such as filtering, summarizing, and analyzing genetic variants in VCF format. | Genetic Variation Analysis, Variant Call Format (Vcf), Population Genetics, Bioinformatics | Bioinformatics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| vclust | mcc | 1.0 | Documentation, Uses, and more | ||||
| vcontact2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| vcontact3 | mcc | 1.0 | Documentation, Uses, and more | ||||
| velocyto | mcc, lcc | 1.0 | A package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. | bioinformatics,single-cell RNA-seq,RNA velocity,data analysis | Molecular Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| velvet | mcc, lcc | 1.0 | Velvet is a sequence assembler for very short reads. | Genomics, Bioinformatics, Sequencing, Assembly | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| verifybamid2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| verkko | mcc | 1.0 | Documentation, Uses, and more | ||||
| verkko-2.2.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| verkko-fillet | mcc | 1.0 | Documentation, Uses, and more | ||||
| vg | mcc | 1.0 | Variation graphs (vg) provides tools for working with genome variation graphs. | genomics, bioinformatics, variant analysis, graph theory | Bioinformatics, Genomics | Command Line Tool | Documentation, Uses, and more |
| vibrant | mcc | 1.0 | Documentation, Uses, and more | ||||
| viennarna | lcc | 1.0 | Viennarna is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. | RNA Secondary Structure, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Prediction & Analysis Tools | Documentation, Uses, and more |
| vina | mcc, lcc | 1.0 | Autodock VINA software. | molecular docking, bioinformatics, computational chemistry | Bioinformatics, Molecular Docking | Open-source | Documentation, Uses, and more |
| virsorter | mcc | 1.0 | VirSorter is a bioinformatics tool designed for the identification and annotation of viral sequences in metagenomic data. It employs a combination of sequence similarity and genomic features to detect viral sequences, making it a valuable resource for viromics studies. | bioinformatics, metagenomics, viral detection, sequence analysis | Genomics, Bioinformatics | Command-line tool | Documentation, Uses, and more |
| visit | lcc | N/A | Visit is an open-source, interactive parallel visualization and graphical analysis tool used for visualizing scientific data. It is particularly focused on large-scale simulations and post-processing of complex data sets, enabling researchers to analyze and present their data in a visually engaging manner. | Visualization, Data Analysis, Scientific Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Visualization Software | Documentation, Uses, and more |
| vmd | lcc | N/A | VMD https://www.ks.uiuc.edu/Research/vmd/ | Molecular Visualization, Molecular Dynamics, Structural Biology | Biophysics, Biochemistry & Molecular Biology, Biological Sciences | Molecular Visualization Tool | Documentation, Uses, and more |
| vpl | mcc, lcc | N/A | VPL (Virtual Programming Lab) is an online platform and learning environment for teaching and practicing programming concepts through interactive coding exercises and assignments. It provides a virtual environment where students can write, compile, and test code, allowing educators to create programming labs and assessments in various programming languages. | Visual Programming, Beginner-Friendly, Graphical Interface | Computer & Information Sciences | Language Programming | Documentation, Uses, and more |
| vscode-tunnel | lcc | N/A | Launch VSCode tunnel sessions on LCC via Singularity | Documentation, Uses, and more | |||
| vtune | mcc, ecc, lcc | N/A | VTune Profiler, also known as Intel VTune, is a performance profiling tool developed by Intel. It enables developers to optimize software performance on Intel architecture platforms by providing detailed insights into application behavior, identifying performance bottlenecks, and suggesting optimizations. | Performance Optimization, Profiling, Intel Architecture | Software Engineering, Computer & Information Sciences | Profiling Tool | Documentation, Uses, and more |
| wget | ecc | N/A | GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. | Download Manager, Command-Line Tool | Computer Science, Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| whatshap | lcc | N/A | Whatshap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. | Genomics, Bioinformatics, Variant Phasing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| winnowmap | mcc | 1.0 | Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. | Mapping, Alignment, Nanopore, Pacbio, Sequencing | Genetics, Biological Sciences | Sequence Alignment Tool | Documentation, Uses, and more |
| wrf | lcc | N/A | The Weather Research and Forecasting (WRF) Model represents a cutting-edge mesoscale system for numerical weather prediction, designed to serve both atmospheric research and practical forecasting needs. Description Source: https://www.mmm.ucar.edu/models/wrf |
Weather Forecasting, Numerical Modeling, Atmospheric Science | Meteorology, Earth & Environmental Sciences | Meteorological Modeling Software | Documentation, Uses, and more |
