Software List
From ACCRE Wiki
This page contains the list of software available through Lmod in the cluster. If the software you need is not present in the list and you think would be useful for multiple groups in the future, you can submit a software installation request.
| Name | Description | Versions Available |
|---|---|---|
| abaqus | Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. | 2020 |
| abinit | ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. | 10.2.3 10.0.3 |
| abseil | Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives. | 20230125.3 |
| abyss | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler | 2.3.7 |
| ACCREJupyterLab | This bundle includes a Python interpreter, the Scientific Python stack, Julia, R, and Jupyter kernel support for Julia, R, and Python. It is intended for use with the JupyterLab application on the ACCRE Visualization Portal. | 2024b 2025a |
| actc | ACTC converts independent triangles into triangle strips or fans. | 1.1 |
| admixture | 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. | 1.3.0 |
| adol-c | The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C. | 2.7.2 |
| adtree | AdTree: Accurate, Detailed, and Automatic Modelling of Laser-Scanned Trees | 1.1.2 |
| advisor | Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain | 2020.3 |
| afni | AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. | 24.1.03 |
| alevin-fry | alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. | 0.8.2 |
| amber | Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. | 24 |
| amber-pmemd | Amber-PMEMD is Amber’s high-performance MD engine, optimized for both CPU and GPU execution. Unlike earlier Amber versions, the amber-pmemd module no longer includes AmberTools. | 24.3 |
| ambertools | AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. | 23.5 25.0 |
| amos | The AMOS consortium is committed to the development of open-source whole genome assembly software | 3.1.0 |
| ampl-mp | An open-source library for mathematical programming. | 3.1.0 |
| amrfinderplus | This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. | 3.12.8 4.2.7 |
| andi | This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes. | 0.14 |
| angsd | Program for analysing NGS data. | 0.940 |
| annovar | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). | 20191024 |
| anserini | An open-source information retreival toolkit built on Lucene that aims to bridge the gap between academic information retrieval and the practice of building real-world search applications. Usage: Binaries located in Anserini's target/appassembler/bin are on path. Anserini's folders bin, collections, docs, indexes, logs, runs, src, target, tools, as well as the files pom.xml and README.md are available at $EBROOTANSERINI. Eg. Indexing command for help: IndexCollection -h | 0.9.4 |
| ansys | ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. | 2025R1.02 2024R2 2025R1 2024R2.04 |
| ansysedt | ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. | 2024R2.1 |
| ant | Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. | 1.9.15 1.10.14 1.10.8 |
| antlr | ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. | 2.7.7 |
| ants | ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. | 2.6.0 2.6.1 2.5.0 2.6.2 |
| aocl-blas | AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs. | 5.1 |
| aocl-blascore | AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs. | .5.1 |
| aocl-lapack | AOCL-LAPACK is AMD's optimized version of LAPACK targeted for AMD EPYC and Ryzen CPUs. | 5.1 |
| aocl-lapackcore | AOCL-LAPACK is AMD's optimized version of LAPACK targeted for AMD EPYC and Ryzen CPUs. | .5.1 |
| apptainer | Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. | 1.3.4 1.4.5 1.3.5 1.1.6 1.1.5 1.1.8 1.2.4 1.1.3 1.0 |
| apptainer-suid | Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. - Website: https://apptainer.org - CC-Wiki: Apptainer | 1.1 |
| aragorn | a program to detect tRNA genes and tmRNA genes in nucleotide sequences | 1.2.41 |
| arch | No description available | avx2 avx512 sse3 avx |
| arcs | Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. | 1.2.7 |
| armadillo | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. | 12.6.4 |
| arpack-ng | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | 3.9.1 |
| arrayfire | ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. | 3.10.0 3.9.0 |
| arrow | Apache Arrow is a cross-language development platform for in-memory data. | 21.0.0 22.0.0 16.1.0 15.0.1 18.1.0 14.0.1 14.0.0 19.0.1 17.0.0 |
| ascp | Aspera ASCP is a high speed file transfer software | 3.5.4 |
| aspect | ASPECT: Advanced Solver for Problems in Earth's ConvecTion. An extensible code written in C++ to support research in simulating convection in the Earth's mantle and elsewhere to provide the geosciences with a well-documented and extensible code base for their research needs and to create an open, inclusive, participatory community providing users and developers with a state-of-the-art, comprehensive software that performs well while being simple to extend. | 3.0.0 |
| aspera-cli | IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows. | 3.9.6 |
| assimp | Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. | 5.2.5 |
| atompaw | AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library. | 4.2.0.3 |
| augustus | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | 3.5.0 |
| autodock-gpu | OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | 1.6 |
| autodock-vina | AutoDock Vina is an open-source program for doing molecular docking. | 1.2.6 |
| autodock_vina | AutoDock Vina is an open-source program for doing molecular docking. | 1.1.2 |
| babel | Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications. | 2.17.0 |
| bacio | This library performs binary I/O for the NCEP models, processing unformatted byte-addressable data records, and transforming the little endian files and big endian files. This is part of the NCEPLIBS project. | 2.6.0 |
| bamtools | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. | 2.5.2 |
| bbmap | BBMap short read aligner, and other bioinformatic tools. | 38.86 39.06 |
| bcftools | Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants | 1.22 1.19 1.18 |
| bcl-convert | The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. | 4.2.4 4.2.7 |
| beagle | Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. | 5.4 5.4-240301 |
| beagle-lib | beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | 4.0.1 |
| beast | BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. | 2.7.7 |
| bedops | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. | 2.4.41 |
| bedtools | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. | 2.31.0 |
| beef | BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. | 0.1.1 |
| berkeleygw | The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). | 4.0 |
| bigdft | BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. | 1.9.5 |
| bioawk | 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. | 1.0 |
| bioperl | Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. | 1.7.7 1.7.8 |
| bismark | A tool to map bisulfite converted sequence reads and determine cytosine methylation states | 0.25.1 0.24.1 |
| blast | Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. | 2.2.26 |
| blast+ | Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. | 2.14.1 |
| blat | BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | 3.7 |
| blender | Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. | 4.0.2 4.2.8 3.6.0 |
| blis | BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | 2.0 0.9.0 1.0 |
| bliscore | BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. | .2.0 .0.9.0 .1.0 |
| blosc2 | Blosc, an extremely fast, multi-threaded, meta-compressor library | 2.21.1 2.10.5 |
| boost | Boost provides free peer-reviewed portable C++ source libraries. | 1.82.0 1.88.0 1.85.0 |
| boost-core | Boost provides free peer-reviewed portable C++ source libraries. | .1.87.0 .1.82.0 |
| boost-mpi | Boost provides free peer-reviewed portable C++ source libraries. | 1.82.0 |
| bowtie | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. | 1.3.1 |
| bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. | 2.5.2 2.5.4 |
| bracken | Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. | 3.0 |
| breseq | breseq is a computational pipeline for the analysis of short-read re-sequencing data | 0.38.2 |
| brunsli | Brunsli is a lossless JPEG repacking library. | 0.1 |
| btllib | Bioinformatics Technology Lab common code library | 1.6.2 |
| bufr | The NCEPLIBS-bufr library contains routines and utilites for working with the WMO BUFR format. It is part of the NCEPLIBS project. | 12.0.1 |
| bustools | bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. | 0.40.0 |
| bwa | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. | 0.7.17 0.7.18 |
| bwa-mem2 | The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. The original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license. | 2.2.1 |
| calibre | calibre is a powerful and easy to use e-book manager. Users say it’s outstanding and a must-have. It’ll allow you to do nearly everything and it takes things a step beyond normal e-book software. It’s also completely free and open source and great for both casual users and computer experts. | 8.6.0 |
| campari | CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. | 5.0 |
| cantera | Chemical kinetics, thermodynamics, and transport tool suite | 3.2.0 |
| canu | Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences | 2.3 |
| cap3 | CAP3 assembly program | 20151002 |
| capnproto | Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. | 1.0.2 |
| casacore | A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them. | 3.7.1 3.6.1 |
