Modules avx512¶
| Module | Type | Versions | Description |
|---|---|---|---|
| 4ti2 | - | 1.6.9 | !!! note "Full Details" |
| A software package for algebraic, geometric and combinatorial problems on linear spaces |
[Homepage](https://4ti2.github.io/) |
| abaqus | phys | 2021, 2026 | Abaqus
Full Details
Finite Element Analysis (FEA) software for advanced engineering simulations involving stress analysis, conductive and convective heat transfer, mass diffusion, acoustics, piezoelectricity, electrochemistry independently, sequentially coupled, fully coupled using implicit and explicit robust solvers. This module contains the initial release Abaqus 2026 Golden with SIMULIA Abaqus, Isight, fe-safe, Tosca.
Homepage |
| abinit | chem | 9.2.2, 9.6.2, 10.0.3, 10.2.3, 10.4.7 | ABINIT
Full Details
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
Homepage |
| abricate | - | 1.0.0 | !!! note "Full Details" Mass screening of contigs for antimicrobial and virulence genes
[Homepage](https://github.com/tseemann/abricate) |
| abseil | - | 20230125.3 | !!! note "Full Details" Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
[Homepage](https://abseil.io/) |
| abyss | bio | 2.2.5, 2.3.7 | !!! note "Full Details" Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
[Homepage](https://www.bcgsc.ca/platform/bioinfo/software/abyss) |
| actc | - | 1.1 | !!! note "Full Details" ACTC converts independent triangles into triangle strips or fans.
[Homepage](https://sourceforge.net/projects/actc) |
| admixture | bio | 1.3.0 | !!! note "Full Details" ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
[Homepage](http://software.genetics.ucla.edu/admixture) |
| adol-c | - | 2.7.2 | !!! note "Full Details" 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.
[Homepage](https://projects.coin-or.org/ADOL-C) |
| adtree | - | 1.1.2 | !!! note "Full Details" AdTree: Accurate, Detailed, and Automatic Modelling of Laser-Scanned Trees
[Homepage](https://github.com/tudelft3d/AdTree) |
| advisor | tools | 2020.3 | !!! note "Full Details" Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain
[Homepage](https://software.intel.com/intel-advisor-xe) |
| afni | bio | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 24.1.03, 26.0.09 | !!! note "Full Details" AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
[Homepage](http://afni.nimh.nih.gov/) |
| alevin-fry | - | 0.8.2 | !!! note "Full Details" alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
[Homepage](https://github.com/COMBINE-lab/alevin-fry) |
| alm | - | 2.0.0_dev.2 | !!! note "Full Details" Spglib is a software for calculating harmonic and anharmonic interatomic force constants in solids and molecules
[Homepage](https://github.com/ttadano/ALM) |
| almosthere | - | 1.0.10 | !!! note "Full Details" Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program.
[Homepage](https://github.com/horta/almosthere) |
| alpscore | phys | 2.2.0 | !!! note "Full Details" The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT
[Homepage](https://github.com/ALPSCore/ALPSCore) |
| amber | chem | 18.14-18.17, 20.12-20.15, 20.9-20.15, 22.5-23.5 | !!! note "Full Details" Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
[Homepage](https://ambermd.org/) |
| amber-pmemd | - | 24.3 | !!! note "Full Details" 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.
[Homepage](https://ambermd.org/AmberTools.php) |
| ambertools | chem | 20, 21, 22, 23.5, 25.0 | !!! note "Full Details" AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
[Homepage](https://ambermd.org/AmberTools.php) |
| amos | - | 3.1.0 | !!! note "Full Details" The AMOS consortium is committed to the development of open-source whole genome assembly software
[Homepage](http://amos.sourceforge.net) |
| ampl-mp | - | 3.1.0 | !!! note "Full Details" An open-source library for mathematical programming.
[Homepage](https://github.com/ampl/mp) |
| amrfinderplus | - | 3.11.18, 3.11.26, 3.12.8, 4.2.7 | !!! note "Full Details" This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.
[Homepage](https://github.com/ncbi/amr) |
| amrplusplus | - | 2.0-20200114 | !!! note "Full Details" AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database.
[Homepage](https://megares.meglab.org/amrplusplus/latest/html/v2) |
| andi | - | 0.14 | !!! note "Full Details" 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.
[Homepage](https://github.com/evolbioinf/andi/) |
| angsd | bio | 0.933, 0.935, 0.936, 0.939, 0.940 | !!! note "Full Details" Program for analysing NGS data.
[Homepage](http://www.popgen.dk/angsd) |
| annovar | bio | 20191024 | !!! note "Full Details" ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
[Homepage](http://annovar.openbioinformatics.org/en/latest/) |
| anserini | - | 0.9.4 | !!! note "Full Details"
An open-source information retreival toolkit built on Lucene that aims to bridge the gap between academic information retrieval and the practice of building real-world search applications. Usage: Binaries located in Anserini's target/appassembler/bin are on path. Anserini's folders bin, collections, docs, indexes, logs, runs, src, target, tools, as well as the files pom.xml and README.md are available at $EBROOTANSERINI. Eg. Indexing command for help: IndexCollection -h
[Homepage](https://github.com/castorini/anserini) |
| ansys | phys | 2025R1.02, 2024R1.03, 2025R2.04, 2024R2.04, 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2, 2024R2, 2025R2 | Ansys
Full Details
ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
Homepage |
| ansysedt | - | 2024R2.1, 2021R2, 2023R2 | !!! note "Full Details" ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
[Homepage](http://www.ansys.com) |
| ant | tools | 1.9.15, 1.10.8, 1.10.14 | !!! note "Full Details" Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
[Homepage](https://ant.apache.org/) |
| antlr | - | 2.7.7 | !!! note "Full Details" ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.
[Homepage](https://www.antlr2.org/) |
| ants | vis | 2.3.2, 2.3.5, 2.4.4, 2.5.0, 2.6.0, 2.6.1, 2.6.2, 2.6.5 | !!! note "Full Details" ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
[Homepage](https://stnava.github.io/ANTs/) |
| any2fasta | - | 0.4.2 | !!! note "Full Details" Convert various sequence formats to FASTA
[Homepage](https://github.com/tseemann/any2fasta) |
| aocl-blas | - | 5.1 | !!! note "Full Details" AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs.
[Homepage](https://github.com/amd/blis) |
| aocl-lapack | - | 5.1 | !!! note "Full Details" AOCL-LAPACK is AMD's optimized version of LAPACK targeted for AMD EPYC and Ryzen CPUs.
[Homepage](https://github.com/amd/libflame) |
| apbs | chem | 1.3 | !!! note "Full Details" APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.
[Homepage](http://www.poissonboltzmann.org/apbs) |
| apptainer | - | 1.1.3, 1.1.5, 1.1.6, 1.1.8, 1.2.4, 1.3.4, 1.3.5, 1.4.5 | !!! note "Full Details" Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems.
[Homepage](https://apptainer.org) |
| aragorn | - | 1.2.38, 1.2.41 | !!! note "Full Details" a program to detect tRNA genes and tmRNA genes in nucleotide sequences
[Homepage](http://www.ansikte.se/ARAGORN/) |
| arcs | bio | 1.2.1, 1.2.5, 1.2.7 | !!! note "Full Details" Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.
[Homepage](https://github.com/bcgsc/arcs) |
| argtable | tools | 2.13 | !!! note "Full Details" Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
[Homepage](http://argtable.sourceforge.net/) |
| arioc | - | 1.43 | !!! note "Full Details" ACTC converts independent triangles into triangle strips or fans.
[Homepage](https://sourceforge.net/projects/actc) |
| arks | - | 1.0.4 | !!! note "Full Details" Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.
[Homepage](https://github.com/bcgsc/arcs) |
| armadillo | math | 9.900.2, 12.6.4 | !!! note "Full Details" Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
[Homepage](https://arma.sourceforge.net/) |
| arpack-ng | math | 3.7.0, 3.8.0, 3.9.0, 3.9.1 | !!! note "Full Details" ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
[Homepage](https://github.com/opencollab/arpack-ng) |
| arrayfire | - | 3.7.3, 3.8.2, 3.9.0, 3.10.0 | !!! note "Full Details" ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
[Homepage](https://arrayfire.com/) |
| arrow | tools | 0.16.0, 0.17.1, 2.0.0, 5.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0, 17.0.0, 18.1.0, 19.0.1, 21.0.0, 22.0.0, 23.0.1 | !!! note "Full Details" Apache Arrow is a cross-language development platform for in-memory data.
[Homepage](https://arrow.apache.org)
* Compatible modules:
* `python/3.14`
* `python/3.13`
* `python/3.12`
* `python/3.11`
* Extensions:
* `None` |
| ascp | tools | 3.5.4 | !!! note "Full Details" Aspera ASCP is a high speed file transfer software
[Homepage](http://downloads.asperasoft.com/) |
| aspect | - | 2.4.0, 3.0.0 | !!! note "Full Details" 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.
[Homepage](https://aspect.geodynamics.org/) |
| assimp | - | 5.0.0, 5.2.5 | !!! note "Full Details" 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.
[Homepage](https://github.com/assimp/assimp) |
| astrid | - | 2.2.1 | !!! note "Full Details" ASTRID-2 is a method for estimating species trees from gene trees.
[Homepage](https://github.com/pranjalv123/ASTRID) |
| atat | - | 3.36 | !!! note "Full Details" ATAT is a generic name that refers to a collection of alloy theory tools developped by Axel van de Walle, in collaboration with various research groups and with various sources of financial support.
[Homepage](https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/) |
| atom | chem | 4.2.7_2 | !!! note "Full Details" ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere.
[Homepage](https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html) |
| atomicrex | chem | 1.0.20181114 | !!! note "Full Details" atomicrex is a versatile tool for the construction of advanced atomistic models. It is written in C++ and Python. It was primarily developed to fit interatomic potential models. Thanks to its flexible generic structure its application range, however, is much larger. In a general sense, it allows one to develop models that describe a given property as a function of an atomic (or atom-like) configuration. The property in question can be scalar or vectorial in nature, and could represent e.g., total energies and forces, or eventually electronic eigen energies. It thus provides already the basic framework for constructing in the future for example tight binding models.
[Homepage](http://atomicrex.gitlab.io/atomicrex/) |
| atompaw | chem | 4.1.0.6, 4.2.0.3 | !!! note "Full Details" AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.
[Homepage](http://users.wfu.edu/natalie/papers/pwpaw/man.html) |
| augustus | bio | 3.3.3, 3.4.0, 3.5.0 | !!! note "Full Details" AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
[Homepage](https://bioinf.uni-greifswald.de/augustus/) |
| autodiff | - | 0.6.0, 0.6.12 | !!! note "Full Details" autodiff is a C++17 library that uses modern and advanced programming techniques to enable automatic computation of derivatives in an efficient, easy, and intuitive way.
[Homepage](https://github.com/autodiff/autodiff)
* Compatible modules:
* `python/3.8`
* `python/3.9`
* `python/3.10` |
| autodock-gpu | - | 1.5.3, 1.6 | !!! note "Full Details" 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.
[Homepage](https://github.com/ccsb-scripps/AutoDock-GPU) |
| autodock-vina | - | 1.2.6 | !!! note "Full Details" AutoDock Vina is an open-source program for doing molecular docking.
[Homepage](https://vina.scripps.edu/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* `python/3.13`
* Extensions:
* `vina-1.2.6` |
| autodock_vina | chem | 1.1.2 | !!! note "Full Details" AutoDock Vina is an open-source program for doing molecular docking.
[Homepage](http://vina.scripps.edu/index.html) |
| babel | - | 2.17.0 | !!! note "Full Details" Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications.
[Homepage](https://babel.pocoo.org/en/latest/) |
| bacio | - | 2.6.0 | !!! note "Full Details" This library performs binary I/O for the NCEP models, processing unformatted byte-addressable data records, and transforming the little endian files and big endian files. This is part of the NCEPLIBS project.
