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List of supported software

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EasyBuild supports 3470 different software packages (incl. toolchains, bundles):

a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z

3

3d-dna - 3to2

3d-dna

3D de novo assembly (3D DNA) pipeline

homepage: https://github.com/theaidenlab/3d-dna

version versionsuffix toolchain
180922 -Python-2.7.15 GCCcore/8.2.0

3to2

lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.

homepage: https://pypi.python.org/pypi/3to2

version versionsuffix toolchain
1.1.1 -Python-2.7.12 foss/2016b, intel/2016b
1.1.1 -Python-2.7.13 intel/2017a

4

4ti2

4ti2

A software package for algebraic, geometric and combinatorial problems on linear spaces

homepage: https://4ti2.github.io/

version toolchain
1.6.9 GCC/11.3.0, GCC/8.2.0-2.31.1, intel/2018b

A

ABAQUS - ABINIT - ABRA2 - ABRicate - Abseil - abTEM - ABySS - ack - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - affinity - AFNI - AGAT - AGeNT - AGFusion - AICSImageIO - AIMAll - aiohttp - ALADIN - ALAMODE - Albacore - Albumentations - alevin-fry - ALFA - Alfred - ALL - alleleCount - alleleIntegrator - Allinea - ALLPATHS-LG - almosthere - Alpha - AlphaFold - AlphaPulldown - ALPS - alsa-lib - AMAPVox - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMD-uProf - AMICA - AMOS - AMPHORA2 - AMPL-MP - amplimap - AMPtk - AMRFinderPlus - AmrPlusPlus - AMS - Anaconda2 - Anaconda3 - anadama2 - aNCI - andi - ANGEL - angsd - ANIcalculator - anndata - Annif - Annocript - annovar - ANSYS - ANSYS_CFD - ant - ANTIC - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - AOFlagger - AOMP - APBS - apex - APR - APR-util - AptaSUITE - ARAGORN - Arb - Arcade-Learning-Environment - arcasHLA - ARCH - Archive-Zip - ArchR - archspec - AreTomo2 - ARGoS - argtable - aria2 - Arlequin - Armadillo - arosics - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - arrow-R - ART - Artemis - artic-ncov2019 - ARTS - ArviZ - ARWEN - ASAP - ASAP3 - ASCAT - ASE - ASF-SearchAPI - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astro-tulips - astropy - at-spi2-atk - at-spi2-core - ATAT - ATK - ATLAS - atomate - AtomPAW - atools - atropos - ATSAS - attr - attrdict - attrdict3 - augur - AUGUSTUS - Austin - AUTO-07p - Autoconf - Autoconf-archive - AutoDock - AutoDock-GPU - AutoDock-Vina - AutoDockSuite - AutoGeneS - AutoGrid - Automake - AutoMap - autopep8 - Autotools - Avogadro2 - avro-cpp - awscli - Ax - axel

ABAQUS

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

homepage: http://www.simulia.com/products/abaqus_fea.html

version versionsuffix toolchain
6.12.1 -linux-x86_64 system
6.13.5 -linux-x86_64 system
6.14.1 -linux-x86_64 system
2017 -hotfix-1721 system
2018 -hotfix-1806 system
2020 system
2021 -hotfix-2132 system
2022 system
2022 -hotfix-2214 system
2022 -hotfix-2223 system

ABINIT

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

homepage: https://www.abinit.org/

version versionsuffix toolchain
7.0.3 -x86_64_linux_gnu4.5 system
7.0.5 -x86_64_linux_gnu4.5 system
7.2.1 -x86_64_linux_gnu4.5 system
7.10.5 intel/2016.02-GCC-4.9
7.10.5 -libxc intel/2016.02-GCC-4.9
8.0.8 intel/2016a
8.0.8b foss/2016b, intel/2016b
8.2.2 foss/2016b, intel/2016b
8.4.4 intel/2017b
8.6.3 intel/2018a
8.10.2 intel/2018b
8.10.3 intel/2018b
9.2.1 foss/2019b, intel/2019b, intel/2020a
9.4.1 foss/2020b, intel/2020a, intel/2020b
9.4.2 foss/2021a, intel/2021a
9.6.2 foss/2022a, intel/2021a, intel/2021b, intel/2022a
9.10.3 intel/2022a