| casadi | CasADi is an open-source tool for nonlinear optimization and algorithmic differentiation. | 3.6.7 |
| catch2 | A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) | 2.11.0 |
| CCconfig | No description available | |
| ccsm | The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. | 4_0_a02 |
| cd-hit | CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. | 4.8.1 |
| cdo | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. | 2.2.2 |
| cellranger | Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. | 2.1.0 |
| centrifuge | [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers | 1.0.4.2 |
| cereal | cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. | 1.3.2 1.3.0 |
| ceres-solver | Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010. Ceres Solver can solve two kinds of problems: - Non-linear Least Squares problems with bounds constraints. - General unconstrained optimization problems. | 2.2.0 |
| cesm | The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. | 2.1.3 |
| cfitsio | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | 4.3.0 4.5.0 |
| cgal | The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. | 6.0.1 5.5.2 |
| cgns | The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. | 4.5.0 |
| chapel-multicore | Chapel is a programming language designed for productive parallel computing on large-scale systems. | 2.3.0 2.4.0 |
| chapel-ucx | Chapel is a programming language designed for productive parallel computing on large-scale systems. | 2.3.0 2.4.0 |
| chapel-ucx-cuda | Chapel is a programming language designed for productive parallel computing on large-scale systems. | 2.3.0 2.4.0 |
| charm-gems | This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations. | 1.3.3 |
| circos | 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. | 0.69-9 |
| cjson | Ultralightweight JSON parser in ANSI C | 1.7.18 |
| clang | C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. | 18.1.8 17.0.6 |
| clhep | The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. | 2.4.6.2 2.4.7.1 |
| cmake | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | 3.18.4 3.31.0 3.27.7 3.22.1 3.20.1 3.21.4 3.23.1 |
| cnvnator | a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads | 0.4.1 |
| code-server | Run VS Code on any machine anywhere and access it in the browser. | 4.101.2 4.92.2 3.5.0 3.12.0 |
| coinmp | CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects. | 1.8.4 |
| colmap | COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for reconstruction of ordered and unordered image collections. The software is licensed under the new BSD license. | 3.12.6 |
| comet-ms | Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool written primarily in C/C++. | 2025.03.0 |
| comsol | COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. | 6.4 |
| COMSOL | COMSOL Multiphysics - Simulation Tool for Electrical, Mechanical, Fluid Flow, and Chemical Applications | 6.1 6.0 5.6 |
| connectomeworkbench | Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. | 2.0.1 |
| coordgenlibs | Schrodinger-developed 2D Coordinate Generation | 1.4.2 |
| corset | Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. | 1.09 |
| cp2k | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. | 2023.1 2025.2 |
| cppzmq | cppzmq is a C++ binding for libzmq | 4.7.1 |
| crest | Conformer-Rotamer Ensemble Sampling Tool | 3.0.2 3.0.1 |
| cromwell | Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ | 58 |
| cst | CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. | 2024 |
| csvtk | Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts. | 0.23.0 |
| cuba | Cuba – a library for multidimensional numerical integration | 4.2.2 |
| cuda | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. | 12.9 12.6 11.8 12.2 |
| cudacompat | Using the CUDA Forward Compatibility package, system administrators can run applications built using a newer toolkit even when an older driver that does not satisfy the minimum required driver version is installed on the system. This forward compatibility allows the CUDA deployments in data centers and enterprises to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. | .13.0 .12.9 |
| cudacore | CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. | .12.2.2 .12.6.3 .11.2.2 .12.5.0 .11.1.1 .11.0.2 .12.9.1 .11.4.2 .11.8.0 .10.2.89 .11.7.0 .12.6.2 |
| cudnn | The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | 9.13.1.26 9.2.1.18 8.0.3 8.2.0 8.9.5.29 8.6.0.163 9.5.1.17 9.10.0.56 8.7.0.84 |
| cudss | The NVIDIA cuDSS: A high-performance CUDA Library for Direct Sparse Solvers. | 0.6.0.5 0.7.1.4 |
| cusparselt | NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix | 0.6.1.0 0.5.0.1 0.8.1.1 0.7.1.0 0.4.0.7 |
| custom-ctypes | This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names. | 1.2 1.4 1.1 |
| cutensor | cuTENSOR is a high-performance CUDA library for tensor primitives. | 1.5.0.3 1.7.0.1 2.4.1.4 2.0.0.7 2.3.1.0 2.0.1.2 |
| cvit | A genomic linkage feature visualization tools based on Perl. | 1.2.1 |
| dakota | The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. | 6.22.0 |
| dalton | The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html. | 2020.0 2020.1 |
| das_tool | DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. | 1.1.6 |
| db | Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. | 18.1.32 |
| dcm2niix | dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. | 1.0.20230411 |
| dealii | A C++ software library supporting the creation of finite element codes and an open community of users and developers. | 9.6.2 |
| deepvariant | 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. DeepVariant supports germline variant-calling in diploid organisms. | 1.8.0 |
| deepvariant-gpu | 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. DeepVariant supports germline variant-calling in diploid organisms. | 1.8.0 |
| delly | Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. | 0.8.5 1.1.8 |
| dftbplus | DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. | 24.1 |
| dftd4 | Generally Applicable Atomic-Charge Dependent London Dispersion Correction. | 3.7.0 3.6.0 |
| diamond | Accelerated BLAST compatible local sequence aligner | 2.1.11 2.1.8 |
| dl_poly4 | DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. | 5.1.0 |
| dnmtools | DNMTools is a set of tools for analyzing DNA methylation data from high-throughput sequencing experiments, especially whole genome bisulfite sequencing (WGBS), but also reduced representation bisulfite sequencing (RRBS). These tools focus on overcoming the computing challenges imposed by the scale of genome-wide DNA methylation data, which is usually the early parts of data analysis. | 1.4.4 |
| dorado | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | 0.3.0 1.3.0 0.5.3 0.4.1 0.7.2 0.2.1 0.6.1 0.9.5 0.7.0 0.2.2 0.8.0 1.0.2 0.4.3 0.8.3 |
| dotnet-core | .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. | 8.0.407 5.0.12 3.1.8 6.0.0 9.0.202 |
| ecbuild | A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems | 3.8.0 |
| eccodes | ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). | 2.31.0 |
| edirect | Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. | 20.9.20231210 |
| eigen | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | 3.3.7 3.4.0 |
| elpa | Eigenvalue SoLvers for Petaflop-Applications. | 2024.05.001 2023.05.001 |
| embree | Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. | 4.3.0 |
| energyplus | EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings. | 23.2.0 9.3.0 |
| epa-ng | Massively parallel phylogenetic placement of genetic sequences | 0.3.8 |
| esmf | The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. | 8.8.0 8.6.0 8.7.0 |
| etsf_io | A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. | 1.0.4 |
| everybeam | Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc. | 0.7.4 0.8.0 |
| expat | 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) | 2.2.9 2.2.10 |
| faiss | Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. | 1.8.0 1.7.4 1.12.0 |
| fasta | The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. | 36.3.8i |
| fastahack | Utilities for indexing and sequence extraction from FASTA files. | 1.0.0 |
| fastp | A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. | 1.0.1 0.24.0 0.23.4 |
| fastqc | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. | 0.12.1 0.11.9 0.12.0 |
| fastsimcoal2 | While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. | 2.7.0.9 2.6.0.3 |
| fcl | FCL is a library for performing three types of proximity queries on a pair of geometric models composed of triangles. | 0.7.0 |
| fds | Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. | 6.9.1 |
| febio | FEBio is a nonlinear finite element (FE) solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics. The software is open-source, and pre-compiled executables for Windows, OS-X and Linux platforms are available. | 4.7 |
| fermi-lite | Standalone C library for assembling Illumina short reads in small regions. | 20190320 |
| ferret | Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. Ferret 7.6.0 is the final available version of Classic Ferret. The developers recommend using PyFerret instead. | 7.6.0 |
| ffmpeg | A complete, cross-platform solution to record, convert and stream audio and video. | 7.1.1 |
| ffnvcodec | FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). | 13.0.19.0 |
| 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. | 3.3.10 |
| fftw-mpi | 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. | 3.3.10 |
| filevercmp | filevercmp function as in sort --version-sort. | 20191210 |
| filtlong | 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 | 0.2.0 0.2.1 |
| flatbuffers | FlatBuffers: Memory Efficient Serialization Library | 24.12.23 23.3.3 |
| flexiblas | FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. | 3.4.5 3.0.4 .3.4.4 .3.4.5 3.3.1 3.4.4 .3.3.1 |