[Homepage](https://github.com/NOAA-EMC/NCEPLIBS-bacio/) |
| bamm | bio | 2.5.0 | !!! note "Full Details" BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution.
[Homepage](http://bamm-project.org/) |
| bamtools | bio | 2.5.1, 2.5.2 | !!! note "Full Details" BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
[Homepage](https://github.com/pezmaster31/bamtools) |
| bamutil | bio | 1.0.14 | !!! note "Full Details" BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
[Homepage](http://genome.sph.umich.edu/wiki/BamUtil) |
| barracuda | - | 0.7.107h | !!! note "Full Details" Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
[Homepage](https://sourceforge.net/projects/seqbarracuda/) |
| barrnap | - | 0.9 | !!! note "Full Details" Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new nhmmer tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.
[Homepage](https://github.com/tseemann/barrnap) |
| bayesass | bio | 3.0.4 | !!! note "Full Details" BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
[Homepage](http://www.rannala.org/?page_id=245) |
| bayesass3-snps | - | 1.1 | !!! note "Full Details" Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols. This is an enhancement of the code produced by the Rannala Research Group: Homepage Most changes will not be obvious to the average user. However, the most important changes will now allow the user to input large SNP datasets that previously would have caused BayesAss to crash with a "segmentation fault" error. The upper limit of 420 loci has been removed.
[Homepage](https://github.com/stevemussmann/BayesAss3-SNPs) |
| bayescan | bio | 2.1 | !!! note "Full Details" BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
[Homepage](http://cmpg.unibe.ch/software/BayeScan/) |
| baypass | bio | 2.1, 2.2 | !!! note "Full Details" The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).
[Homepage](http://www1.montpellier.inra.fr/CBGP/software/baypass/) |
| bazel | tools | 3.6.0 | !!! note "Full Details" Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
[Homepage](https://bazel.io/) |
| bbmap | bio | 37.78, 38.86, 39.06 | !!! note "Full Details" BBMap short read aligner, and other bioinformatic tools.
[Homepage](https://sourceforge.net/projects/bbmap/) |
| bcftools | bio | 1.9, 1.10.2, 1.11, 1.13, 1.16, 1.18, 1.19, 1.22 | !!! note "Full Details" Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
[Homepage](https://www.htslib.org/) |
| bcl-convert | - | 4.2.4, 4.2.7 | !!! note "Full Details" The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.
[Homepage](https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html) |
| bcl2fastq2 | bio | 2.20.0 | !!! note "Full Details" bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
[Homepage](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html) |
| beagle | - | 5.4-240301 | !!! note "Full Details" Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
[Homepage](https://faculty.washington.edu/browning/beagle/beagle.html) |
| beagle-lib | bio | 3.1.2, 4.0.0, 4.0.1 | !!! note "Full Details" beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
[Homepage](https://github.com/beagle-dev/beagle-lib) |
| beast | bio | 2.6.3, 2.7.5, 2.7.7 | !!! note "Full Details" 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.
[Homepage](http://beast2.org) |
| bedops | - | 2.4.39, 2.4.41 | !!! note "Full Details" BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
[Homepage](http://bedops.readthedocs.io/en/latest/index.html) |
| bedtools | bio | 2.29.2, 2.30.0, 2.31.0 | !!! note "Full Details" The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
[Homepage](https://github.com/arq5x/bedtools2) |
| beef | chem | 0.1.1 | !!! note "Full Details" BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
[Homepage](http://suncat.stanford.edu/facility/software/functional) |
| berkeleygw.) | phys | 2.1.0, 3.0.1, 4.0 | !!! note "Full Details" The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429).
[Homepage](http://www.berkeleygw.org) |
| bgcdist | - | 1.03 | !!! note "Full Details" bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data.
[Homepage](https://sites.google.com/site/bgcsoftware/) |
| bgen-lib | - | 1.1.7 | !!! note "Full Details"
This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. What's included? This repository contains the library itself, a set of example data files, and a number of example programs (e.g. bgen_to_vcf) that demonstrate the use of the library API. In addition, a number of utilities built using the library are also included in this repository: bgenix - a tool to index and efficiently retrieve subsets of a BGEN file. cat-bgen - a tool to efficiently concatenate BGEN files. edit-bgen - a tool to edit BGEN file metadata. An R package called rbgen is also constructed in the build directory. See the rbgen wiki page for more information on using this package.
[Homepage](https://enkre.net/cgi-bin/code/bgen) |
| bigdft | chem | 1.8.3, 1.9.5 | !!! note "Full Details" 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.
[Homepage](http://bigdft.org/Wiki/index.php?title=BigDFT_website)
* Compatible modules:
* `python/3.12`
* `python/3.11`
* `python/3.10` |
| bio-searchio-hmmer | - | 1.7.3 | !!! note "Full Details" Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org.
[Homepage](https://metacpan.org/pod/Bio::SearchIO::hmmer3) |
| bioawk | - | 1.0 | !!! note "Full Details" Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
[Homepage](https://github.com/lh3/bioawk) |
| biobloomtools | - | 2.3.2-20200731 | !!! note "Full Details" BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes. This tool is intended to be a pipeline component to replace costly alignment steps.
[Homepage](https://github.com/bcgsc/biobloom) |
| bioperl | bio | 1.7.7, 1.7.8 | !!! note "Full Details" Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
[Homepage](https://bioperl.org/)
* Extensions:
* `Bio::Procedural-1.7.4`
* `BioPerl-1.7.8`
* `XML::DOM::XPath-0.14`
* `XML::Writer-0.900` |
| biopp | - | 2.4.1 | !!! note "Full Details" Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.
[Homepage](https://github.com/BioPP/bpp-core) |
| bismark | - | 0.22.3, 0.24.1, 0.25.1 | !!! note "Full Details" A tool to map bisulfite converted sequence reads and determine cytosine methylation states
[Homepage](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) |
| bison | - | 3.7.1, 3.8.2 | !!! note "Full Details" Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
[Homepage](https://www.gnu.org/software/bison) |
| blacs | math | 1.1 | !!! note "Full Details" The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
[Homepage](http://www.netlib.org/blacs/) |
| blasr | bio | 5.3.3 | !!! note "Full Details" The PacBio long read aligner
[Homepage](https://github.com/PacificBiosciences/blasr) |
| blasr_libcpp | bio | 5.3.4 | !!! note "Full Details" Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences
[Homepage](https://github.com/PacificBiosciences/blasr_libcpp) |
| blast | bio | 2.2.26 | !!! note "Full Details" Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
[Homepage](http://blast.ncbi.nlm.nih.gov/) |
| blast+ | bio | 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.1, 2.15.0, 2.17.0 | BLAST
Full Details
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
Homepage |
| blat | bio | 3.5, 3.7 | !!! note "Full Details" BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
[Homepage](https://genome.ucsc.edu/goldenPath/help/blatSpec.html) |
| blender | vis | 2.92.0, 3.6.0, 4.0.2, 4.2.8 | !!! note "Full Details" Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
[Homepage](https://www.blender.org/) |
| blis | - | 0.8.1, 0.9.0, 1.0, 2.0 | !!! note "Full Details" BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
[Homepage](https://github.com/flame/blis/) |
| blitz++ | tools | 1.0.2 | !!! note "Full Details" Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
[Homepage](https://github.com/blitzpp/blitz) |
| blosc | - | 1.17.1, 1.21.3 | !!! note "Full Details" Blosc, an extremely fast, multi-threaded, meta-compressor library
[Homepage](https://www.blosc.org/) |
| blosc2 | - | 2.10.3, 2.10.5, 2.21.1 | !!! note "Full Details" Blosc, an extremely fast, multi-threaded, meta-compressor library
[Homepage](https://www.blosc.org/) |
| bmtagger | - | 3.101 | !!! note "Full Details" Best Match Tagger for removing human reads from metagenomics datasets
Homepage |
| bolt-lmm | bio | 2.3.4, 2.4 | !!! note "Full Details" The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. Like the GCTA software.
[Homepage](https://data.broadinstitute.org/alkesgroup/BOLT-LMM/) |
| boltztrap | phys | 1.2.5 | !!! note "Full Details" Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients.
[Homepage](http://www.icams.de/content/departments/cmat/boltztrap/) |
| boost | tools | 1.72.0, 1.76.0, 1.80.0, 1.82.0, 1.85.0, 1.88.0 | !!! note "Full Details" Boost provides free peer-reviewed portable C++ source libraries.
[Homepage](https://www.boost.org/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| boost-build | - | 1.80.0 | !!! note "Full Details" Boost provides free peer-reviewed portable C++ source libraries.
[Homepage](https://www.boost.org/) |
| boost-mpi | tools | 1.72.0, 1.80.0, 1.82.0 | !!! note "Full Details" Boost provides free peer-reviewed portable C++ source libraries.
[Homepage](https://www.boost.org/)
* Compatible modules:
* `python/3.10`
* `python/3.11` |
| bowtie | bio | 1.3.0 | !!! note "Full Details" Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
[Homepage](http://bowtie-bio.sourceforge.net/index.shtml) |
| bowtie2 | bio | 2.4.1, 2.4.2, 2.4.4, 2.5.1, 2.5.2, 2.5.4 | !!! note "Full Details" Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
[Homepage](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |
| bpp | - | 4.3.8, 4.6.1 | !!! note "Full Details" The aim of this project is to implement a versatile high-performance version of the BPP software. BPP implements four methods: * Estimation of the parameters of species divergence times and population sizes under the multi-species coalescent (MSC) model when the species phylogeny is given * Inference of the species tree when the assignments are given by the user * Species delimitation using a user-specified guide treed * Joint species delimitation and species tree estimation
[Homepage](https://github.com/bpp/bpp) |
| bracken | - | 2.6.0, 2.7, 3.0 | !!! note "Full Details" 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.
[Homepage](https://ccb.jhu.edu/software/bracken/) |
| breseq | - | 0.35.2, 0.36.1, 0.38.2 | !!! note "Full Details" breseq is a computational pipeline for the analysis of short-read re-sequencing data
[Homepage](https://barricklab.org/breseq) |
| brotli | - | 1.0.9 | !!! note "Full Details" Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
[Homepage](https://github.com/google/brotli) |
| brunsli | - | 0.1 | !!! note "Full Details" Brunsli is a lossless JPEG repacking library.
[Homepage](https://github.com/google/brunsli/) |
| btllib | - | 1.6.2 | !!! note "Full Details" Bioinformatics Technology Lab common code library
[Homepage](https://github.com/bcgsc/btllib) |
| bufr | - | 12.0.1 | !!! note "Full Details" The NCEPLIBS-bufr library contains routines and utilites for working with the WMO BUFR format. It is part of the NCEPLIBS project.
[Homepage](https://github.com/NOAA-EMC/NCEPLIBS-bufr/) |
| bufrlib | geo | 11.3.0.2 | !!! note "Full Details" NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself.
[Homepage](https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB) |
| bullet | - | 2.89, 3.24 | !!! note "Full Details" Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics.
[Homepage](http://bulletphysics.org/)
* Compatible modules:
* `python/3.8`
* `python/3.9`
* `python/3.10`
* Extensions:
* `pybullet-3.2.4` |
| bustools | - | 0.40.0 | !!! note "Full Details" bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
[Homepage](https://github.com/BUStools/bustools) |
| bwa | bio | 0.7.17, 0.7.18 | !!! note "Full Details" Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
[Homepage](http://bio-bwa.sourceforge.net/) |
| bwa-mem2 | - | 2.2.1 | !!! note "Full Details" The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. The original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license.
[Homepage](https://github.com/bwa-mem2/bwa-mem2) |
| bwidget | - | 1.9.14 | !!! note "Full Details" The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.
[Homepage](https://core.tcl-lang.org/bwidget/home) |
| cafe5 | - | 5.1.0 | !!! note "Full Details" Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
[Homepage](https://github.com/hahnlab/CAFE5) |
| calibre | - | 8.6.0 | !!! note "Full Details" 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.