ABRA2

Assembly Based ReAligner

homepage: https://github.com/mozack/abra2

version toolchain
2.22 iccifort/2019.5.281
2.23 GCC/10.2.0, GCC/9.3.0

ABRicate

Mass screening of contigs for antimicrobial and virulence genes

homepage: https://github.com/tseemann/abricate

version versionsuffix toolchain
0.9.9 gompi/2019b
0.9.9 -Perl-5.28.1 gompi/2019a
1.0.0 gompi/2021a

Abseil

Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.

homepage: https://abseil.io/

version toolchain
20210324.2 GCCcore/11.2.0
20230125.2 GCCcore/11.3.0, GCCcore/12.2.0
20230125.3 GCCcore/12.3.0
20240116.1 GCCcore/13.2.0

abTEM

abTEM provides a Python API for running simulations of Transmission Electron Microscopy images.

homepage: https://github.com/jacobjma/abTEM

version versionsuffix toolchain
1.0.0b24 -ASE-3.22.0 fosscuda/2020b
1.0.0b26 -ASE-3.22.0 foss/2020b, fosscuda/2020b

ABySS

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss

version toolchain
1.9.0 foss/2016a
2.0.2 foss/2016b, foss/2018a, gompi/2019a, intel/2016b
2.0.3 foss/2017b, intel/2017b
2.1.5 foss/2019b
2.2.5 foss/2020b
2.3.7 foss/2023a

ack

ack is a tool like grep, optimized for programmers

homepage: https://beyondgrep.com

version toolchain
2.14 system
3.4.0 GCCcore/10.2.0
3.5.0 GCCcore/10.3.0

ACTC

ACTC converts independent triangles into triangle strips or fans.

homepage: https://sourceforge.net/projects/actc

version toolchain
1.1 GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2016b

ada

Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.

homepage: https://cran.r-project.org/web/packages/ada/index.html

version versionsuffix toolchain
2.0-5 -R-3.4.0 intel/2017a

AdapterRemoval

AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.

homepage: https://github.com/MikkelSchubert/adapterremoval

version toolchain
2.2.0 foss/2016b
2.2.2 foss/2018b
2.3.1 foss/2018b
2.3.2 GCC/10.2.0, GCC/10.3.0, GCC/11.2.0
2.3.3 GCC/11.3.0

ADDA

ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes.

homepage: https://github.com/adda-team/adda/wiki

version toolchain
1.3b4 foss/2019a

ADF

ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).

homepage: https://www.scm.com/ADF/

version versionsuffix toolchain
2009.01a.pc64_linux.intelmpi system
2014.02 system
2014.11.r48287 intel/2016a
2016.101 system
2019.303 -intelmpi system

ADIOS

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

homepage: https://www.olcf.ornl.gov/center-projects/adios/

version versionsuffix toolchain
1.13.1 -Python-2.7.15 foss/2019a
1.13.1 -Python-3.8.2 foss/2020a
20210804 -Python-3.8.2 foss/2020a

adjustText

A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

homepage: https://github.com/Phlya/adjustText

version versionsuffix toolchain
0.7.3 foss/2021b
0.7.3 -Python-3.6.6 foss/2018b
0.7.3 -Python-3.7.2 intel/2019a

ADMIXTURE

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

homepage: https://dalexander.github.io/admixture/

version toolchain
1.3.0 system

ADOL-C

The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C.