| flexiblascore | FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. | .3.0.4 .3.4.4 .3.2.0 .3.4.5 .3.3.1 |
| flint | FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. | 3.0.0 |
| fmlrc2 | FMLRC v2, based on the same methodology used by the original FMLRC. In benchmarks, the results between FMLRC v1 and v2 are nearly identical, but tests have shown that v2 uses approximately 50% of the run and CPU time compared to v1. | 0.1.8 |
| fmm3d | Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine. | 1.0.4 |
| fmriprep | fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI). | 23.1.3 25.1.1 23.0.2 |
| fmt | fmt (formerly cppformat) is an open-source formatting library. | 5.3.0 7.0.3 6.2.1 |
| foss | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | .2020a .2024a .2022a .2023a |
| fosscuda | GNU Compiler Collection (GCC) based compiler toolchain, alongside Open MPI, FlexiBLAS, ScaLAPACK, FFTW, and Cuda | .2024a .2023.2.415.216 .2023.2.415.126 .2023a .2022a |
| fpc | Free Pascal is a mature, versatile, open source Pascal compiler. | 3.2.2 |
| fplll | fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name. | 5.4.5 |
| freebayes | 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. | 1.3.7 |
| freesurfer | FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. | 5.3.0 7.2.0 |
| freexl | FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. | 2.0.0 |
| fsl | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | 6.0.7.18 6.0.7.17 |
| fsom | A tiny C library for managing SOM (Self-Organizing Maps) neural networks. | 20151117 |
| g2clib | This library contains C decoder/encoder routines for GRIB edition 2. This is part of the NCEPLIBS project. | 1.8.0 |
| g2lib | Library contains GRIB2 encoder/decoder and search/indexing routines. | 3.4.8 |
| gappa | gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files. | 0.9.0 |
| gate | GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography | 9.3 9.4 |
| gatk | The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. | 4.6.1.0 4.2.5.0 4.4.0.0 4.1.8.1 4.2.2.0 4.2.4.0 4.1.8.0 |
| Gaussian | Gaussian provides state-of-the-art capabilities for electronic structure modeling. | 16.B.01 .16.B.01-SSE4.2 .16.B.01-AVX .16.B.01-AVX2 |
| gblocks | Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis | 0.91b |
| gcc | 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,...). | 12.3 11.3.0 10.2.0 13.3 10.3.0 8.4.0 14.3 9.3.0 |
| gcccore | 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,...). | .8.4.0 .14.3 .13.3 .11.3.0 .13.2.0 .12.3 .10.3.0 .10.2.0 .9.3.0 |
| gcccorecuda | GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit (Core level). | .2024a .2023.2.126 .2020.1.112 .2023.2.129 .2025b .2020a .2020.1.114 .2019.6.102 .2023a |
| gcccoreflexiblas | GNU Compiler Collection (GCC) based compiler toolchain, alongside FlexiBLAS, at Core level. | .2020a .2024a .2023a |
| gcccoremkl | GNU Compiler Collection (GCC) based compiler toolchain, alongside Intel MKL, at Core level. | .2020a |
| gcccuda | GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. | .2024a .2023.2.126 .2020.1.112 .2020a .2020.1.114 .2019.6.102 .2023a .2022a .2023.2.216 |
| gccflexiblas | GNU Compiler Collection (GCC) based compiler toolchain, alongside FlexiBLAS. | .2020a .2024a .2022a .2023a |
| gccflexiblascuda | GNU Compiler Collection (GCC) based compiler toolchain, alongside FlexiBLAS and CUDA. | .2024a .2023.2.126 .2020.1.114 .2023a .2022a |
| gcta | GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). | 1.94.1 |
| gd | GD.pm - Interface to Gd Graphics Library | 2.77 |
| gdal | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. | 3.7.2 3.9.1 |
| gdrcopy | A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. | 2.4.1 2.5 2.3.1 |
| geant4 | 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. | 11.3.0 11.1.2 11.2.1 |
| geant4-data | Datasets for Geant4. | 11.3.0 10.7.3 11.1.2 11.1.0 11.2.1 |
| gemma | GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. | 0.98.5 |
| genometools | A comprehensive software library for efficient processing of structured genome annotations. | 1.6.5 |
| gentoo | No description available | 2023 2020 |
| geos | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) | 3.12.0 |
| gfbf | GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. | .2024a .2022a .2023a |
| gfbfc | GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support), (serial) FFTW, and CUDA. | .2024a .2023.2.126 .2023a |
| gffcompare | GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. | 0.12.6 |
| gh | GitHub’s official command line tool | 2.52.0 |
| git-annex | git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. | 10.20221003 8.20200810 10.20231129 |
| git-lfs | Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com | 3.3.0 2.11.0 3.4.0 |
| glew | The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. | 2.2.0 |
| glfw | GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop | 3.4 3.3.8 |
| glimpse | GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies. Main features of the method: 1. Accurate imputed genotype calls. Our method takes advantage of reference panels to produce high quality genotype calls. 2. Accurate phasing. GLIMPSE outputs accurate phased haplotypes for the low-coverage sequenced dataset. 3. Low-coverage sequencing outperforms SNP arrays. Imputation using low-coverage sequencing data is competitive to SNP array imputation. Results for European and African-American populations are interactively available on the website. 4. A cost-effective paradigm. GLIMPSE realises whole genome imputation from the HRC reference panel for less than 1$. 5. An easy-to-use framework for diploid, haploid and mixed ploidy imputation. Our method is able to perform imputation of samples with different ploidy without the need to split the data. | 2.0.1 |
| glm | OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. | 0.9.9.8 |
| globalarrays | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | 5.8.2 |
| glost | This is GLOST, the Greedy Launcher Of Small Tasks. | 0.3.1 |
| gmap-gsnap | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program | 2024-08-20 2024-10-20 |
| gmkl | GNU Compiler Collection (GCC) based compiler toolchain, alongside Intel MKL. | .2020a |
| gmklc | GNU Compiler Collection (GCC) based compiler toolchain, alongside Intel MKL and CUDA | .2020a .2020.1.114 .2019.6.102 .2020.1.112 |
| gmsh | Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. | 4.13.1 4.12.2 |
| gmt | GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. | 6.5.0 |
| gnina | gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina. | 1.3.1 |
| gnuplot | Portable interactive, function plotting utility | 5.4.8 6.0.3 |
| go | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. | 1.18.3 1.21.3 1.22.1 1.14.1 |
| gofb | GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and FlexiBLAS | .2024a .2021a .2020a .2023a .2022a |
| gofbc | GNU Compiler Collection (GCC) based compiler toolchain, alongside Open MPI, FlexiBLAS and CUDA. | .2020.1.403.114 .2024a .2023.2.415.126 .2023a .2022a |
| gofbf | GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and FlexiBLAS | .2020a .2021a |
| gofbfc | GNU Compiler Collection (GCC) based compiler toolchain, alongside Open MPI, FlexiBLAS, ScaLAPACK, FFTW, and Cuda | .2020.1.403.114 .2022a |
| gomkl | GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL | .2020a .2020b |
| gomklc | GNU Compiler Collection (GCC) based compiler toolchain, Intel MKL & OpenMPI. and Cuda | .2020a |
| gompi | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | .2024a .2021a .2025b .2020a .2020b .2023a .2022a |
| gompic | GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. | .2020.1.403.114 .2024a .2020.1.403.112 .2020a .2023.2.415.126 .2019.6.102 .2023a .2019.6.403.102 .2022a |
| googlebenchmark | Google's library to benchmark code snippets, similar to unit tests. | 1.8.3 |
| googletest | Google's framework for writing C++ tests on a variety of platforms | 1.14.0 |
| grenedalf | Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments. | 0.6.3 |
| groff | Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. | 1.22.4 |
| gromacs | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. | 2024.1 2023.3 2023.5 2024.6 2025.4 2024.4 2016.6 |
| gromacs-ls | GROMACS-LS is a modified version of GROMACS that has been modified to enable the calculation of local stress fields from molecular dynamics simulations. This is a CPU only build. Note that GROMACS-LS does not support MPI, GPUs(CUDA) or Hardware accelleration (SIMD) and is therefore much slower than unmodified versions of GROMACS. CC-Wiki: GROMACS | 2016.3 |
| gromacs-plumed | GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS | 2020.7 2023.5 |
| gromacs-ramd | GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a GPU enabled build, containing both MPI and threadMPI binaries. CC-Wiki: GROMACS | 2024.1-RAMD-2.1 |
| gromacs-swaxs | Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS | 2021.7-0.5.1 |
| gsl | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. | 2.7 2.8 |
| gsl-lite | A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later | 0.41.0 0.40.0 |
| guile | Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. | 2.2.2 |
| gurobi | The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. | 12.0.3 13.0.0 |
| hapgen2 | 'HAPGEN2' simulates case control datasets at SNP markers. | 2.2.0 |
| haploview | Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. | 4.2 |
| harminv | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. | 1.4.2 1.4.1 |
| hdf | HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. | 4.2.16 |
| hdf5 | HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. | 1.14.2 1.14.5 1.14.6 |
| hdf5-mpi | HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. | 1.14.2 1.14.5 1.14.4 1.14.6 |