[Homepage](https://calibre-ebook.com/about) |
| campari | - | 5.0 | !!! note "Full Details" 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.
[Homepage](http://campari.sourceforge.net/V5/index.html) |
| cantera | chem | 2.5.1, 2.6.0, 3.2.0 | !!! note "Full Details" Chemical kinetics, thermodynamics, and transport tool suite
[Homepage](https://github.com/Cantera/cantera)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| canu | bio | 2.0, 2.1.1, 2.2, 2.3 | !!! note "Full Details" 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
[Homepage](https://github.com/marbl/canu) |
| cap3 | bio | 20151002 | !!! note "Full Details" CAP3 assembly program
[Homepage](http://seq.cs.iastate.edu/) |
| capnproto | - | 0.7.0, 1.0.2 | !!! note "Full Details" Cap'n Proto is an insanely fast data interchange format and capability-based RPC system.
[Homepage](https://capnproto.org) |
| casacore | - | 3.6.1, 3.7.1 | !!! note "Full Details" 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.
[Homepage](https://github.com/casacore/casacore)
* Compatible modules:
* `python/3.13`
* `python/3.11`
* `python/3.12`
* Extensions:
* `python_casacore-3.7.1` |
| casadi | - | 3.6.3, 3.6.7 | !!! note "Full Details" CasADi is an open-source tool for nonlinear optimization and algorithmic differentiation.
[Homepage](https://github.com/casadi/casadi)
* Compatible modules:
* `python/3.10`
* `python/3.11` |
| casper | bio | 0.8.2 | !!! note "Full Details" CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.
[Homepage](http://best.snu.ac.kr/casper/) |
| catch2 | - | 2.11.0, 3.2.1 | !!! note "Full Details" A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)
[Homepage](https://github.com/catchorg/Catch2) |
| ccfits | vis | 2.5 | !!! note "Full Details" CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.
[Homepage](http://heasarc.gsfc.nasa.gov/fitsio/CCfits/) |
| ccsm | geo | 4_0_a02 | !!! note "Full Details" The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states.
[Homepage](http://www.cesm.ucar.edu/models/ccsm4.0/) |
| cd-hit | bio | 4.8.1 | !!! note "Full Details" CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
[Homepage](http://weizhongli-lab.org/cd-hit/) |
| cdbfasta | - | 0.99 | !!! note "Full Details" Fasta file indexing and retrival tool
[Homepage](https://sourceforge.net/projects/cdbfasta) |
| cdo | geo | 1.9.8, 1.9.10, 2.0.4, 2.0.5, 2.2.2 | !!! note "Full Details" CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
[Homepage](https://code.zmaw.de/projects/cdo) |
| cellranger | bio | 2.1.0 | !!! note "Full Details"
Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information.
[Homepage](https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) |
| cellsnp-lite | - | 1.2.2, 1.2.3 | !!! note "Full Details" Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each allele of given or detected SNPs.
[Homepage](https://cellsnp-lite.readthedocs.io/en/latest) |
| centrifuge | bio | 1.0.4-beta, 1.0.4, 1.0.4.2 | !!! note "Full Details" [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
[Homepage](https://github.com/infphilo/centrifuge) |
| cereal | - | 1.3.0, 1.3.2 | !!! note "Full Details" cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
[Homepage](https://uscilab.github.io/cereal/) |
| ceres-solver | - | 1.14.0, 2.2.0 | !!! note "Full Details" 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.
[Homepage](https://ceres-solver.googlesource.com/ceres-solver/) |
| cesm | geo | 2.1.3 | !!! note "Full Details" The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
[Homepage](http://www.cesm.ucar.edu/models/cesm2/) |
| cfitsio | vis | 3.41, 3.48, 3.49, 4.1.0, 4.3.0, 4.5.0 | !!! note "Full Details" CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
[Homepage](https://heasarc.gsfc.nasa.gov/fitsio/) |
| cfour | chem | 2.1 | !!! note "Full Details" Serial version of CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download
[Homepage](http://www.cfour.de/) |
| cfour-mpi | chem | 2.1 | !!! note "Full Details" CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download
[Homepage](http://www.cfour.de/) |
| cgal | math | 4.14.3, 5.2.4, 5.5.2, 6.0.1 | !!! note "Full Details" The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
[Homepage](https://www.cgal.org/) |
| cgns | phys | 3.4.1, 4.1.0, 4.1.2, 4.5.0 | !!! note "Full Details" The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.
[Homepage](https://cgns.github.io/) |
| chapel-multicore | - | 2.3.0, 2.4.0 | !!! note "Full Details" Chapel is a programming language designed for productive parallel computing on large-scale systems.
[Homepage](https://chapel-lang.org) |
| chapel-ofi | - | 1.31.0 | !!! note "Full Details" Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI.
[Homepage](https://chapel-lang.org) |
| chapel-ucx | - | 2.3.0, 2.4.0 | !!! note "Full Details" Chapel is a programming language designed for productive parallel computing on large-scale systems.
[Homepage](https://chapel-lang.org) |
| chapel-ucx-cuda | - | 2.3.0, 2.4.0 | !!! note "Full Details" Chapel is a programming language designed for productive parallel computing on large-scale systems.
[Homepage](https://chapel-lang.org) |
| charm-gems | - | 1.3.3 | !!! note "Full Details" This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations.
[Homepage](https://github.com/simnibs/charm-gems)
* Compatible modules:
* `python/3.11`
* `python/3.10`
* Extensions:
* `charm-gems-1.3.3` |
| chemps2 | chem | 1.8.9 | !!! note "Full Details" CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
[Homepage](https://github.com/SebWouters/CheMPS2) |
| chrom3d | - | 1.0.2 | !!! note "Full Details" Chrom3D is a computational framework for efficient reconstruction of 3D genome structures using chromosome contact data (Hi-C, TCC and 5C data) and optionally lamin ChIP-seq data.
[Homepage](https://github.com/Chrom3D/Chrom3D) |
| circos | vis | 0.69-9 | !!! note "Full Details" Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
[Homepage](http://www.circos.ca/) |
| cjson | - | 1.7.18 | !!! note "Full Details" Ultralightweight JSON parser in ANSI C
[Homepage](https://github.com/DaveGamble/cJSON) |
| clang | tools | 9.0.1, 11.0.0, 13.0.1, 17.0.6, 18.1.8 | !!! note "Full Details" C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
[Homepage](https://clang.llvm.org/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| clhep | math | 2.4.1.3, 2.4.4.0, 2.4.6.2, 2.4.7.1 | !!! note "Full Details" The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
[Homepage](https://proj-clhep.web.cern.ch/proj-clhep/) |
| clustal-omega | bio | 1.2.4 | !!! note "Full Details" Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
[Homepage](http://www.clustal.org/omega/) |
| cmake | tools | 3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7, 3.31.0 | !!! note "Full Details" CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
[Homepage](https://www.cmake.org) |
| cnvnator | bio | 0.4.1 | !!! note "Full Details" a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
[Homepage](https://github.com/abyzovlab/CNVnator) |
| code-server | - | 3.5.0, 3.12.0, 4.92.2, 4.101.2 | !!! note "Full Details" Run VS Code on any machine anywhere and access it in the browser.
[Homepage](https://github.com/coder/code-server)
* Extensions:
* `anwar.resourcemonitor-1.0.10`
* `DavidAnson.vscode-markdownlint-0.60.0`
* `foxundermoon.shell-format-7.0.1`
* `GitHub.vscode-github-actions-0.27.2`
* `GitHub.vscode-pull-request-github-0.112.0`
* `gitlens-17.3.0`
* `hashicorp.terraform-2.34.5`
* `hediet.vscode-drawio-1.6.6`
* `IBM.output-colorizer-0.1.2`
* `jeff-hykin.better-cpp-syntax-1.27.1`
* `julialang.language-julia-1.146.2`
* `mechatroner.rainbow-csv-3.3.0`
* `monokai.theme-monokai-pro-vscode-2.0.7`
* `MS-CEINTL.vscode-language-pack-fr-1.101.0`
* `ms-python.black-formatter-2024.6.0`
* `ms-python.debugpy-2025.6.0`
* `ms-python.pylint-2024.2.0`
* `ms-python.python-2025.4.0`
* `ms-toolsai.jupyter-2025.5.0`
* `ms-toolsai.jupyter-keymap-1.1.2`
* `ms-toolsai.vscode-jupyter-cell-tags-0.1.9`
* `ms-vscode.cmake-tools-1.20.53`
* `ms-vscode.cpptools-themes-1.0.0`
* `ms-vscode.hexeditor-1.11.1`
* `ms-vscode.live-server-0.4.15`
* `ms-vscode.makefile-tools-0.12.17`
* `nsight-vscode-edition-2024.1.34572442`
* `oderwat.indent-rainbow-8.3.1`
* `onnovalkering.vscode-singularity-0.7.0`
* `puppet.puppet-vscode-1.5.5`
* `RDebugger.r-debugger-0.5.5`
* `redhat.ansible-25.4.0`
* `redhat.vscode-xml-0.29.2025051008`
* `redhat.vscode-yaml-1.18.0`
* `REditorSupport.r-2.8.6`
* `rust-lang.rust-analyzer-0.4.2512`
* `streetsidesoftware.code-spell-checker-4.2.0` |
| coinmp | - | 1.8.4 | !!! note "Full Details" CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects.
[Homepage](https://projects.coin-or.org/CoinMP) |
| colmap | - | 3.6, 3.12.6 | !!! note "Full Details" 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.
[Homepage](https://github.com/colmap/colmap) |
| combblas | - | 1.6.2 | !!! note "Full Details" The Combinatorial BLAS (CombBLAS) is an extensible distributed-memory parallel graph library offering a small but powerful set of linear algebra primitives specifically targeting graph analytics.
[Homepage](https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/) |
| comet-ms | - | 2025.03.0 | !!! note "Full Details" Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool written primarily in C/C++.
[Homepage](https://github.com/UWPR/Comet/) |
| comsol | phys | 5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2, 6.2.0.415, 6.3, 6.4 | !!! note "Full Details" COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.
[Homepage](https://www.comsol.com) |
| connectomeworkbench | - | 2.0.1 | !!! note "Full Details" 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.
[Homepage](https://www.humanconnectome.org/software/connectome-workbench) |
| coordgenlibs | chem | 1.4.2 | !!! note "Full Details" Schrodinger-developed 2D Coordinate Generation
[Homepage](https://github.com/schrodinger/coordgenlibs) |
| coretran | - | 1.0.1 | !!! note "Full Details" An easy to follow library to make Fortran easier in general with wrapped interfaces, sorting routines, kD-Trees, and other algorithms to handle scientific data and concepts. The library contains core fortran routines and object-oriented classes.
[Homepage](https://github.com/leonfoks/coretran#compile) |
| corset | bio | 1.09 | !!! note "Full Details" Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq.
[Homepage](https://github.com/Oshlack/Corset/wiki) |
| cp2k | chem | 7.1, 8.2, 9.1, 2023.1, 2025.2 | !!! note "Full Details" 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.
[Homepage](https://www.cp2k.org/) |
Full Details
The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Homepage |
| cppzmq | - | 4.7.1 | !!! note "Full Details" cppzmq is a C++ binding for libzmq
[Homepage](https://github.com/zeromq/cppzmq) |
| cpu_features | - | 0.6.0 | !!! note "Full Details" A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.
[Homepage](https://github.com/google/cpu_features) |
| cram | - | 0.7 | !!! note "Full Details" Cram is a functional testing framework for command line applications.
[Homepage](https://bitheap.org/cram)
* Compatible modules:
* `None` |
| crest | chem | 2.11, 2.12, 3.0.1, 3.0.2 | !!! note "Full Details" CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation ConformerRotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNnxTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.
[Homepage](https://xtb-docs.readthedocs.io/en/latest/crest.html) |
| cromwell | tools | 58 | !!! note "Full Details" Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/
[Homepage](https://cromwell.readthedocs.io/) |
| csblast | - | 2.2.4 | !!! note "Full Details" Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.