| wrf-python | lcc | 1.0 | A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model. | Meteorology, Data Analysis, Visualization, Python, Scientific Computing | Meteorology, Weather Forecasting | Library | Documentation, Uses, and more |
| xcb-proto | mcc, lcc | N/A | Documentation, Uses, and more | ||||
| xextproto | mcc, lcc | N/A | X11 Extension protocols and auxiliary headers | Linux, X11, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xf86vidmodeproto | mcc | N/A | Documentation, Uses, and more | ||||
| xineramaproto | mcc | N/A | Documentation, Uses, and more | ||||
| xkbcomp | mcc | N/A | xkbcomp is a utility for compiling XKB (X Keyboard Extension) descriptions into binary files that can be used by the X server. | X Window System, Keyboard Configuration, Linux, Unix | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| xkbdata | mcc | N/A | Documentation, Uses, and more | ||||
| xorg-macros | lcc | N/A | X.org macros utilities. | Build Tools, Autoconf Macros | Computer & Information Sciences | Library/Dependency | Documentation, Uses, and more |
| xproto | mcc, lcc | N/A | X protocol and ancillary headers | Software Development, Protocol Development, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xrandr | mcc, lcc | N/A | xrandr is a command-line tool for managing and configuring display settings in the X Window System. It allows users to set the size, orientation, and reflection of the outputs for the display. | Display Management, X Window System, Linux, Command Line Tool | Software Engineering, Other Computer and Information Sciences | Command Line Utility | Documentation, Uses, and more |
| xtea | mcc | 1.0 | Documentation, Uses, and more | ||||
| xtrans | mcc, lcc | N/A | xtrans is a general-purpose transducer-based approach for defining translations between various formats and data representations. It provides a flexible framework for specifying bidirectional transformations between different data structures. | Data Transformation, Format Conversion, Transducer-Based Tool | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| xxhash | mcc | N/A | xxHash is an extremely fast non-cryptographic hash algorithm, providing high-speed hashing for data integrity checks. | hashing, performance, data integrity | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| xz | mcc, ecc, lcc | N/A | xz: XZ utilities | Compression, Data Compression, Open-Source | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| yahs | mcc | 1.0 | YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. | Hi-C scaffolding, genome assembly, chromosome-scale assembly | Life Sciences, Bioinformatics | Documentation, Uses, and more | |
| yak | mcc | 1.0 | Documentation, Uses, and more | ||||
| ytorch | ecc | 1.0 | Documentation, Uses, and more | ||||
| z3 | mcc | N/A | Z3 is a high-performance theorem prover developed by Microsoft Research that is used for solving satisfiability modulo theories (SMT) problems. It provides capabilities for automated reasoning and constraint solving in various domains such as software verification, automated planning, and formal methods. | Theorem Prover, Satisfiability Modulo Theories (Smt) Solver, Software Verification, Hardware Verification, Security, Ai, Machine Learning | Artificial Intelligence, Computer & Information Sciences | Theorem Prover | Documentation, Uses, and more |
| zfp | mcc, lcc | N/A | zfp is a compressed numerical array library providing high-throughput, low-overhead fixed-rate, fixed-precision encoding and compression of 1D and 2D scientific data. | Numerical Array, Compression, Scientific Data | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| zip | mcc | N/A | Zip is a popular utility for compressing and archiving files and directories into a single zip file. It provides a convenient way to reduce file sizes, organize data for storage or transmission, and create compressed archives that can be easily shared and extracted. | Compression, File Packaging, Utility | Computer Science, Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| zlib | mcc, lcc | N/A | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. | Compression, Data Compression, File Compression, Deflate Algorithm | Software Engineering, Computer & Information Sciences | Data Compression | Documentation, Uses, and more |
| zlib-ng | ecc | N/A | zlib-ng is a fast, efficient, and portable data compression library that is a drop-in replacement for zlib. It is designed to be compatible with zlib while providing improved performance and additional features. | compression, data processing, library, performance | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| zsh | mcc | N/A | Z shell (zsh) version 5.9, built with ncurses from source. | Unix Shell, Customizable Shell, Command Line Interface | Software Engineering, Computer & Information Sciences | Command Line Interface | Documentation, Uses, and more |
| zstd | mcc, ecc, lcc | N/A | zstd (Zstandard) is a high-performance data compression library and command-line tool that offers fast compression and decompression speeds with the ability to achieve high compression ratios. It is designed to balance efficient compression and decompression with speed, making it suitable for various data processing and storage applications. | Compression, Data Compression, Algorithm | Computer Science, Computer & Information Sciences | Compression Algorithm | Documentation, Uses, and more |