| hdfview | HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. | 2.14 |
| healpix | Hierarchical Equal Area isoLatitude Pixelation of a sphere. | 3.82 3.83 |
| hh-suite | HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. | 3.3.0 |
| highfive | HighFive is a modern header-only C++11 friendly interface for libhdf5. | 2.9.0 |
| hisat2 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). | 2.2.1 |
| hmmer | HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. | 3.4 |
| hoomd-blue | HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface. | 5.1.1 |
| hpl | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. | 2.3 |
| htslib | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix | 1.19 1.18 1.22.1 |
| hwloc | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. | 2.10.0 2.7.1 2.9.1 2.12.1 2.4.0 |
| hypre | Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. | 2.33.0 |
| iccifortcuda | Intel C, C++ & Fortran compilers with CUDA toolkit | .2020a .2020.1.114 .2020.1.112 |
| iccifortflexiblas | Intel C, C++ & Fortran compiler toolchain, alongside FlexiBLAS. | .2020a |
| iccifortflexiblascuda | Intel C, C++ & Fortran compiler toolchain, alongside FlexiBLAS and CUDA. | .2020.1.114 |
| idg | Image Domain Gridding (IDG) is a fast method for convolutional resampling (gridding/degridding) of radio astronomical data (visibilities). Direction dependent effects (DDEs) or A-tems can be applied in the gridding process. The algorithm is described in "Image Domain Gridding: a fast method for convolutional resampling of visibilities", Van der Tol (2018). The implementation is described in "Radio-astronomical imaging on graphics processors", Veenboer (2020). Please cite these papers in publications using IDG. | 1.2.0 |
| ifb | Intel C, C++ & Fortran compiler toolchain, alongside FlexiBLAS. | .2022a .2023a |
| ifbc | Intel C, C++ & Fortran compiler toolchain, alongside FlexiBLAS and CUDA. | .2023.2.126 .2022a .2023.2.118 .2023a |
| ifbf | Intel based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. | .2022a .2023a |
| ifbfc | Intel based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support), (serial) FFTW, and CUDA | .2023.2.126 .2023.2.118 .2023a |
| igblast | IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. | 1.17.0 1.18.0 |
| igraph | igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. | 0.10.7 0.10.13 0.10.16 |
| igv | This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. | 2.9.2 |
| iifb | Intel Compilers based compiler toolchain, alongside Intel MPI and FlexiBLAS. | .2023a |
| iimkl | Intel C/C++ and Fortran compilers, alongside Intel MKL. | .2020a .2021a |
| iimklc | Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL, CUDA & | .2020a |
| iimpi | Intel C/C++ and Fortran compilers, alongside Intel MPI. | .2020a .2022a .2021a .2023a |
| ijulia | Julia kernel for Jupyter | .1.24.0 |
| ijulia-kernel | IJulia kernelspec for Julia 1.10 | 1.10 |
| imb | The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes | 2021.3 |
| imkl | Intel oneAPI Math Kernel Library | 2024.1.0 2023.2.0 2020.1.217 2022.1.0 2021.2.0 2021.4.0 2025.2.0 2024.2.0 |
| impute2 | IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 | 2.3.2 |
| impute5 | IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1 | 1.1.5 |
| infernal | Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. | 1.1.5 |
| intel | Intel C, C++ & Fortran compilers (classic and oneAPI) | .2020a 2025.2.0 .2021a |
| intel-opencl | Intel's OpenCL CPU runtime | 2021.2.0 |
| intelcompilerscuda | Intel C, C++ & Fortran compilers with CUDA toolkit | .2023.2.126 .2022a .2023.2.118 .2023a |
| intelmpi | Intel MPI Library, compatible with MPICH ABI | 2021.9.0 |
| intelxed | The X86 Encoder Decoder (XED), is a software library (and associated headers) for encoding and decoding X86 (IA32 and Intel64) instructions. | 12.0.1 |
| interproscan | InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. | 5.55-88.0 5.56-89.0 5.52-86.0 5.64-96.0 5.63-95.0 5.53-87.0 5.73-104.0 5.50-84.0 |
| interproscan_data | This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. | 5.73-104.0 5.64-96.0 5.63-95.0 |
| intervaltree | An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. | 0.1 |
| iofb | Intel Compilers based compiler toolchain, alongside Open MPI and FlexiBLAS. | .2020a .2024a .2022a .2023a |
| iofbc | Intel Compilers based compiler toolchain, alongside Open MPI, FlexiBLAS and CUDA. | .2020.1.403.114 .2023a .2022a .2023.2.415.126 |
| iofbf | Intel Compilers based compiler toolchain, alongside Open MPI, FlexiBLAS, FFTW and ScaLAPACK. | .2020a .2024a .2022a .2023a |
| iofbfc | Intel Compilers based compiler toolchain, alongside Open MPI, FlexiBLAS, ScaLAPACK, FFTW, and CUDA. | .2023a .2022a .2023.2.415.126 |
| iomkl | Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). | .2020a .2021a |
| iomklc | Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL, CUDA & OpenMPI. | .2020a |
| iompi | Intel C/C++ and Fortran compilers, alongside Open MPI. | .2024a .2021a .2025b .2020a .2023a .2022a |
| iompic | Intel based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support. | .2020.1.403.114 .2020a .2023.2.415.126 .2023a .2022a |
| ipopt | IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. | 3.14.14 |
| ipp | Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. | 2020.1.217 |
| ipykernel | Bundle which contains ipykernel 2023b and its dependencies | 2026a 2023b 2025a 2024b 2024a |
| ipython-kernel | IPython kernelspec for Python 3.10 | 2.7 3.10 3.12 3.13 3.11 |
| iq-tree | Efficient phylogenomic software by maximum likelihood | 2.3.6 |
| ir-kernel | The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network. | 4.4 |
| ispc | Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. | 1.18.0 1.10.0 1.21.1 1.13.0 |
| itk | Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. | 5.3.0 5.4.0 |
| ivar | iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. | 1.4.2 |
| jags | JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation | 4.3.2 |
| jasper | 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. | 4.2.4 4.0.0 |
| java | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. | 13.0.2 17.0.6 1.8.0_292 11.0.2 21.0.1 17.0.2 14.0.2 11.0.22 11.0.16_8 |
| jbigkit | JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. | 2.1 |
| jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. | 2.3.1 |
| jemalloc | jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. | 5.3.0 |
| json-fortran | JSON-Fortran: A Modern Fortran JSON API | 8.3.0 |
| jsoncpp | 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. | 1.9.5 |
| judy | A C library that implements a dynamic array. | 1.0.5 |
| julia | Julia is a high-level, high-performance dynamic programming language for numerical computing | 1.9.3 1.11.3 1.10.0 1.10.10 |
| jupyterhub_node | Bundle to run jupyterhub | .6.8.2 .7.0.1 |
| jupyterlab-apps | jupyterlab-apps is a collection of modules that make applications available in JupyterLab | 1.0 |
| kahip | The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. | 3.16 3.14 |
| kaiju | Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments | 1.10.1 |
| kalign | Kalign is a fast multiple sequence alignment program for biological sequences. | 3.3.5 |
| kallisto | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | 0.51.1 |
| kent_tools | Kent utilities: collection of tools used by the UCSC genome browser. | 486 |
| kim-api | Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. | 2.4.1 2.3.0 |
| kma | KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | 1.4.14 1.3.0 |
| kraken2 | Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. | 2.1.6 2.1.3 |
| kyotocabinet | Kyoto Cabinet is a library of routines for managing a database. | 1.2.80 |
| lammps-omp | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. | 20240829 20230802 20250722 |
| last | LAST: find & align related regions of sequences | 1642 |
| ldc | The LLVM-based D Compiler | 1.30.0 0.17.6 |
| legacy_load | legacy_load (Run software from legacy CentOS 7 stack in containerized environment) | 1.0 |
| lerc | LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds). | 4.0.0 |
| libaec | Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. | 1.0.6 |
| libbeef | BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. | 0.1.2 |
| libccd | libccd is library for a collision detection between two convex shapes. libccd implements variation on Gilbert–Johnson–Keerthi algorithm plus Expand Polytope Algorithm (EPA) and also implements algorithm Minkowski Portal Refinement (MPR, a.k.a. XenoCollide) as described in Game Programming Gems 7. | 2.1 |
| libcerf | libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. | 2.4 |
| libctl | libctl is a free Guile-based library implementing flexible control files for scientific simulations. | 4.5.1 |
| libdap | A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. | 3.20.11 3.21.1 |
| libdivsufsort | libdivsufsort is a software library that implements a lightweight suffix array construction algorithm. | 2.0.1 |
| libfabric | Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. | 2.1.0 1.21.0 1.18.0 |
| libfdf | LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF). | 0.2.2 |
| libffi | 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. | 3.3 |
| libgdsii | libGDSII is a C++ library for working with GDSII binary data files, intended primarily for use with the computational electromagnetism codes scuff-em and meep but sufficiently general-purpose to allow other uses as well. | 0.21 |
| libgeotiff | Library for reading and writing coordinate system information from/to GeoTIFF files | 1.7.1 |
| libint | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. | 2.7.2 |
| libmbd | A general-purpose package for scalable quantum many-body dispersion calculations. | 0.12.8 |