[Homepage](https://github.com/soedinglab/csblast/) |
| cslib | - | 20180813 | !!! note "Full Details" The client/server model is a messaging paradigm, used ubiquitously by web-based applications, where one or more clients (e.g. your phone) communicate with a server (e.g. a website). In the context of the CSlib, it can used to couple two scientific applications (apps) together where one app acts as the client and the other as the server. The client sends messages to the server requesting it perform specific computations and return the results.
[Homepage](https://cslib.sandia.gov/index.html) |
| cst | phys | 2020, 2024 | !!! note "Full Details" CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST.
[Homepage](https://www.cst.com/) |
| csvtk | - | 0.23.0 | !!! note "Full Details" Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts.
[Homepage](https://github.com/shenwei356/csvtk) |
| ctffind | chem | 4.1.14 | !!! note "Full Details" Program for finding CTFs of electron micrographs.
[Homepage](https://grigoriefflab.umassmed.edu/ctffind4) |
| cuba | - | 4.2.2 | !!! note "Full Details" Cuba a library for multidimensional numerical integration
[Homepage](https://feynarts.de/cuba/) |
| cubegui | - | 4.4.4 | !!! note "Full Details" Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.
[Homepage](https://www.scalasca.org/software/cube-4.x/download.html) |
| cubelib | - | 4.4.4 | !!! note "Full Details" Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.
[Homepage](https://www.scalasca.org/software/cube-4.x/download.html) |
| cubewriter | - | 4.4.3 | !!! note "Full Details" Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.
[Homepage](https://www.scalasca.org/software/cube-4.x/download.html) |
| cubic_interpolation | - | 0.1.5 | !!! note "Full Details" A leightweight interpolation library based on boost and eigen. It provides the utilities to handle tables which are runtime intensive to build and reduces interpolation failures to axis transformation.
[Homepage](https://github.com/tudo-astroparticlephysics/cubic_interpolation) |
| cuda | tools | 10.1, 10.2, 11.0, 11.1.1, 11.2.2, 11.4, 11.7, 11.8, 11.8.0, 12.2, 12.6, 12.9, 13.2 | CUDA
Full Details
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.
Homepage |
| cudnn | math | 8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29, 9.2.1.18, 9.5.1.17, 9.10.0.56, 9.13.1.26 | !!! note "Full Details" The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
[Homepage](https://developer.nvidia.com/cudnn) |
| cudss | - | 0.6.0.5, 0.7.1.4 | !!! note "Full Details" The NVIDIA cuDSS: A high-performance CUDA Library for Direct Sparse Solvers.
[Homepage](https://developer.nvidia.com/cudss) |
| cufflinks | bio | 2.2.1 | !!! note "Full Details" Transcript assembly, differential expression, and differential regulation for RNA-Seq
[Homepage](http://cole-trapnell-lab.github.io/cufflinks/) |
| cuquantum | - | 23.06.1.8, 24.03.0.4, 25.06.0.10 | !!! note "Full Details" NVIDIA cuQuantum SDK is a high-performance library for quantum information science and beyond
[Homepage](https://developer.nvidia.com/cuquantum-sdk)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* Extensions:
* `cuquantum-25.06.0` |
| cusparselt | - | 0.4.0.7, 0.5.0.1, 0.6.1.0, 0.7.1.0, 0.8.1.1 | !!! note "Full Details" NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix
[Homepage](https://docs.nvidia.com/cuda/cusparselt/index.html) |
| custom-ctypes | - | 1.1, 1.2, 1.4 | !!! note "Full Details" This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names.
[Homepage](https://github.com/ComputeCanada/custom_ctypes/) |
| cutensor | - | 1.5.0.3, 1.7.0.1, 2.0.0.7, 2.0.1.2, 2.3.1.0, 2.4.1.4 | !!! note "Full Details" cuTENSOR is a high-performance CUDA library for tensor primitives.
[Homepage](https://developer.nvidia.com/cutensor) |
| cvit | - | 1.2.1 | !!! note "Full Details" A genomic linkage feature visualization tools based on Perl.
[Homepage](https://sourceforge.net/projects/cvit/)
* Extensions:
* `Config::IniFiles-3.000002`
* `Data::Dumper-2.173`
* `ExtUtils::PkgConfig-1.16`
* `GD-2.71`
* `GD::Arrow-0.01`
* `GD::SVG-0.33`
* `GD::Text-0.86`
* `SVG-2.84`
* `Test::Fork-0.02` |
| dakota | tools | 6.13, 6.22.0 | !!! note "Full Details" The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.
[Homepage](https://dakota.sandia.gov/) |
| dalton | chem | 2020.0, 2020.1 | !!! note "Full Details" 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.
[Homepage](https://daltonprogram.org/) |
| das_tool | - | 1.1.6 | !!! note "Full Details" DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
[Homepage](https://github.com/cmks/DAS_Tool)
* Extensions:
* `data.table-1.14.8`
* `docopt-0.7.1`
* `magrittr-2.0.3` |
| db | - | 18.1.32 | !!! note "Full Details" Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
[Homepage](https://www.oracle.com/technetwork/products/berkeleydb) |
| db_file | - | 1.859 | !!! note "Full Details" Perl5 access to Berkeley DB version 1.x.
[Homepage](https://perldoc.perl.org/DB_File.html) |
| dcm2niix | bio | 1.0.20200331, 1.0.20230411 | !!! note "Full Details" dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
[Homepage](https://github.com/rordenlab/dcm2niix) |
| dcmtk | - | 3.6.7 | !!! note "Full Details" DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
[Homepage](https://dicom.offis.de/dcmtk) |
| ddt-cpu | tools | 20.2, 22.0.1, 23.1.1 | ARM software
| ddt-gpu | tools | 20.2, 22.0.1, 23.1.1 | ARM software
| dealii | math | 9.2.0, 9.3.1, 9.4.1, 9.6.2 | !!! note "Full Details" A C++ software library supporting the creation of finite element codes and an open community of users and developers.
[Homepage](http://www.dealii.org/) |
| deepvariant | - | 1.8.0 | !!! note "Full Details" 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.
[Homepage](https://github.com/google/deepvariant) |
| deepvariant-gpu | - | 1.8.0 | !!! note "Full Details" 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.
[Homepage](https://github.com/google/deepvariant) |
| delft3d | geo | 62441 | Delft3D
Full Details
Delft3D is a powerful modelling suite focusing primarily on coastal, estuarine, river, rural and urban environments Delft3D FM Suite can simulate storm surges, hurricanes, tsunamis, detailed flows and water levels, waves, sediment transport and morphology, water quality and ecology, and is capable of handling the interactions between these processes.
Homepage |
| delly | - | 0.8.5, 1.1.6, 1.1.8 | !!! note "Full Details" Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
[Homepage](https://github.com/dellytools/delly/) |
| detonate | bio | 1.11 | !!! note "Full Details" DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
[Homepage](http://deweylab.biostat.wisc.edu/detonate/) |
| dftbplus | chem | 21.1, 21.2, 24.1 | !!! note "Full Details" 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.
[Homepage](https://www.dftb-plus.info)
* Compatible modules:
* `python/3.11`
* `python/3.10`
* Extensions:
* `dptools-24.1` |
| dftd3-lib | chem | 0.10 | !!! note "Full Details" This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.
[Homepage](https://github.com/dftbplus/dftd3-lib) |
| dftd4 | chem | 3.3.0, 3.6.0, 3.7.0 | !!! note "Full Details" DFTD4 van-der-Waals functional is generally Applicable Atomic-Charge Dependent London Dispersion Correction.
[Homepage](https://github.com/dftd4/dftd4/) |
| diamond | bio | 0.9.36, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7, 2.1.8, 2.1.11, 2.1.22 | !!! note "Full Details" Accelerated BLAST compatible local sequence aligner
[Homepage](https://github.com/bbuchfink/diamond) |
| dirac | - | 21.1, 23.0 | !!! note "Full Details" DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
[Homepage](http://www.diracprogram.org) |
| dl_monte | - | 2.07 | !!! note "Full Details" General-purpose Monte Carlo molecular simulation
[Homepage](https://gitlab.com/dl_monte) |
| dl_poly4 | chem | 4.10.0, 5.1.0 | !!! note "Full Details" DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
[Homepage](http://www.scd.stfc.ac.uk/SCD/44516.aspx) |
| dmalloc | tools | 5.5.2 | !!! note "Full Details" The debug memory allocation or dmalloc library has been designed as a drop in replacement for the system s malloc, realloc, calloc, free and other memory management routines while providing powerful debugging facilities configurable at runtime. These facilities include such things as memory-leak tracking, fence-post write detection, file/line number reporting, and general logging of statistics. The library is reasonably portable having been run successfully on at least the following operating systems: AIX, BSD/OS, DG/UX, Free/Net/OpenBSD, GNU/Hurd, HPUX, Irix, Linux, MS-DOG, NeXT, OSF, SCO, Solaris, SunOS, Ultrix, Unixware, Windoze, and even Unicos on a Cray T3E. It also provides support for the debugging of threaded programs. The package includes the library, configuration scripts, debug utility application, test program, and documentation.
[Homepage](http://dmalloc.com/) |
| dnmtools | - | 1.4.4 | !!! note "Full Details" 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.
[Homepage](https://github.com/smithlabcode/dnmtools) |
| dorado | - | 0.2.1, 0.2.2, 0.3.0, 0.4.1, 0.4.3, 0.5.3, 0.6.1, 0.7.0, 0.7.2, 0.8.0, 0.8.3, 0.9.5, 1.0.2, 1.3.0, 1.4.0 | !!! note "Full Details" Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
[Homepage](https://github.com/nanoporetech/dorado) |
| dotnet-core | - | 3.1.8, 5.0.12, 6.0.0, 8.0.407, 9.0.202 | !!! note "Full Details" .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime.
[Homepage](https://www.microsoft.com/net/) |
| double-conversion | - | 3.1.5, 3.2.1 | !!! note "Full Details" Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
[Homepage](https://github.com/google/double-conversion) |
| dpc++ | - | 2022-06, 2022-12 | !!! note "Full Details" DPC++ is a LLVM-based compiler project that implements compiler and runtime support for the SYCL language.
[Homepage](https://github.com/intel/llvm) |
| dragmap | - | 1.3.0 | !!! note "Full Details" Dragmap is the Dragen mapper/aligner Open Source Software.
[Homepage](https://github.com/Illumina/DRAGMAP) |
| dssp | chem | 2.3.0, 3.1.4 | !!! note "Full Details" The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. If you use DSSP, please quote these two articles: 1) A series of PDB related databases for everyday needs. Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Research 2015 January; 43(Database issue): D364-D368. 2) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824.
[Homepage](https://swift.cmbi.umcn.nl/gv/dssp/) |
| ecbuild | - | 3.8.0 | !!! note "Full Details" A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems
[Homepage](https://ecbuild.readthedocs.io/) |
| eccodes | geo | 2.15.0, 2.19.0, 2.22.1, 2.25.0, 2.31.0 | !!! note "Full Details" ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
[Homepage](https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* Extensions:
* `cfgrib-0.9.10.4`
* `eccodes-1.6.1` |
| ecogen | - | 5.0 | !!! note "Full Details" A CFD open source code dedicated to multiphase compressible flows
[Homepage](https://code-mphi.github.io/ECOGEN/) |
| edirect | - | 20.9.20231210 | !!! note "Full Details" Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats.
[Homepage](https://www.ncbi.nlm.nih.gov/books/NBK25501/) |
| eigen | math | 3.3.7, 3.4.0 | !!! note "Full Details" Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
[Homepage](https://eigen.tuxfamily.org) |
| eigensoft | bio | 7.2.1 | !!! note "Full Details" The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
[Homepage](http://www.hsph.harvard.edu/alkes-price/software/) |
| elastix | - | 5.0.1 | !!! note "Full Details" elastix: a toolbox for rigid and nonrigid registration of images.