homepage: https://projects.coin-or.org/ADOL-C

version toolchain
2.7.0 gompi/2019a
2.7.2 gompi/2020a

Advisor

Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain

homepage: https://software.intel.com/intel-advisor-xe

version toolchain
2016_update2 system
2017_update1 system
2018_update1 system
2018_update3 system
2019_update2 system
2019_update3 system
2019_update5 system
2021.2.0 system
2021.4.0 system
2022.1.0 system
2023.0.0 system
2023.2.0 system

affinity

A small C++ wrapper for managing Linux CPU sets and CPU affinity. It also includes a tool to report binding, which is useful for testing different binding options

homepage: https://github.com/vkarak/affinity

version toolchain
20230524 foss/2022a, intel/2022a

AFNI

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/

version versionsuffix toolchain
18.1.09 -Python-3.6.4 intel/2018a
18.3.00 -Python-3.6.6 foss/2018b
19.0.01 -Python-2.7.14 foss/2017b, intel/2017b
20160329 -Python-2.7.11 intel/2016a

AGAT

AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.

homepage: https://agat.readthedocs.io/en/latest/

version toolchain
0.9.2 GCC/11.2.0
1.1.0 GCC/12.2.0

AGeNT

The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format. The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.

homepage: https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879

version toolchain
3.0.6 system

AGFusion

AGFusion is a python package for annotating gene fusions from the human or mouse genomes.

homepage: https://github.com/murphycj/AGFusion

version versionsuffix toolchain
1.2 -Python-3.7.2 foss/2019a

AICSImageIO

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python

homepage: https://github.com/AllenCellModeling/aicsimageio

version toolchain
4.14.0 foss/2022a

AIMAll

AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.

homepage: http://aim.tkgristmill.com

version versionsuffix toolchain
19.10.12 -linux_64bit intel/2020b

aiohttp

Asynchronous HTTP client/server framework for asyncio and Python.

homepage: https://github.com/aio-libs/aiohttp

version versionsuffix toolchain
3.5.4 -Python-3.6.6 foss/2018b
3.8.1 GCCcore/10.3.0, GCCcore/11.2.0
3.8.3 GCCcore/11.3.0
3.8.5 GCCcore/12.2.0, GCCcore/12.3.0

ALADIN

ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the differences between the two softwares as small as possible.

homepage: http://www.cnrm.meteo.fr/aladin/

version toolchain
36t1_op2bf1 intel/2016a

ALAMODE

ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.

homepage: http://alamode.readthedocs.io/en/latest/index.html

version toolchain
1.4.2 foss/2022b

Albacore

Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.

homepage: https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016

version versionsuffix toolchain
2.0.2 -Python-3.6.1 intel/2017a

Albumentations

Albumentations is a Python library for fast and flexible image augmentations

homepage: https://albumentations.ai

version versionsuffix toolchain
1.1.0 foss/2021b
1.1.0 -CUDA-11.3.1 foss/2021a
1.3.0 foss/2022a
1.3.0 -CUDA-11.7.0 foss/2022a

alevin-fry

alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

homepage: https://github.com/COMBINE-lab/alevin-fry

version toolchain
0.4.3 GCCcore/11.2.0
0.6.0 GCCcore/10.3.0

ALFA

ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.

homepage: https://github.com/biocompibens/ALFA

version versionsuffix toolchain
1.1.1 -Python-3.7.2 foss/2019a

Alfred

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments.

homepage: https://www.gear-genomics.com/alfred/

version toolchain
0.2.6 GCC/11.2.0

ALL

A Load Balancing Library (ALL) aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the Jülich Supercomputing Centre at Forschungszentrum Jülich.

homepage: https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing

version toolchain
0.9.2 foss/2022b, foss/2023a

alleleCount

The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing.

homepage: http://cancerit.github.io/alleleCount/

version toolchain
4.0.0 GCCcore/6.4.0
4.2.1 GCC/11.3.0
4.3.0 GCC/12.2.0

alleleIntegrator

R package to generate allele specific counts for scRNA data and use it to identify cancer cells

homepage: https://github.com/constantAmateur/alleleIntegrator

version versionsuffix toolchain
0.8.8 -R-4.2.1 foss/2022a
0.8.8 -R-4.2.2 foss/2022b