| libmesh | The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. | 1.7.5 |
| libpsml | A library to handle pseudopotentials in PSML format | 1.1.12 |
| libraw | The LibRaw library provides a simple and unified interface for extracting out of RAW files generated by digital photo cameras the following: - RAW data (pixel values) - Metadata necessary for processing RAW (geometry, CFA / Bayer pattern, black level, white balance, etc.) - Embedded preview / thumbnail. | 0.21.2 |
| libreqda | LibreQDA is an open-source web-based document tagging tool for qualitative data analysis. Using this tool, you can upload a collection of documents, create a hierarchy of codes, and annotate portions of documents with codes and notes that you can recall and organize later. | 1.0.1 |
| librmn | rmnlib is a library of functions for numerical weather prediction used primarily by Environment and and Climate Change Canada. Its main components are Standard RPN files and the EZ interpolator. | 20.0.9 |
| librt-compat | No description available | centos7 |
| librttopo | The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. | 1.1.0 |
| libspatialindex | C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API | 1.9.3 |
| libspatialite | SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. | 5.1.0 |
| libvori | C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package. | 220621 |
| libxc | Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. | 7.0.0 6.2.2 |
| libxsmm | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). | 1.17 |
| libyaml | LibYAML is a YAML parser and emitter written in C. | 0.2.5 |
| links | LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer). | 2.0.1 |
| lldb | The debugger component of the LLVM project | 11.0.0 |
| llvm | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. | 16.0.6 8.0.1 9.0.1 20.1.8 18.1.8 14.0.3 21.1.5 |
| llvmcore | The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. | .21.1.5 |
| lmdb | LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. | 0.9.31 |
| lpsolve | Mixed Integer Linear Programming (MILP) solver | 5.5.2.11 |
| ls-prepost | LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. | 4.8.11 |
| lsd2 | Least-squares methods to estimate rates and dates from phylogenies | 2.4.1 |
| ltr_retriever | LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. | 3.0.4 |
| m4ri | M4RI is a library for fast arithmetic with dense matrices over F2. | 20251207 |
| m4rie | M4RIE is a library for fast arithmetic with dense matrices. | 20250128 |
| maeparser | maeparser is a parser for Schrodinger Maestro files. | 1.2.4 |
| mafft | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. | 7.526 |
| mafft-mpi | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. | 7.526 |
| magma | The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. | 2.9.0 2.8.0 2.7.2 |
| mariadb | MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. | 11.5.0 |
| mariadb-connector-c | MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. | 3.1.7 3.3.7 |
| mash | Fast genome and metagenome distance estimation using MinHash | 2.3 |
| Mathematica | Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. | 12.0.0 12.3.0 |
| matio | matio is an C library for reading and writing Matlab MAT files. | 1.5.26 |
| matlab | MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. | 2022b 2021b 2025b.1 2023b 2021a 2023a |
| maven | Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. | 3.9.10 3.9.6 3.6.3 |
| mcr | The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. | R2024b R2020b R2022b R2025a R2025b R2021b R2024a |
| mctc-lib | Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats. | 0.3.1 |
| mdi | The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods. | 1.4.30 |
| meep | Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications. | 1.29.0 |
| megahit | An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | 1.2.9 |
| meme | The MEME Suite allows you to: - discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, - search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, - compare a motif to all motifs in a database of motifs, - associate motifs with Gene Ontology terms via their putative target genes, - analyse motif enrichment using SpaMo or CentriMo. | 5.5.7 |
| mesa-astrophysics | MESA Modules for Experiments in Stellar Astrophysics | r24.03.1 |
| meta-farm | Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). | 1.0.2 1.0.3 |
| metabat | An efficient tool for accurately reconstructing single genomes from complex microbial communities | 2.12.1 2.18 2.17 |
| metaeuk | MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. | 7 |
| metageneannotator | MetaGeneAnnotator is a gene-finding program for prokaryote and phage. | 20080819 |
| metis | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. | 5.1.0 |
| metis-64idx | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. | 5.1.0 |
| mii | A smart search engine for module environments. | 1.1.1 1.1.2 |
| mila_dataset | Test dataset designed by MILA. This is intended to test the behaviour and performance of Machine Learning data loading pipelines. | .1.0 |
| minc-toolkit | Medical Imaging NetCDF Toolkit | 1.9.18.3 |
| minced | Mining CRISPRs in Environmental Datasets | 0.4.2 |
| miniasm | Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. | 0.3-20191007 |
| miniconda3 | Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. | 23.9.0-0 |
| minimap2 | Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. | 2.26 2.28 |
| minpath | MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. | 1.6 |
| mixcr | MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. | 4.7.0 4.1.2 |
| mlflow | MLflow is an open-source developer platform to build AI/LLM applications and models with confidence. Enhance your AI applications with end-to-end experiment tracking, observability, and evaluations, all in one integrated platform. | 3.8.1 |
| mlip | MLIP is a software for Machine Learning Interatomic Potentials. It has been developed at Skoltech (Moscow) by Alexander Shapeev, Evgeny Podryabinkin, Konstantin Gubaev, and Ivan Novikov | 2.1 |
| mmg | Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries. | 5.7.3 |
| mmseqs2 | MMseqs2: ultra fast and sensitive search and clustering suite | 17-b804f 15-6f452 |
| modflow | MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions. | 6.5.0 |
| mothur | Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. | 1.48.3 |
| mpas | The Model for Prediction Across Scales (MPAS) is a collaborative project for developing atmosphere, ocean and other earth-system simulation components for use in climate, regional climate and weather studies. | 8.3.1 |
| mpb | MPB is a software package to compute definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. It can compute optical dispersion relations and eigenstates for structures such as strip waveguides and optical fibers. MPB is well suited for the study of photonic crystals: periodic dielectric structures exhibiting a band gap in their optical modes, prohibiting propagation of light in that frequency range. | 1.11.1 |
| mpb-mpi | MPB is a software package to compute definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. It can compute optical dispersion relations and eigenstates for structures such as strip waveguides and optical fibers. MPB is well suited for the study of photonic crystals: periodic dielectric structures exhibiting a band gap in their optical modes, prohibiting propagation of light in that frequency range. | 1.11.1 |
| mpi4py | MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. | 4.0.0 3.1.6 4.0.3 3.1.4 4.1.0 |
| mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | 3.2.7 |
| mrtrix | MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. | 3.0.4 |
| mstore | Molecular structure store for testing | 0.3.0 0.2.0 |
| mujoco | MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment. | 3.1.6 3.3.0 3.0.1 |
| multicharge | Electronegativity equilibration model for atomic partial charges. | 0.3.0 0.2.0 |
| multichoose | generate multiset combinations (n multichoose k). | 1.0.3 |
| multiwfn | A multifunctional wavefunction analyzer. | 3.8 |
| mummer | MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. | 4.0.0rc1 |
| muparser | muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. | 2.3.4 |
| muparserx | A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more. | 4.0.12 |
| muscle | MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. | 5.1.0 |
| mustang | MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the Cα atoms in the set. | 3.2.4 |
| mysql | MySQL is one of the world's most widely used open-source relational database management system (RDBMS). | 8.3.0 |
| n2p2 | A neural network potential package: high-dimensional neural network potentials in computational physics and chemistry. | 2.2.0 |
| namd-multicore | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | 3.0.2 3.0.1 |
| namd-ucx | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | 3.0.2 3.0.1 |
| nanoflann | nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies | 1.3.2 1.7.1 |
| nccl | The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. | 2.7.8 2.11.4 2.8.4 |
| ncl | NCL is an interpreted language designed specifically for scientific data analysis and visualization. | 6.6.2 |
| nco | manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 | 5.1.7 |
| ncview | 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. | 2.1.8 |
| nektar++ | Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. | 5.7.0 |
| netcdf | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.9.3 4.9.2 |
| netcdf-c++4 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.3.1 |
| netcdf-c++4-mpi | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.3.1 |
| netcdf-fortran | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.6.1 |