[Homepage](http://elastix.isi.uu.nl/) |
| elixir | tools | 1.13 | !!! note "Full Details" Elixir is a dynamic, functional language designed for building scalable and maintainable applications.
[Homepage](https://elixir-lang.org/) |
| elmerfem | - | scc20, 8.4, 9.0 | !!! note "Full Details" Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After it's open source publication in 2005, the use and development of Elmer has become international. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).
[Homepage](https://www.csc.fi/web/elmer) |
| elpa | math | 2020.05.001, 2023.05.001, 2024.05.001 | !!! note "Full Details" Eigenvalue SoLvers for Petaflop-Applications.
[Homepage](https://elpa.mpcdf.mpg.de/) |
| emboss | bio | 6.6.0 | !!! note "Full Details" EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
[Homepage](https://emboss.sourceforge.net/) |
| embree | - | 2.17.7, 3.11.0, 3.13.5, 4.3.0 | !!! note "Full Details" Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU.
[Homepage](https://github.com/embree/embree) |
| energyplus | - | 9.3.0, 23.2.0 | !!! note "Full Details" EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings.
[Homepage](https://energyplus.net/downloads) |
| epa-ng | - | 0.3.8 | !!! note "Full Details" Massively parallel phylogenetic placement of genetic sequences
[Homepage](https://github.com/pierrebarbera/epa-ng) |
| erlangotp | tools | 23.3, 24.2 | !!! note "Full Details" Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system.
[Homepage](http://www.erlang.org/) |
| esmf | geo | 8.0.1, 8.2.0, 8.4.0, 8.6.0, 8.7.0, 8.8.0 | !!! note "Full Details" The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.
[Homepage](https://www.earthsystemcog.org/projects/esmf/)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* Extensions:
* `esmpy-8.8.0` |
| espeak-ng | - | 1.51 | !!! note "Full Details" The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.
[Homepage](https://github.com/espeak-ng/espeak-ng) |
| etsf_io | io | 1.0.4 | !!! note "Full Details" A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
[Homepage](http://www.etsf.eu/resources/software/libraries_and_tools) |
| etsf_io-mpi | - | 1.0.4 | !!! note "Full Details" A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
[Homepage](http://www.etsf.eu/resources/software/libraries_and_tools) |
| everybeam | - | 0.7.4, 0.8.0 | !!! note "Full Details" Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.
[Homepage](https://everybeam.readthedocs.io/)
* Compatible modules:
* `python/3.11` |
| exonerate | bio | 2.4.0 | !!! note "Full Details" Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
[Homepage](https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate) |
| expat | tools | 2.2.9, 2.2.10, 2.4.1 | !!! note "Full Details" Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
[Homepage](https://libexpat.github.io) |
| faiss | - | 1.6.5, 1.7.1, 1.7.3, 1.7.4, 1.8.0, 1.12.0 | !!! note "Full Details" Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU.
[Homepage](https://github.com/facebookresearch/faiss)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| fann | - | 2.2.0 | !!! note "Full Details" Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.
[Homepage](http://leenissen.dk) |
| fasta | bio | 36.3.8h, 36.3.8i | !!! note "Full Details" 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.
[Homepage](http://fasta.bioch.virginia.edu) |
| fastahack | - | 1.0.0 | !!! note "Full Details" Utilities for indexing and sequence extraction from FASTA files.
[Homepage](https://github.com/ekg/fastahack) |
| fastani | - | 1.32 | !!! note "Full Details" FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
[Homepage](https://github.com/ParBLiSS/FastANI) |
| fastme | bio | 2.1.6.2 | !!! note "Full Details" FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.
[Homepage](http://www.atgc-montpellier.fr/fastme/) |
| fastp | bio | 0.20.1, 0.23.1, 0.23.4, 0.24.0, 1.0.1 | !!! note "Full Details" 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.
[Homepage](https://github.com/OpenGene/fastp) |
| fastq-join | - | 1.3.1 | !!! note "Full Details" fastq-join: Joins two paired-end reads on the overlapping ends.
[Homepage](https://github.com/brwnj/fastq-join) |
| fastq-multx | - | 1.4.0 | !!! note "Full Details" fastq-multx
[Homepage](https://github.com/brwnj/fastq-multx) |
| fastq-tools | - | 0.8 | !!! note "Full Details" This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.
[Homepage](https://homes.cs.washington.edu/~dcjones/fastq-tools/) |
| fastq_screen | bio | 0.11.4 | !!! note "Full Details" FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
[Homepage](http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) |
| fastqc | bio | 0.11.9, 0.12.0, 0.12.1 | !!! note "Full Details" FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
[Homepage](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) |
| fastsimcoal2 | bio | 2.6.0.3, 2.7.0.9 | !!! note "Full Details" While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.
[Homepage](http://cmpg.unibe.ch/software/fastsimcoal2/) |
| fastspar | - | 1.0.0 | !!! note "Full Details" FastSpar is a C++ implementation of the SparCC algorithm which is up to several thousand times faster than the original Python2 release and uses much less memory. The FastSpar implementation provides threading support and a p-value estimator which accounts for the possibility of repetitious data permutations (see this paper for further details).
[Homepage](https://github.com/scwatts/fastspar) |
| fasttree | bio | 2.1.11 | FastTree
Full Details
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
Homepage |
| fasttree-double | - | 2.1.11, 2.2.0 | FastTree
Full Details
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
Homepage |
| fastx-toolkit | bio | 0.0.14 | !!! note "Full Details" The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
[Homepage](http://hannonlab.cshl.edu/fastx_toolkit/) |
| fcl | - | 0.7.0 | !!! note "Full Details" FCL is a library for performing three types of proximity queries on a pair of geometric models composed of triangles.
[Homepage](https://github.com/flexible-collision-library/fcl)
* Compatible modules:
* `python/3.11`
* `python/3.10`
* `python/3.12`
* Extensions:
* `python-fcl-0.7.0.7` |
| fds | - | 6.7.5, 6.7.6, 6.7.7, 6.7.8, 6.7.9, 6.8.0 | !!! note "Full Details" 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.
[Homepage](https://pages.nist.gov/fds-smv/) |
| febio | - | 4.7 | !!! note "Full Details" 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.
[Homepage](https://github.com/febiosoftware/FEBio) |
| fermi-lite | - | 20190320 | !!! note "Full Details" Standalone C library for assembling Illumina short reads in small regions.
[Homepage](https://github.com/lh3/fermi-lite) |
| ferret | vis | 7.3, 7.6.0 | !!! note "Full Details" Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. Ferret 7.6.0 is the final available version of Classic Ferret. The developers recommend using PyFerret instead.
[Homepage](http://ferret.pmel.noaa.gov/) |
| ffmpeg | - | 4.2.2, 4.3.2, 7.1.1 | !!! note "Full Details" A complete, cross-platform solution to record, convert and stream audio and video.
[Homepage](https://www.ffmpeg.org/) |
| ffnvcodec | - | 13.0.19.0 | !!! note "Full Details" FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).
[Homepage](https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git) |
| fftw | math | 3.3.8, 3.3.10 | !!! note "Full Details" FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
[Homepage](https://www.fftw.org) |
| fftw-mpi | math | 3.3.8, 3.3.9, 3.3.10 | !!! note "Full Details" FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
[Homepage](https://www.fftw.org) |
| filevercmp | - | 20191210 | !!! note "Full Details" filevercmp function as in sort --version-sort.
[Homepage](https://github.com/ekg/filevercmp) |
| filtlong | bio | 0.2.0, 0.2.1 | !!! note "Full Details" Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter
[Homepage](https://github.com/rrwick/Filtlong) |
| flash | - | 1.2.11 | !!! note "Full Details" FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
[Homepage](https://ccb.jhu.edu/software/FLASH/) |
| flashpca | - | 2.0 | !!! note "Full Details" Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter
[Homepage](https://github.com/gabraham/flashpca/) |
| flatbuffers | - | 22.9.24, 23.3.3, 24.12.23 | !!! note "Full Details" FlatBuffers: Memory Efficient Serialization Library
[Homepage](https://github.com/google/flatbuffers/) |
| flexiblas | - | 3.0.4, 3.2.0, 3.3.1, 3.4.4, 3.4.5 | !!! note "Full Details" FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
[Homepage](https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release)
* Extensions:
* `LAPACK-3.12.1` |
| flint | math | 2.7.1, 2.9.0, 3.0.0 | !!! note "Full Details" FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.
[Homepage](http://www.flintlib.org/) |
| fmlrc2 | - | 0.1.8 | !!! note "Full Details" FMLRC v2, based on the same methodology used by the original FMLRC. In benchmarks, the results between FMLRC v1 and v2 are nearly identical, but tests have shown that v2 uses approximately 50% of the run and CPU time compared to v1.
[Homepage](https://github.com/HudsonAlpha/fmlrc2) |
| fmm3d | - | 1.0.1, 1.0.4 | !!! note "Full Details" Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.
[Homepage](https://fmm3d.readthedocs.io)
* Compatible modules:
* `python/3.11`
* `python/3.10` |
| fmriprep | - | 23.0.2, 23.1.3, 25.1.1 | !!! note "Full Details" fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI).
[Homepage](https://fmriprep.org/) |
| fmt | - | 5.3.0, 6.2.1, 7.0.3, 9.1.0 | !!! note "Full Details" fmt (formerly cppformat) is an open-source formatting library.
[Homepage](http://fmtlib.net/) |
| fpc | tools | 3.2.2 | !!! note "Full Details" Free Pascal is a mature, versatile, open source Pascal compiler.
[Homepage](https://www.freepascal.org) |
| fplll | - | 5.4.5 | !!! note "Full Details" fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.
[Homepage](https://github.com/fplll/fplll) |
| fraggenescan | bio | 1.30, 1.31 | !!! note "Full Details" FragGeneScan is an application for finding (fragmented) genes in short reads.
[Homepage](http://omics.informatics.indiana.edu/FragGeneScan/) |
| freebayes | bio | 1.2.0, 1.3.6, 1.3.7 | !!! note "Full Details" FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
[Homepage](https://github.com/freebayes/freebayes) |
| freesasa | - | 2.1.0 | !!! note "Full Details" FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).
[Homepage](https://freesasa.github.io) |
| freesurfer | bio | 5.3.0, 7.4.1, 8.0.0-1 | !!! note "Full Details" 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.
[Homepage](https://surfer.nmr.mgh.harvard.edu/) |
| freexl | tools | 1.0.5, 2.0.0 | !!! note "Full Details" FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
[Homepage](https://www.gaia-gis.it/fossil/freexl/index) |
| fsl | bio | 6.0.3, 6.0.4, 6.0.7.7, 6.0.7.18, 6.0.7.20 | !!! note "Full Details" FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
[Homepage](https://www.fmrib.ox.ac.uk/fsl/) |
| fsom | - | 20141119, 20151117 | !!! note "Full Details" A tiny C library for managing SOM (Self-Organizing Maps) neural networks.
[Homepage](https://github.com/ekg/fsom) |
| g2clib | geo | 1.6.0, 1.8.0 | !!! note "Full Details" This library contains C decoder/encoder routines for GRIB edition 2. This is part of the NCEPLIBS project.
[Homepage](https://github.com/NOAA-EMC/NCEPLIBS-g2c) |
| g2lib | geo | 3.1.0, 3.4.8 | !!! note "Full Details" Library contains GRIB2 encoder/decoder and search/indexing routines.
[Homepage](https://github.com/NOAA-EMC/NCEPLIBS-g2/) |
| ga | tools | 5.7.2 | !!! note "Full Details" Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency. I8 version.
[Homepage](http://hpc.pnl.gov/globalarrays/) |
| gamess-us | chem | 20210930-R2P1, 2020.2, 20220930-R2, 20230630-R1, 20230930-R2 | GAMESS-US
Full Details
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS-US is built with Intel compilers, mixed DDI, and OpenMPI 4.1.
Homepage |
| gapcloser | - | 1.12-r6 | !!! note "Full Details" GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads.
[Homepage](https://sourceforge.net/projects/soapdenovo2/files/GapCloser/) |
| gappa | - | 0.9.0 | !!! note "Full Details" 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.
[Homepage](https://github.com/lczech/gappa) |
| gate | bio | 9.3, 9.4 | !!! note "Full Details" GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography
[Homepage](http://www.opengatecollaboration.org/) |
| gatk | bio | 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0, 4.6.1.0 | !!! note "Full Details" The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
[Homepage](http://www.broadinstitute.org/gatk/) |
| gazebo | - | 11.7.0 | !!! note "Full Details" This is the Gazebo simulator. Gazebo simulates multiple robots in a 3D environment, with extensive dynamic interaction between objects.
[Homepage](https://gazebosim.org) |
| gblocks | - | 0.91b | !!! note "Full Details" Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
[Homepage](http://molevol.cmima.csic.es/castresana/Gblocks.html) |
| gcc | tools | 8.4.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3, 13.3, 14.3 | !!! note "Full Details" The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
[Homepage](https://gcc.gnu.org/) |
| gclust | - | 355z3 | !!! note "Full Details" Gclust software was developed to make clusters of protein sequences from all predicted protein sequences in a selected set of genomes. The clusters are homolog groups, but not ortholog clusters (see below for the distinction), and therefore, contain all homologous sequences encoded by the selected genomes. An ortholog cluster, such as the one in KEGG Orthologs or COG in NCBI, contains only a single sequence for each genome, and such a single representative is usually selected by a criterion called bi-directional best hit
[Homepage](http://gclust.c.u-tokyo.ac.jp/) |
| gcta | bio | 1.26.0, 1.93.2, 1.94.1 | !!! note "Full Details" 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).
[Homepage](https://yanglab.westlake.edu.cn/software/gcta/) |
| gd | - | 2.71, 2.77 | !!! note "Full Details" GD.pm - Interface to Gd Graphics Library
[Homepage](https://github.com/lstein/Perl-GD)
* Extensions:
* `ExtUtils::PkgConfig-1.16`
* `GD-2.77` |
| gdal | geo | 3.0.4, 3.2.3, 3.4.1, 3.5.1, 3.7.2, 3.9.1 | !!! note "Full Details" GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
[Homepage](https://www.gdal.org/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* Extensions:
* `osgeo-3.9.1` |
| gdcm | - | 2.6.8, 3.0.8 | !!! note "Full Details" Grassroots DICOM: Cross-platform DICOM implementation
[Homepage](https://sourceforge.net/projects/gdcm) |
| gdrcopy | - | 2.1, 2.3.1, 2.4.1, 2.5 | !!! note "Full Details" A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
[Homepage](https://github.com/NVIDIA/gdrcopy) |
| geant4 | phys | 10.06, 10.7.3, 11.1.0, 11.1.2, 11.2.1, 11.3.0 | !!! note "Full Details" Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
[Homepage](http://geant4.cern.ch/) |
| geant4-data | - | 10.7.3, 11.1.0, 11.1.2, 11.2.1, 11.3.0 | !!! note "Full Details" Datasets for Geant4.
[Homepage](https://geant4.cern.ch/) |
| geant4-seq | - | 11.1.0 | !!! note "Full Details" Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
[Homepage](http://geant4.cern.ch/) |
| geant4-topasmc3.9 | - | 10.7.3 | !!! note "Full Details" Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
[Homepage](http://geant4.cern.ch/) |
| gem | - | 5.1.1 | !!! note "Full Details" The Global Environmental Multiscale Model (GEM) is an integrated forecasting and data assimilation system developed by the Atmospheric Numerical Prediction Research Section, Meteorological Research Division, of Environment and Climate Change Canada.
[Homepage](https://github.com/ECCC-ASTD-MRD/gem) |
| gemma | bio | 0.98.3, 0.98.5 | !!! note "Full Details" GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.
[Homepage](http://veda.cs.uiuc.edu/Seq2Expr/) |
| gengetopt | - | 2.23 | !!! note "Full Details" Gengetopt is a tool to write command line option parsing code for C programs.
[Homepage](https://www.gnu.org/software/gengetopt/gengetopt.html) |
| genmap | - | 1.3.0 | !!! note "Full Details" GenMap - Fast and Exact Computation of Genome Mappability GenMap computes the uniqueness of k-mers for each position in the genome while allowing for up to e mismatches. More formally, the uniqueness or (k,e)-mappability can be described for every position as the reciprocal value of how often each k-mer occurs approximately in the genome, i.e., with up to e mismatches. Hence, a mappability value of 1 at position i indicates that the k-mer in the sequence at position i occurs only once in the sequence with up to e errors. A low mappability value indicates that this k-mer belongs to a repetitive region. GenMap can be applied to single or multiple genomes and helps finding regions that are unique or shared by many or all genomes.
[Homepage](https://github.com/cpockrandt/genmap) |
| genometools | bio | 1.6.1, 1.6.5 | !!! note "Full Details" A comprehensive software library for efficient processing of structured genome annotations.
[Homepage](http://genometools.org) |
| gentoo | - | 2020, 2023 | !!! note "Full Details" Gentoo prefix is Gentoo Linux installed in a prefix -
[Homepage](https://wiki.gentoo.org/wiki/Project:Prefix) |
| geopsy | - | 3.4.2 | !!! note "Full Details" Geopsy team is developing, distributing and maintaining open source software for geophysical research and applications. Born during SESAME European Project, it has provided tools for processing ambient vibrations with site characterization in mind since 2005. Progressively, more conventional techniques (such as MASW or refraction) are included to offer a high quality, comprehensive and free platform for the interpretation of geophysical experiments.
[Homepage](https://www.geopsy.org/) |
| geos | geo | 3.7.3, 3.8.1, 3.9.1, 3.10.2, 3.12.0 | !!! note "Full Details" GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
[Homepage](https://trac.osgeo.org/geos) |
| gerris | - | 20131206 | !!! note "Full Details" Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow
[Homepage](http://gfs.sourceforge.net/wiki/index.php/Main_Page) |
| gffcompare | - | 0.12.6 | !!! note "Full Details" GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.
[Homepage](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) |
| gffread | - | 0.11.7, 0.12.3 | !!! note "Full Details" GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
[Homepage](https://github.com/gpertea/gffread) |
| gflags | - | 2.2.2 | !!! note "Full Details" The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.
[Homepage](https://github.com/gflags/gflags) |
| gibbs2 | - | 1.0 | !!! note "Full Details" Gibbs2 is a program for the calculation of thermodynamic properties in periodic solids under arbitrary conditions of temperature and pressure. Gibbs2 uses the results of periodic solid-state quantum-mechanical calculations, specifically the energy-volume curve and possibly the harmonic phonon frequencies, to compute the thermodynamic properties of the solid within the framework of the quasiharmonic approximation.
[Homepage](https://aoterodelaroza.github.io/gibbs2/) |
| ginkgo | - | 1.6.0 | !!! note "Full Details" FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
[Homepage](https://ginkgo-project.github.io/) |
| git-annex | tools | 8.20200810, 10.20221003, 10.20231129 | !!! note "Full Details" git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space.
[Homepage](http://git-annex.branchable.com/) |
| git-lfs | - | 2.11.0, 3.3.0, 3.4.0 | !!! note "Full Details" Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
[Homepage](https://git-lfs.github.com) |
| givaro | - | 4.2.0 | !!! note "Full Details" C++ library for arithmetic and algebraic computations
[Homepage](http://givaro.forge.imag.fr/) |
| glew | - | 2.1.0, 2.2.0 | !!! note "Full Details" The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.
[Homepage](http://glew.sourceforge.net/) |
| glfw | - | 3.3.2, 3.3.8, 3.4 | !!! note "Full Details" GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop
[Homepage](https://www.glfw.org)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* Extensions:
* `glfw-2.8.0` |
| glimmerhmm | - | 3.0.4 | !!! note "Full Details" GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.
[Homepage](https://ccb.jhu.edu/software/glimmerhmm) |
| glimpse | - | 1.1.1, 2.0.0, 2.0.1 | !!! note "Full Details" 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.
[Homepage](https://odelaneau.github.io/GLIMPSE/) |
| glm | vis | 0.9.9.8 | !!! note "Full Details" OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
[Homepage](https://github.com/g-truc/glm) |
| globalarrays | - | 5.7.2, 5.8.2 | !!! note "Full Details" Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
[Homepage](https://hpc.pnl.gov/globalarrays) |
| glost | tools | 0.3.1 | !!! note "Full Details" This is GLOST, the Greedy Launcher Of Small Tasks.
[Homepage](https://github.com/cea-hpc/glost) |
| glpk | math | 4.65, 5.0 | !!! note "Full Details" The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
[Homepage](https://www.gnu.org/software/glpk/) |
| gmap-gsnap | bio | 2024-10-20, 2024-08-20, 2020-11-14, 2019-09-12 | !!! note "Full Details" GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
[Homepage](http://research-pub.gene.com/gmap/) |
| gmp | - | 6.2.0 | !!! note "Full Details" GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
[Homepage](https://gmplib.org/) |
| gmsh | phys | 4.7.0, 4.10.5, 4.11.1, 4.12.2, 4.13.1 | !!! note "Full Details" Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.
[Homepage](https://gmsh.info/) |
| gmt | geo | 6.5.0 | !!! note "Full Details" GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
[Homepage](https://www.generic-mapping-tools.org/) |
| gmtk | - | 1.4.4 | !!! note "Full Details" GMTK: The Graphical Models Toolkit
[Homepage](http://melodi.ee.washington.edu/) |
| gnina | - | 1.0.1, 1.3.1 | !!! note "Full Details" 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.
[Homepage](https://github.com/gnina/gnina) |
| gnuplot | vis | 5.2.8, 5.4.2, 5.4.6, 5.4.8, 6.0.3 | !!! note "Full Details" Portable interactive, function plotting utility
[Homepage](http://gnuplot.sourceforge.net) |
| go | tools | 1.14.1, 1.18.3, 1.21.3 | !!! note "Full Details" Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
[Homepage](https://www.golang.org) |
| goldrush | - | 1.2.2 | !!! note "Full Details" Linear-time de novo Long Read Assembler.
[Homepage](https://github.com/bcgsc/goldrush) |
| gomc | - | 2.75a | !!! note "Full Details" GOMC - GPU Optimized Monte Carlo is a parallel molecular simulation code designed for high-performance simulation of large systems.
[Homepage](https://gomc-wsu.org/) |
| googlebenchmark | - | 1.7.1, 1.8.3 | !!! note "Full Details" Google's library to benchmark code snippets, similar to unit tests.
[Homepage](https://github.com/google/benchmark) |
| googletest | tools | 1.10.0, 1.13.0, 1.14.0 | !!! note "Full Details" Google's framework for writing C++ tests on a variety of platforms
[Homepage](https://github.com/google/googletest) |
| grace | vis | 5.99.0 | !!! note "Full Details" Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
[Homepage](http://freecode.com/projects/grace) |
| graph-tool | - | 2.37, 2.45, 2.56, 2.98 | !!! note "Full Details" Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.
[Homepage](https://graph-tool.skewed.de/)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| graphaligner | - | 1.0.20 | !!! note "Full Details" Seed-and-extend program for aligning long error-prone reads to genome graphs.
[Homepage](https://github.com/maickrau/GraphAligner) |
| grass | geo | 7.8.4, 8.2.1 | !!! note "Full Details" The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
[Homepage](https://grass.osgeo.org) |
| grenedalf | - | 0.6.3 | !!! note "Full Details" Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments.
[Homepage](https://github.com/lczech/grenedalf) |
| groff | - | 1.22.4 | !!! note "Full Details" Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
[Homepage](https://www.gnu.org/software/groff) |
| gromacs | chem | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2023.5, 2024.1, 2024.4, 2024.6, 2025.4, 2026.1 | GROMACS
Full Details
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds.