| netcdf-fortran-mpi | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.6.1 |
| netcdf-mpi | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | 4.9.2 |
| nextflow | Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data | 22.10.6 22.04.3 23.04.3 23.10.0 25.04.6 21.10.3 21.04.3 24.04.4 25.10.2 22.10.8 20.10.0 24.10.2 |
| nextgenmap | NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. | 0.5.5 |
| nextstrain.cli | This is the source code repository for a program called nextstrain, the Nextstrain command-line interface (CLI). It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch. | 3.1.0 |
| ngstools | ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data. An application note illustrating its application has published (Fumagalli et al., 2014). | 1.0.1 |
| nibabel | NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. | 5.2.0 |
| ninja-phylogenetics | Nearly Infinite Neighbor Joining Application Compute correct neighbor-joining phylogenies for inputs of more than 10,000 sequences. This is a C++/SSE port of the original Java code described in: Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin. (LNCS webpage,preprint) The Java version of NINJA was the fastest available tool computing neighbor-joining phylogenies ( 10x faster than the fastest implemenation of the canonical neighbor-joining algorithm - QuickTree ) at the time of it's release. In addition to generating phylogenies, Ninja can be used to output pairwise distances using several common sequence distance measures, and cluster sequences using a nearest-neighbor approach. | 0.97-cluster_only |
| nixpkgs | No description available | 16.09 |
| nlohmann_json | JSON for Modern C++ | 3.10.2 |
| nlopt | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. | 2.10.0 2.7.1 2.9.1 |
| nodejs | Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. | 18.17.1 20.16.0 |
| nvhpccuda | NVHPC Compiler and CUDA toolkit | .2020a |
| nvompi | NVHPC Compiler including OpenMPI for MPI support. | .2024a .2023a |
| nwchem | NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. | 7.2.3 |
| occt | Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. | 7.7.1 7.8.1 |
| octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations. | 7.2.0 |
| octomap | The OctoMap library implements a 3D occupancy grid mapping approach, providing data structures and mapping algorithms in C++ particularly suited for robotics. | 1.10.0 |
| octopus | Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. | 16.2 |
| oldest-supported-numpy | Oldest supported version of numpy for each version of python on our stack | .2023b |
| ont-guppy | Guppy is a bioinformatics toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. For Research Use Only | 6.1.5 |
| opa-psm2 | Low-level user-space communications interface for the Intel(R) OPA family of products. | .11.2.206 .11.2.185 .12.0.1 |
| openbabel | 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. | 3.1.1 |
| openbabel-omp | 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. | 3.1.1 |
| openblas | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | 0.3.24 0.3.27 0.3.30 |
| openblascore | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | .0.3.27 .0.3.24 .0.3.30 |
| opencolorio | OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. | 2.3.0 |
| opencv | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. | 4.13.0 4.9.0 4.11.0 4.12.0 4.10.0 4.10.0-2 4.8.1 |
| openfoam | OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. | 12 v2406 v2306 11 v2412 v2312 13 |
| openfst | OpenFst is a library for constructing, combining, optimizing, and searching weighted finite-state transducers (FSTs). | 1.8.4 1.8.3 |
| openimagedenoise | Intel Open Image Denoise is an open source library of high-performance, high-quality denoising filters for images rendered with ray tracing. | 2.1.0 2.0.1 |
| openimageio | OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. | 2.4.14.0 |
| openmc | OpenMC is a community-developed Monte Carlo neutron and photon transport simulation code. It is capable of performing fixed source, k-eigenvalue, and subcritical multiplication calculations on models built using either a constructive solid geometry or CAD representation. OpenMC supports both continuous-energy and multigroup transport. The continuous-energy particle interaction data is based on a native HDF5 format that can be generated from ACE files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP programming model. | 0.15.0 |
| openmm | OpenMM is a toolkit for molecular simulation. | 8.0.0 8.1.1 8.2.0 |
| openmolcas | OpenMolcas is a quantum chemistry software package | 25.06 |
| openmpi | The Open MPI Project is an open source MPI-3 implementation. | 5.0.8 5.0.3 4.1.5 |
| openrefine | OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. | 3.9.3 3.4.1 |
| opensees | OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. | 3.7.1 |
| opensim | OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. | 4.5.1 |
| openslide | C library for reading virtual slide images | 4.0.0 |
| openvdb | OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. | 10.1.0 |
| openvkl | Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKL’s performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. | 1.3.2 |
| optix | OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. | 8.0.0 7.7.0 |
| orad | DRAGEN ORA Decompression software decompresses *.fastq.ora files that have been compressed using DRAGEN ORA Compression software with the default human reference and with the additional supported references. | 2.6.1 |
| orca | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. | 6.1.1 6.1.0 |
| orthomcl | OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. | 2.0.9 |
| oskar | The OSKAR package consists of a number of applications for the simulation of astronomical radio interferometers. OSKAR has been designed primarily to produce simulated data from telescopes that use aperture arrays, as envisaged for the SKA. | 2.11.1 |
| ospray | Intel OSPRay is an open source, scalable, and portable ray tracing engine for high-performance, high-fidelity visualization on Intel Architecture CPUs. | 2.12.0 |
| osu-micro-benchmarks | OSU Micro-Benchmarks | 7.2 7.1-1 7.4 |
| ovito | OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes. The program is freely available for all major platforms under an open source license. It has served in a growing number of computational simulation studies as a powerful tool to analyze, understand and illustrate simulation results. | 3.3.3 |
| p4est | The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scales to hundreds of thousands of processor cores. It is free software released under GNU General Public Licence version 2, or (at your option) any later version. | 2.8.6 |
| p7zip | p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. | 17.05 |
| paml | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | 4.10.7 |
| panther | Panther is the database part of InterProScan software. It contains only data. | 14.1 |
| parallelio | A high-level Parallel I/O Library for structured grid applications | 2.6.3 |
| parasail | parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. | 2.6.2 |
| paraview | ParaView is a scientific parallel visualizer. | 5.11.2 5.13.1 6.0.0 |
| pari-gp | PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. | 2.15.5 |
| parmetis | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. | 4.0.3 |
| pcl | The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. | 1.14.1 |
| pdal | PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications for translating and processing point cloud data. It is not limited to LiDAR data, although the focus and impetus for many of the tools in the library have their origins in LiDAR. | 2.7.1 |
| penncnv | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. | 1.0.5 |
| percolator | Semi-supervised learning for peptide identification from shotgun proteomics datasets | 3.8 |
| perl | Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. | 5.36.1 5.30.2 |
| perl-no-thread | Larry Wall's Practical Extraction and Report Language This version has no threading support. | .5.30.2 |
| petsc | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | 3.21.6 3.20.0 3.23.4 |
| petsc-64bits | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | 3.21.6 3.23.4 |
| petsc-complex | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | 3.20.0 |
| pflotran | PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. | 5.0.0 6.0.0 |
| pgplot | The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. | 5.2.2 |
| photospline | Detector response to a high-energy physics process is often estimated by Monte Carlo simulation. For purposes of data analysis, the results of this simulation are typically stored in large multi-dimensional histograms, which can quickly become unwieldy in terms of size or numerically problematic due to unfilled bins or interpolation artifacts. Photospline is a library that uses the penalized spline technique to efficiently compute, store, and evaluate B-spline representations of such tables. | 2.2.1 |
| phylip | PHYLIP is a free package of programs for inferring phylogenies. | 3.698 |
| phylobayes-mpi | A Bayesian software for phylogenetic reconstruction using mixture models | 1.9 |
| picard | A set of tools (in Java) for working with next generation sequencing data in the BAM format. | 3.1.0 2.23.3 2.26.3 |
| pilercr | PILERCR is public domain software for finding CRISPR repeats. It is part of the PILER family of repeat analysis tools. | 1.06 |
| pilon | Pilon is an automated genome assembly improvement and variant detection tool | 1.24 1.23 |
| plink | Whole-genome association analysis toolset | 2.00a5.8 2.0.0-a.6.32 2.00-20251019-avx2 2.00-10252019-avx2 1.9b_6.21-x86_64 2.00-20231024-avx2 |