Homepage |
| gromacs-colvars | chem | 2020.6 | GROMACS
Full Details
GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS
Homepage |
| gromacs-cp2k | chem | 2022.2 | GROMACS
Full Details
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 version has been compiled with CP2K for QM/MM calculations. Note: only 'gmx_mpi' and 'gmx_mpi_d' executables are available. See also: https://www.cp2k.org/tools:gromacs - CC-Wiki: GROMACS
Homepage |
| gromacs-ls | - | 2016.3 | GROMACS
Full Details
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
Homepage |
| gromacs-plumed | chem | 2019.6, 2020.7, 2021.2, 2021.4, 2021.6, 2021.7, 2022.3, 2022.6, 2023.5 | GROMACS
Full Details
GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS
Homepage |
| gromacs-ramd | chem | 2024.1-RAMD-2.1, 2020.5-RAMD-2.0 | GROMACS
Full Details
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 CPU only build, containing both MPI and threadMPI builds. CC-Wiki: GROMACS
Homepage |
| gromacs-swaxs | chem | 2021.7-0.5.1 | GROMACS
Full Details
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
Homepage |
| gsl | math | 1.16, 2.6, 2.7, 2.8 | !!! note "Full Details" The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
[Homepage](https://www.gnu.org/software/gsl/) |
| gsl-lite | - | 0.40.0, 0.41.0 | !!! note "Full Details" A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later
[Homepage](https://github.com/gsl-lite/gsl-lite) |
| gts | - | 20121130 | !!! note "Full Details" GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
[Homepage](http://gts.sourceforge.net/) |
| gudhi | - | 3.4.1, 3.7.1 | !!! note "Full Details" The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology. The library comes with data sets, demos, examples and test suites.
[Homepage](https://gudhi.inria.fr/)
* Compatible modules:
* `python/3.10`
* `python/3.9`
* `python/3.8` |
| guile | tools | 2.2.2 | !!! note "Full Details" 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.
[Homepage](https://www.gnu.org/software/guile/) |
| gurobi | math | 9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0, 11.0.1, 11.0.3, 12.0.0, 12.0.3, 13.0.0 | !!! note "Full Details" The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.
[Homepage](https://www.gurobi.com) |
| hal | bio | 2.2 | !!! note "Full Details" HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree. This package includes the HAL API and several analysis and conversion tools which are described below. HAL files are presently stored in either HDF5 or mmap format, but we note that the tools and most of the API are format-independent, so other databases could be implemented in the future.
[Homepage](https://github.com/ComparativeGenomicsToolkit/hal)
* Extensions:
* `addict-2.2.1`
* `blessed-1.18.1`
* `dill-0.3.4`
* `docker-4.3.1`
* `enlighten-1.10.1`
* `newick-1.3.0`
* `prefixed-0.3.2`
* `psutil-5.9.2`
* `PyYAML-5.4.1`
* `toil-5.3.0`
* `websocket-client-1.1.0` |
| hapgen2 | - | 2.2.0 | !!! note "Full Details" 'HAPGEN2' simulates case control datasets at SNP markers.
[Homepage](https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html) |
| haploview | - | 4.2 | !!! note "Full Details" Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
[Homepage](https://www.broadinstitute.org/haploview/haploview) |
| harminv | math | 1.4.1, 1.4.2 | !!! note "Full Details" 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.
[Homepage](https://github.com/NanoComp/harminv) |
| hdf | io | 4.2.15, 4.2.16 | !!! note "Full Details" HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
[Homepage](https://www.hdfgroup.org/products/hdf4/) |
| hdf-eos5 | - | 5.1.16 | !!! note "Full Details" HDF is the prescribed format for standard data products that are derived from EOS missions. HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura. Two versions of HDF-EOS libraries: HDF-EOS2 (v2.20) based on HDF4 and HDF-EOS5 (v5.1.16) based on HDF5 are developed.
[Homepage](https://hdfeos.org) |
| hdf-fortran | - | 4.2.15 | !!! note "Full Details" HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
[Homepage](https://www.hdfgroup.org/products/hdf4/) |
| hdf5 | io | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2, 1.14.5, 1.14.6 | !!! note "Full Details" HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
[Homepage](https://portal.hdfgroup.org/display/support)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* `python/3.14`
* Extensions:
* `blosc2-3.12.2`
* `cached-property-2.0.1`
* `h5py-3.15.1`
* `hdf5-blosc-1.0.1`
* `ndindex-1.10.1`
* `numexpr-2.14.1`
* `pkgconfig-1.5.5`
* `py-cpuinfo-9.0.0`
* `tables-3.11.0` |
| hdf5-mpi | io | 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2, 1.14.4, 1.14.5, 1.14.6 | !!! note "Full Details" HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
[Homepage](https://portal.hdfgroup.org/display/support)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* `python/3.14`
* Extensions:
* `blosc2-3.12.2`
* `cached-property-2.0.1`
* `h5py-3.15.1`
* `hdf5-blosc-1.0.1`
* `ndindex-1.10.1`
* `numexpr-2.14.1`
* `pkgconfig-1.5.5`
* `py-cpuinfo-9.0.0`
* `tables-3.11.0` |
| hdfview | - | 2.14 | !!! note "Full Details" HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.
[Homepage](https://support.hdfgroup.org/products/java/hdfview/) |
| healpix | - | 3.81, 3.82, 3.83 | !!! note "Full Details" Hierarchical Equal Area isoLatitude Pixelation of a sphere.
[Homepage](http://healpix.sourceforge.net/) |
| heasoft | phys | 6.32.1 | !!! note "Full Details" A Unified Release of the FTOOLS and XANADU Software Packages XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases
[Homepage](https://heasarc.nasa.gov/lheasoft/)
* Extensions:
* `Env-1.04`
* `ExtUtils::MakeMaker-7.70`
* `modules-0.04` |
| hh-suite | bio | 3.3.0 | !!! note "Full Details" HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases.
[Homepage](https://github.com/soedinglab/hh-suite) |
| hifiasm | - | 0.16.1, 0.19.5 | !!! note "Full Details" Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.
[Homepage](https://github.com/chhylp123/hifiasm) |
| highfive | - | 2.9.0 | !!! note "Full Details" HighFive is a modern header-only C++11 friendly interface for libhdf5.
[Homepage](https://github.com/BlueBrain/HighFive) |
| hisat2 | bio | 2.2.1 | !!! note "Full Details" HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
[Homepage](https://daehwankimlab.github.io/hisat2/) |
| hmmer | bio | 3.2.1, 3.3.2, 3.4 | !!! note "Full Details" HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
[Homepage](http://hmmer.org/) |
| hoomd-blue | - | 2.9.3, 3.6.0, 5.1.1 | !!! note "Full Details" HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface.
[Homepage](http://glotzerlab.engin.umich.edu/hoomd-blue/)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| hoomd-blue-mpi | - | 3.6.0 | !!! note "Full Details" HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface.
[Homepage](http://glotzerlab.engin.umich.edu/hoomd-blue/)
* Compatible modules:
* `python/3.8`
* `python/3.9`
* `python/3.10` |
| hpcspades | - | 3.15.0 | !!! note "Full Details" Genome assembler for single-cell and isolates data sets
[Homepage](http://cab.spbu.ru/software/spades/) |
| hpctoolkit | - | 2020.08 | !!! note "Full Details" HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to supercomputers.
[Homepage](http://hpctoolkit.org/) |
| hpl | tools | 2.3 | !!! note "Full Details" 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.
[Homepage](https://www.netlib.org/benchmark/hpl/) |
| htslib | bio | 1.9, 1.10.2, 1.11, 1.13, 1.14, 1.15.1, 1.16, 1.17, 1.18, 1.19, 1.22.1 | !!! note "Full Details" A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
[Homepage](https://www.htslib.org/) |
| hwloc | - | 2.4.0, 2.7.1, 2.9.1, 2.10.0, 2.12.1 | !!! note "Full Details" The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
[Homepage](https://www.open-mpi.org/projects/hwloc/) |
| hyphy | bio | 2.5.26, 2.5.49 | !!! note "Full Details" HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
[Homepage](https://veg.github.io/hyphy-site/) |
| hypre | math | 2.20.0, 2.33.0 | !!! note "Full Details" 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.
[Homepage](https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods) |
| idba-ud | - | 1.1.3 | !!! note "Full Details" IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
[Homepage](http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/) |
| idg | - | 1.2.0 | !!! note "Full Details" 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.
[Homepage](https://idg.readthedocs.io/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* `python/3.13` |
| igblast | bio | 1.17.0, 1.18.0 | !!! note "Full Details" IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm.
[Homepage](https://www.ncbi.nlm.nih.gov/igblast/intro.html) |
| ignition | - | citadel | !!! note "Full Details" Tools and libraries for robotics applications.
[Homepage](https://ignitionrobotics.org/) |
| igraph | math | 0.8.2, 0.9.10, 0.10.2, 0.10.7, 0.10.13, 0.10.16, 1.0.1 | !!! note "Full Details" igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.
[Homepage](https://igraph.org)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* `python/3.14`
* Extensions:
* `python-igraph-1.0.0` |
| igv | - | 2.9.2 | !!! note "Full Details" This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.
[Homepage](https://www.broadinstitute.org/software/igv/) |
| ijulia-kernel | - | 1.5, 1.8, 1.10 | !!! note "Full Details" IJulia kernelspec for Julia 1.10
[Homepage](https://julialang.org/) |
| ima3 | - | 1.12, 20210120 | !!! note "Full Details" IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models. For a given phylogenetic tree IMa3 addresses the same model as IMa2. Like IMa2-p, IMa3 can run on multiple processors.
[Homepage](https://github.com/jodyhey/IMa3) |
| imb | - | 2021.3 | !!! note "Full Details" The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes
[Homepage](https://software.intel.com/en-us/articles/intel-mpi-benchmarks) |
| imkl | math | 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0, 2023.2.0, 2024.1.0, 2024.2.0, 2025.2.0 | !!! note "Full Details" Intel oneAPI Math Kernel Library
[Homepage](https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html) |
| impute2 | bio | 2.3.2 | !!! note "Full Details" IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
[Homepage](http://mathgen.stats.ox.ac.uk/impute/impute_v2.html) |
| impute5 | - | 1.1.5 | !!! note "Full Details" IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1
[Homepage](https://jmarchini.org/software/#impute-5) |
| infernal | bio | 1.1.3, 1.1.4, 1.1.5 | !!! note "Full Details" Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.
[Homepage](http://eddylab.org/infernal/) |
| intel | tools | 2020.1.217, 2021.2.0, 2022.1.0, 2023.2.1, 2024.2.0, 2025.2.0 | !!! note "Full Details" Intel C, C++ and Fortran compilers with CodePlay SYCL support for NVIDIA GPUs
[Homepage](https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html) |
| intel-opencl | - | 2021.2.0 | !!! note "Full Details" Intel's OpenCL CPU runtime
[Homepage](https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html) |
| intelmpi | mpi | 2019.7.217, 2021.2.0, 2021.9.0, 2021.16.1 | !!! note "Full Details" Intel MPI Library, compatible with MPICH ABI
[Homepage](https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html) |
| intelxed | - | 12.0.1 | !!! note "Full Details" The X86 Encoder Decoder (XED), is a software library (and associated headers) for encoding and decoding X86 (IA32 and Intel64) instructions.
[Homepage](https://intelxed.github.io/) |
| interproscan | bio | 5.55-88.0, 5.64-96.0, 5.73-104.0, 5.52-86.0, 5.53-87.0, 5.63-95.0, 5.50-84.0, 5.56-89.0 | !!! note "Full Details" InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.
[Homepage](http://www.ebi.ac.uk/interpro/) |
| interproscan_data | - | 5.73-104.0, 5.63-95.0, 5.64-96.0 | !!! note "Full Details" This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.
[Homepage](http://www.ebi.ac.uk/interpro/) |
| intervaltree | - | 0.1 | !!! note "Full Details" An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.