| plumed | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. | 2.9.4 2.9.0 2.9.2 2.10.0 2.8.4 2.8.3 |
| pmix | Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. | 4.2.4 5.0.2 5.0.8 |
| pnetcdf | PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements). | 1.12.3 |
| podman | Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. | 4.1.1 4.5.0 4.9.5 5.7.1 |
| polymake | polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects. | 4.14 |
| poplddecay | PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files. | 3.43 |
| postgresql | PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. | 16.0 |
| pov-ray | The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. | 3.7.0.10 |
| pplacer | Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. | 1.1.alpha19 |
| primme | PRIMME, pronounced as prime, is a high-performance library for computing a few eigenvalues/eigenvectors, and singular values/vectors. PRIMME is especially optimized for large, difficult problems. Real symmetric and complex Hermitian problems, standard A x = \lambda x and generalized A x = \lambda B x, are supported. Besides, standard eigenvalue problems with a normal matrix are supported. It can find largest, smallest, or interior singular/eigenvalues, and can use preconditioning to accelerate convergence. | 3.2 |
| prinseq | A bioinformatics tool to PRe-process and show INformation of SEQuence data. | 0.20.4 |
| prodigal | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. | 2.6.3 |
| proj | Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates | 9.4.1 9.2.0 |
| protobuf | Google Protocol Buffers | 24.4 |
| prrte | PRRTE is the PMIx Reference RunTime Environment | 3.0.11 3.0.5 |
| psi4 | PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. | 1.9 1.9.1 |
| pullseq | Utility program for extracting sequences from a fasta/fastq file | 1.0.2 |
| pypy | PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). | 7.3.3 5.8.0 |
| pytest | pytest: simple powerful testing with Python | 8.2.2 8.4.1 7.4.0 |
| python | Python is a programming language that lets you work more quickly and integrate your systems more effectively. | 3.11.5 3.12.4 3.13.2 3.10.13 |
| python-build-bundle | Bundle which contains Python packages useful for building | 2025b 2023b 2024a 2025a |
| q6 | Q is a set of Molecular Dynamics (MD) tools tailored to the following specific kinds of free energy calculations: Free Energy Perturbation (FEP) Empirical Valence Bond (EVB) Linear Interaction Energies (LIE) Quantum Classical Path (QCP) | 6.0 |
| qca | Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. | 2.3.7 |
| qcint | libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. | 6.1.2 |
| qgis | QGIS is a user friendly Open Source Geographic Information System (GIS) | 3.28.12 |
| qhull | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. | 2020.2 |
| qiime2 | QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. | 2021.11 2023.5 2024.5 |
| qrupdate | qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. | 1.1.2 |
| qscintilla | QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control | 2.14.1 |
| qt | Qt is a comprehensive cross-platform C++ application framework. | 5.15.11 6.5.3 |
| qtkeychain | Platform-independent Qt API for storing passwords securely. | 0.14.1 |
| qualimap | Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. | 2.3 |
| quantumespresso | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). | 7.5 7.3.1 |
| quest | The Quantum Exact Simulation Toolkit (QuEST) is a high-performance simulator of quantum statevectors and density matrices. It hybridises multithreading, GPU acceleration and distribution to run lightning fast on laptops, desktops and supercomputers, parallelising over multiple cores, CPUs and GPUs. Behind the scenes, QuEST leverages OpenMP, MPI, CUDA, HIP, Thrust, cuQuantum and GPUDirect for cutting-edge performance on modern multi-GPU clusters, and compatibility with older NVIDIA and AMD GPUs. These deployments can be combined in any combination, or automatically decided at runtime, yet are abstracted behind a single, seamless interface, accessible by both C and C++ and all the major compilers. | 4.2.0 |
| qwt | The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. | 6.2.0 |
| r | R is a free software environment for statistical computing and graphics. | 4.4.0 4.3.1 4.5.0 |
| r-bundle-bioconductor | Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. | 3.18 3.21 3.20 |
| racon | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. | 1.5.0 |
| rapidjson | A fast JSON parser/generator for C++ with both SAX/DOM style API | 1.1.0 |
| raqm | Raqm is a small library that encapsulates the logic for complex text layout and provides a convenient API. | 0.10.1 |
| rarray | rarray is a C++ library for reference counted multidimensional arrays. It is a header-only implementation that uses templates, which allows most compilers to generate fast code. | 2.8.0 |
| raspa3 | RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. | 3.0.3 |
| raven | Raven is a de novo genome assembler for long uncorrected reads. | 1.8.3 |
| raxml-ng | 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. | 1.2.0 |
| rdkit | RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. | 2024.03.4 2025.09.1 2024.03.5 2024.09.6 2025.09.4 2023.09.3 2023.09.5 |
| recon | Patched version of RECON to be used with RepeatModeler. | 1.08 |
| reframe | ReFrame is a framework for writing regression tests for HPC systems. | 3.12.0 |
| regtools | RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. | 1.0.0 |
| repeatmasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | 4.2.1 |
| repeatmodeler | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | 2.0.7 |
| repeatscout | De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) | 1.0.7 |
| rkcommon | Intel RenderKit common library | 1.11.0 |
| rmats | MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. | 4.3.0 |
| rmblast | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. | 2.14.1 |
| root | The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. | 6.28.06 |
| rsem | RNA-Seq by Expectation-Maximization | 1.3.3 |
| rstudio-server | RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. | 4.3 4.5 4.4 |
| ruby | 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. | 3.2.2 |
| rust | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. | 1.76.0 1.73.0 1.85.0 1.70.0 1.91.0 1.65.0 1.47.0 1.53.0 1.59.0 |
| saga | System for automated geoscientific analyses | 9.11.0 |
| salmon | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. | 1.10.2 |
| salmonbeta | Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. | 0.6.0 |
| sambamba | Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. | 1.0.1 0.8.0 |
| samblaster | samblaster: a tool to mark duplicates and extract discordant and split reads from sam files | 0.1.26 |
| samtools | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | 1.20 1.18 1.22.1 |
| savvy | Interface to various variant calling formats. | 2.1.0 |
| sbt | sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. | 1.3.13 |
| scafacos | ScaFaCoS is a library of scalable fast coulomb solvers. | 1.0.4 |
| scalapack | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. | 2.2.0 |
| scipoptsuite | SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver. | 9.0.0 |
| scipy-stack | Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. | 2024b 2023b 2024a 2025a |
| scotch | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. | 7.0.3 |
| selscan | selscan -- a program to calculate EHH-based scans for positive selection in genomes selscan currently implements EHH, iHS, XP-EHH, nSL, and iHH12 and requires phased data. It should be run separately for each chromosome and population (or population pair for XP-EHH). selscan is 'dumb' with respect ancestral/derived coding and simply expects haplotype data to be coded 0/1. Unstandardized iHS scores are thus reported as ln(iHH1/iHH0) based on the coding you have provided. | 2.0.3 |
| seqan-library | SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data | 2.4.0 |
| seqkit | FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. | 2.3.1 0.13.2 0.15.0 2.5.1 |
| seqlib | C++ interface to HTSlib, BWA-MEM and Fermi. | 1.2.0 |
| seqtk | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. | 1.4 |
| shapeit | SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. | 2.r904 |
| shapeit5 | SHAPEIT5 estimates haplotypes in large datasets, with a special focus on rare variants. | 5.1.1 |
| shrinkwrap | A std::streambuf wrapper for compression formats. | 1.2.0 |
| siegfried | Siegfried is a signature-based file format identification tool, implementing: the National Archives UK's PRONOM file format signatures freedesktop.org's MIME-info file format signatures the Library of Congress's FDD file format signatures (beta). Wikidata (beta). | 1.11.2 |
| siesta | SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | 5.4.0 5.0 4.1.5 |
| signalp | SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | 4.1f |
| simnibs | SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation | 4.1.0 |
| simple-dftd3 | reimplementation of the DFT-D3 program | 1.0.0 0.7.0 |
| singular | Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. | 4.2.1 |
| singularity | Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Singularity is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. - Website: http://singularity.lbl.gov/ - CC-Wiki: Singularity | 3.8 3.7 |
| sleef | SIMD Library for Evaluating Elementary Functions, vectorized libm and DFT | 3.8 |
| slepc | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. | 3.20.1 3.21.2 |
| slepc-complex | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. | 3.20.1 |
| slicer | 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. | 4.11.20210226 |
| slim | SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. | 4.3 5.0 |