[Homepage](https://github.com/ekg/intervaltree) |
| ioapi | - | 3.2-2020111 | !!! note "Full Details" The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems.
[Homepage](https://www.cmascenter.org/ioapi/) |
| ipopt | - | 3.14.11, 3.14.14 | !!! note "Full Details" IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization.
[Homepage](https://projects.coin-or.org/Ipopt) |
| ipp | tools | 2020.1.217 | !!! note "Full Details" Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
[Homepage](https://software.intel.com/en-us/articles/intel-ipp/) |
| ipykernel | - | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b, 2024a, 2024b, 2025a, 2026a | !!! note "Full Details" Bundle which contains ipykernel 2026a and its dependencies
[Homepage](https://ipython.org/)
* Compatible modules:
* `python/3.10`
* `python/3.11`
* `python/3.12`
* `python/3.13`
* Extensions:
* `asttokens-3.0.1`
* `comm-0.2.3`
* `debugpy-1.8.19`
* `decorator-5.2.1`
* `executing-2.2.1`
* `ipykernel-7.1.0`
* `ipython-9.9.0`
* `ipython_pygments_lexers-1.1.1`
* `ipywidgets-8.1.8`
* `jedi-0.19.2`
* `jupyter_client-8.8.0`
* `jupyter_core-5.9.1`
* `jupyterlab_widgets-3.0.16`
* `matplotlib_inline-0.2.1`
* `nest_asyncio-1.6.0`
* `packaging-26.0`
* `parso-0.8.5`
* `pexpect-4.9.0`
* `pip-25.2`
* `platformdirs-4.5.1`
* `prompt_toolkit-3.0.52`
* `psutil-7.2.2`
* `ptyprocess-0.7.0`
* `pure_eval-0.2.3`
* `pygments-2.19.2`
* `python_dateutil-2.9.0.post0`
* `pyzmq-27.1.0`
* `six-1.17.0`
* `stack_data-0.6.3`
* `tornado-6.5.4`
* `traitlets-5.14.3`
* `wcwidth-0.5.2`
* `widgetsnbextension-4.0.15` |
| ipython-kernel | - | 2.7, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14 | !!! note "Full Details" IPython kernelspec for Python 3.14
[Homepage](https://ipython.org/) |
| iq-tree | bio | 1.6.12, 2.0.7, 2.1.2, 2.2.1, 2.2.2.7, 2.3.6 | !!! note "Full Details" Efficient phylogenomic software by maximum likelihood
[Homepage](http://www.iqtree.org/) |
| ir-kernel | - | 4.2, 4.4 | !!! note "Full Details" 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.
[Homepage](https://irkernel.github.io)
* Extensions:
* `base64enc-0.1-3`
* `cli-3.6.3`
* `crayon-1.5.3`
* `digest-0.6.37`
* `ellipsis-0.3.2`
* `evaluate-1.0.0`
* `fansi-1.0.6`
* `fastmap-1.2.0`
* `glue-1.7.0`
* `htmltools-0.5.8.1`
* `IRdisplay-1.1`
* `IRkernel-1.3.2`
* `jsonlite-1.8.9`
* `lifecycle-1.0.4`
* `pbdZMQ-0.3-13`
* `pillar-1.9.0`
* `repr-1.1.7`
* `rlang-1.1.4`
* `utf8-1.2.4`
* `uuid-1.2-1`
* `vctrs-0.6.5` |
| irfinder | - | 1.3.1 | !!! note "Full Details" Basic STAR (Spliced Transcripts Alignment to a Reference) STAR workflow consists of 2 steps: Generating genoms indexes files and mapping reads to the genomes.
[Homepage](https://github.com/williamritchie/IRFinder/)
* Extensions:
* `Data::Dumper-2.173` |
| isce2 | - | 2.6.3 | !!! note "Full Details" Interferometric synthetic aperture radar Scientific Computing Environment (ISCE) is a framework designed for the purpose of processing Interferometric Synthetic Aperture Radar (InSAR) data. The framework aspects of it have been designed as a general software development framework. It may have additional utility in a general sense for building other types of software packages.
[Homepage](https://github.com/isce-framework/isce2) |
| ispc | - | 1.10.0, 1.13.0, 1.18.0, 1.21.1 | !!! note "Full Details" Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.
[Homepage](https://ispc.github.io/) |
| itac | tools | 2021.5.0 | !!! note "Full Details" The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
[Homepage](https://software.intel.com/en-us/intel-trace-analyzer/) |
| itk | vis | 4.13.3, 5.0.1, 5.1.2, 5.2.1, 5.3.0, 5.4.0, 5.4.5 | !!! note "Full Details" Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.
[Homepage](https://itk.org)
* Compatible modules:
* `python/3.11`
* `python/3.12`
* `python/3.13`
* `python/3.14` |
| ivar | - | 1.4.2 | !!! note "Full Details" iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
[Homepage](https://github.com/andersen-lab/ivar) |
| jags | math | 4.3.0, 4.3.2 | !!! note "Full Details" JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
[Homepage](http://mcmc-jags.sourceforge.net/) |
| jasper | vis | 2.0.16, 4.0.0, 4.2.4 | !!! note "Full Details" The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
[Homepage](https://www.ece.uvic.ca/~frodo/jasper/) |
| java | tools | 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1 | Java
Full Details
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Homepage |
| jbigkit | - | 2.1 | !!! note "Full Details" JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
[Homepage](https://www.cl.cam.ac.uk/~mgk25/jbigkit/) |
| jdftx | chem | 1.7.0 | !!! note "Full Details" JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. It is distributed under the GPL license (version 3 or higher) and publications resulting from its use must cite: R. Sundararaman, K. Letchworth-Weaver, K.A. Schwarz, D. Gunceler, Y. Ozhabes and T.A. Arias, 'JDFTx: software for joint density-functional theory
[Homepage](http://jdftx.org/index.html) |
| jellyfish | bio | 2.3.0, 2.3.1 | !!! note "Full Details" Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
[Homepage](http://www.genome.umd.edu/jellyfish.html) |
| jemalloc | - | 5.2.1, 5.3.0 | !!! note "Full Details" jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
[Homepage](http://jemalloc.net) |
| json-fortran | - | 8.3.0 | !!! note "Full Details" JSON-Fortran: A Modern Fortran JSON API
[Homepage](https://github.com/jacobwilliams/json-fortran) |
| jsoncpp | - | 1.9.4, 1.9.5 | !!! note "Full Details" JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
[Homepage](https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html) |
| judy | - | 1.0.5 | !!! note "Full Details" A C library that implements a dynamic array.
[Homepage](http://judy.sourceforge.net/) |
| julia | tools | 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1, 1.9.3, 1.10.0, 1.10.10, 1.11.3, 1.12.5 | !!! note "Full Details" Julia is a high-level, high-performance dynamic programming language for numerical computing
[Homepage](https://julialang.org) |
| kahip | - | 3.14, 3.16 | !!! note "Full Details" The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.
[Homepage](https://kahip.github.io/) |
| kahypar | - | 1.3.2 | !!! note "Full Details" KaHyPar is a multilevel hypergraph partitioning framework providing direct k-way and recursive bisection based partitioning algorithms that compute solutions of very high quality.
[Homepage](https://kahypar.org/)
* Compatible modules:
* `python/3.8`
* `python/3.9`
* `python/3.10`
* `python/3.11` |
| kaiju | bio | 1.6.2, 1.7.4, 1.10.1 | !!! note "Full Details" Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments
[Homepage](http://kaiju.binf.ku.dk/) |
| kalign | - | 2.03, 3.3.5 | !!! note "Full Details" Kalign is a fast multiple sequence alignment program for biological sequences.
[Homepage](https://github.com/TimoLassmann/kalign) |
| kallisto | bio | 0.46.1, 0.51.1 | !!! note "Full Details" kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
[Homepage](https://pachterlab.github.io/kallisto/) |
| kent_tools | - | 486 | !!! note "Full Details" Kent utilities: collection of tools used by the UCSC genome browser.
[Homepage](https://genome.cse.ucsc.edu/) |
| kentutils | bio | 401 | !!! note "Full Details" Kent utilities: collection of tools used by the UCSC genome browser.
[Homepage](http://genome.cse.ucsc.edu/) |
| kim-api | chem | 2.1.3, 2.3.0, 2.4.1 | !!! note "Full Details"
Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
[Homepage](https://openkim.org/) |
| kma | - | 1.3.0, 1.3.25, 1.4.14 | !!! note "Full Details" KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
[Homepage](https://bitbucket.org/genomicepidemiology/kma) |
| kmergenie | - | 1.7051 | !!! note "Full Details" KmerGenie estimates the best k-mer length for genome de novo assembly.
[Homepage](http://kmergenie.bx.psu.edu/) |
| komplexity | - | 0.3.6 | !!! note "Full Details" A command-line tool built in Rust to quickly calculate and/or mask low-complexity sequences from a FAST[A/Q] file. This uses the number of unique k-mers over a sequence divided by the length to assess complexity.
[Homepage](https://github.com/eclarke/komplexity) |
| kraken | bio | 1.1.1 | !!! note "Full Details" 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.
[Homepage](https://ccb.jhu.edu/software/kraken/) |
| kraken2 | bio | 2.0.9-beta, 2.1.1, 2.1.2, 2.1.3, 2.1.6 | !!! note "Full Details" 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.
[Homepage](https://github.com/DerrickWood/kraken2/wiki) |
| krakenuniq | - | 1.0.2, 1.0.4 | !!! note "Full Details" krakenuniq: confident and fast metagenomics classification using unique k-mer counts. False-positive identifications are a significant problem in metagenomics classification. KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory.
[Homepage](https://github.com/fbreitwieser/krakenuniq) |
| kronatools | - | 2.8.1 | !!! note "Full Details" Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
[Homepage](https://github.com/marbl/Krona/wiki/KronaTools) |
| kyotocabinet | - | 1.2.80 | !!! note "Full Details" Kyoto Cabinet is a library of routines for managing a database.
[Homepage](https://dbmx.net/kyotocabinet/) |
| lammps-omp | chem | 20201029, 20210929, 20220623, 20230802, 20240829, 20250722 | LAMMPS
Full Details
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
Homepage |
| last | bio | 1145, 1642 | !!! note "Full Details" LAST: find and align related regions of sequences
[Homepage](https://gitlab.com/mcfrith/last) |
| lastz | - | 1.04.03 | !!! note "Full Details" LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
[Homepage](https://www.bx.psu.edu/~rsharris/lastz/) |
| latte | chem | 1.2.1 | !!! note "Full Details" Open source density functional tight binding molecular dynamics.
[Homepage](https://github.com/lanl/LATTE) |
| ldc | - | 0.17.6, 1.26.0, 1.30.0 | !!! note "Full Details" The LLVM-based D Compiler
[Homepage](https://wiki.dlang.org/LDC) |
| leptonica | - | 1.82.0 | !!! note "Full Details" Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
[Homepage](http://www.leptonica.org) |
| lerc | - | 4.0.0 | !!! note "Full Details" LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).
[Homepage](https://github.com/Esri/lerc) |
| leveldb | tools | 1.22 | !!! note "Full Details" LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
[Homepage](https://github.com/google/leveldb) |
| lhapdf | - | 6.4.0 | !!! note "Full Details" LHAPDF is a general purpose C++ interpolator, used for evaluating PDFs from discretised data files. Previous versions of LHAPDF were written in Fortran 77/90
[Homepage](https://lhapdf.hepforge.org/index.html) |
| libaec | - | 1.0.6 | !!! note "Full Details" Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
[Homepage](https://gitlab.dkrz.de/k202009/libaec) |
| libbeef | - | 0.1.2 | !!! note "Full Details" BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
[Homepage](https://github.com/vossjo/libbeef) |
| libbigwig | - | 0.4.6 | !!! note "Full Details" A C library for handling bigWig files
[Homepage](https://github.com/dpryan79/libBigWig) |
| [libccd](https://