| slurm-completion | bash completion for Slurm client commands | 23.02.7 |
| smithwaterman | smith-waterman-gotoh alignment algorithm. | 20160702 |
| smrtlink-sequel2 | PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided | 13.1.0.221970 |
| smv | Smokeview is a visualization program that displays output of FDS and CFAST simulations. | 6.9.1 6.9.5 |
| snpeff | SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). | 5.2 5.0 |
| soci | SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. | 4.0.3 |
| soundtouch | SoundTouch is an open-source audio processing library for changing the Tempo, Pitch and Playback Rates of audio streams or audio files. The library additionally supports estimating stable beats-per-minute rates for audio tracks. | 2.3.3 |
| spades | Genome assembler for single-cell and isolates data sets | 4.0.0 3.15.4 4.2.0 |
| spark | Spark is Hadoop MapReduce done in memory | 3.3.0 3.5.6 3.0.0 |
| sparsehash | An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. | 2.0.4 |
| spdlog | Very fast, header-only/compiled, C++ logging library. | 1.11.0 |
| spectra | Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. | 1.0.1 0.9.0 |
| sra-toolkit | The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format | 3.0.9 |
| ssw | SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. | 1.1 1.2.5 |
| stacks | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | 2.67 2.66 |
| star | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. | 2.7.11b 2.7.11a |
| starccm | Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses double precision. | 19.06.009-R8 20.02.008-R8 18.06.007-R8 20.04.007-R8 18.04.009-R8 19.04.009-R8 20.06.010-R8 20.04.008-R8 |
| starccm-mixed | Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. | 20.06.010 18.04.009 19.04.009 20.04.007 20.04.008 20.02.008 19.06.009 18.06.007 |
| Stata | Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. | 16 |
| StdEnv | No description available | 2023 2018.3 2016.4 2020 |
| StdEnvACCRE | No description available | 2023 |
| stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts | 2.2.3 3.0.1 |
| subread | High performance read alignment, quantification and mutation discovery | 2.0.6 |
| suitesparse | SuiteSparse is a collection of libraries manipulate sparse matrices. | 5.13.0 7.6.0 |
| suitesparse-32idx | SuiteSparse is a collection of libraries to manipulate sparse matrices. | 7.6.0 |
| sundials | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers | 6.6.0 |
| superlu | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. | 7.0.1 |
| supernova | Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. | 2.1.1 |
| swat+ | The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed. | 60.5.1 |
| swi-prolog | SWI-Prolog offers a comprehensive free Prolog environment. | 9.0.3 |
| swig | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. | 4.1.1 4.2.1 4.0.1 |
| symengine | SymEngine is a standalone fast C++ symbolic manipulation library. | 0.13.0 0.11.1 0.14.0 0.11.2 |
| tabix | Generic indexer for TAB-delimited genome position files | 0.2.6 |
| tabixpp | C++ wrapper to tabix indexer | 1.1.2 |
| taudem | TauDEM (Terrain Analysis Using Digital Elevation Models) is a suite of Digital Elevation Model (DEM) tools for the extraction and analysis of hydrologic information from topography as represented by a DEM. | 5.3.8 |
| taxonkit | TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. | 0.6.2 |
| tbb | Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. | 2021.10.0 |
| tbl2asn | Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank | 25.8 |
| tblite | Light-weight tight-binding framework | 0.3.0 0.5.0 |
| tensorboard | TensorBoard provides the visualization and tooling needed for machine learning experimentation: Tracking and visualizing metrics such as loss and accuracy Visualizing the model graph (ops and layers) Viewing histograms of weights, biases, or other tensors as they change over time Projecting embeddings to a lower dimensional space Displaying images, text, and audio data Profiling TensorFlow programs | 2.20.0 |
| tensorrt | NVIDIA TensorRT is a platform for high-performance deep learning inference | 8.6.1.6 |
| thrift | The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. | 0.19.0 |
| tiledb | TileDB is a powerful engine for storing and accessing dense and sparse multi-dimensional arrays, which can help you model any complex data efficiently. It is an embeddable C++ library that works on Linux, macOS, and Windows. | 2.29.0 |
| tmhmm | TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. | 2.0c |
| tpp | The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. On Fir we can also provide TPP web interface (tpp_gui) per group upon user request | 7.3.0 |
| transrate | Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. | 1.0.3 |
| travis-analyzer | TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. | 220729 |
| trf | Tandem Repeats Finder: a program to analyze DNA sequences. | 4.09.1 |
| trilinos | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. | 15.1.1 |
| trimmomatic | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. | 0.39 |
| trinity | Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. | 2.15.2 |
| triqs | TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. | 3.3.1 |
| trnascan-se | tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. | 2.0.12 |
| twl-ninja | Nearly Infinite Neighbor Joining Application. | 1.00 |
| ucc | UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. | 1.4.4 1.3.0 1.2.0 |
| ucx | Unified Communication X An open-source production grade communication framework for data centric and high-performance applications | 1.14.1 1.16.0 1.19.0 |
| udunits | UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. | 2.2.28 2.2.26 |
| unixodbc | unixODBC provides a uniform interface between application and database driver | 2.3.9 |
| valgrind-mpi | Valgrind: Debugging and profiling tools | 3.21.0 |
| varscan | Variant calling and somatic mutation/CNV detection for next-generation sequencing data | 2.4.2 2.4.6 |
| vasp | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version VASPsol (https://github.com/henniggroup/VASPsol) and scripts and modules for calculating transition states and VTSTTools (http://theory.cm.utexas.edu/vtsttools/) has been implemented to the original version of vasp. This version of vasp also supports HDF5, Wannier90, and Libxc. | 5.4.4 6.4.2 |
| vaspkit | VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code. | 1.5.1 |
| vcflib | vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. | 1.0.9 |
| vcftools | The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. | 0.1.16 |
| visit | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. | 2.13.3 |
| voro++ | Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. | 0.4.6 |
| vscode | Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos. | 1.100 |
| vsearch | VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. | 2.29.4 |
| vtk | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. | 9.3.0 |
| vtk-mpi | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. | 9.3.1 |
| w3emc | This library contains Fortran decoder/encoder routines for GRIB edition 1. GRIdded Binary or General Regularly-distributed Information in Binary form (GRIB) is a World Meteorological Organization (WMO) standard for gridded data. This is part of the NCEPLIBS project. | 2.11.0 |
| wannier90 | The Maximally-Localised Generalised Wannier Functions calculates the counterpart of localized molecular orbitals for crystalline systems from the wavefuction. | 1.2 3.1.0 |
| wanniertools | WannierTools is an open source software that studies the physical properties of given tight-binding model. | 2.7.0 |
| wasp | The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. | 4.0.3 3.1.4 4.2.0 |
| wcslib | The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header. | 8.3 |
| wfa2 | The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. | 2.3.4 |
| wham | An implementation of WHAM: the Weighted Histogram Analysis Method | 2.1.0 |
| wps | WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. | 4.6.0 |
| wrf | The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. | 4.6.1 4.7.1 |
| wsclean | WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution. | 3.6 |
| wtdbg2 | Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. | 2.5 |
| wxwidgets | wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. | 3.2.9 |
| xalt | XALT 2 is a tool to allow a site to track user executables and library usage on a cluster. When installed it can tell a site what are the top executables by Node-Hours or by the number of users or the number of times it is run. XALT 2 also tracks library usage as well. XALT 2 can also track package use by R, MATLAB or Python. It tracks both MPI and non-MPI programs. | .2.10.15 |
| xbraid | XBraid is a parallel-in-time software package. It implements an optimal-scaling multigrid solver for the (non)linear systems that arise from the discretization of problems with evolutionary behavior. | 3.1.0 |
| xdrfile | library for reading and writing xtc, edr and trr files | 1.1.4 |
| xml-libxml | Perl binding for libxml2 | 2.0205 2.0208 |
| xmlf90 | A fast XML parser and generator in Fortran | 1.6.2 1.5.4 |
| xnnpack | High-efficiency floating-point neural network inference operators for mobile, server, and Web. | 20250930 |
| xtb | xtb - Extended tight-binding semi-empirical quantum mechanics | 6.7.1 6.6.1 |
| xtensor | xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. | 0.24.2 0.25.0 |
| yaml-cpp | yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec | 0.8.0 |
| yaxt | Yet Another eXchange Tool | 0.10.0 |
| zeo++ | Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. | 0.3 |
| zoltan | Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit | 3.901 |