Allinea

The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.

homepage: http://www.allinea.com

version toolchain
4.1-32834-Redhat-5.7-x86_64 system
4.1-32834-Redhat-6.0-x86_64 system
6.1.1-Ubuntu-14.04-x86_64 system

ALLPATHS-LG

ALLPATHS-LG, the new short read genome assembler.

homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/

version toolchain
52488 foss/2016a

almosthere

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

version toolchain
1.0.1 GCCcore/7.3.0
1.0.10 GCCcore/9.3.0
2.0.2 GCCcore/10.2.0

Alpha

Alpha is a tool designed for detailed comparative study of bacteriophage genomes.

homepage: https://www.lirmm.fr/~swenson/alpha/alpha.htm

version versionsuffix toolchain
20200430 -Python-2.7.16 foss/2019b

AlphaFold

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold contains patches for ColabFold.

homepage: https://github.com/sokrypton/alphafold

version versionsuffix toolchain
2.0.0 foss/2020b, fosscuda/2020b
2.0.1 foss/2020b, fosscuda/2020b
2.1.1 fosscuda/2020b
2.1.2 foss/2021a
2.1.2 -CUDA-11.3.1 foss/2021a
2.1.2 -TensorFlow-2.5.0 foss/2020b, fosscuda/2020b
2.2.2 foss/2021a
2.2.2 -CUDA-11.3.1 foss/2021a
2.3.0 -CUDA-11.4.1 foss/2021b
2.3.1 foss/2022a
2.3.1 -CUDA-11.7.0 foss/2022a
2.3.4 -CUDA-11.7.0-ColabFold foss/2022a
2.3.4 -ColabFold foss/2022a

AlphaPulldown

AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer

homepage: https://github.com/KosinskiLab/AlphaPulldown

version toolchain
0.30.4 foss/2020b, fosscuda/2020b

ALPS

The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.

homepage: http://alps.comp-phys.org/

version versionsuffix toolchain
2.2.b4 -Python-2.7.11 intel/2016a
2.3.0 -Python-2.7.12 foss/2016b
2.3.0 -Python-3.5.2 foss/2016b

alsa-lib

The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.

homepage: https://www.alsa-project.org

version toolchain
1.2.4 GCCcore/9.3.0
1.2.8 GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0

AMAPVox

LiDAR data voxelisation software

homepage: https://amap-dev.cirad.fr/projects/amapvox

version versionsuffix toolchain
1.9.4 -Java-11 system

Amara

Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML.

homepage: https://pypi.org/project/Amara

version versionsuffix toolchain
1.2.0.2 -Python-2.7.15 foss/2019a, intel/2019a

amask

amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads in a parallel environment.

homepage: https://github.com/TACC/amask

version toolchain
20171106 foss/2018a
20190404 foss/2018b

Amber

Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.

homepage: https://ambermd.org/amber.html

version versionsuffix toolchain
14 -AmberTools-15-patchlevel-13-13 intel/2016a
16 -AmberTools-16-patchlevel-5-14 iomkl/2016.07
16 -AmberTools-16-patchlevel-5-14-CUDA iomkl/2016.09-GCC-4.9.3-2.25
16 -AmberTools-16-patchlevel-5-14-serial iomkl/2016.07
16 -AmberTools-17-patchlevel-10-15 foss/2018b, fosscuda/2018b, intel/2018b
16 -AmberTools-17-patchlevel-10-15-Python-2.7.14 foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
16 -AmberTools-17-patchlevel-8-12 intel/2017b
18 -AmberTools-18-patchlevel-10-8 foss/2018b, fosscuda/2018b, intel/2017b
18 -AmberTools-19-patchlevel-12-17-Python-2.7.16 foss/2019b, fosscuda/2019b
20.11 -AmberTools-20.15-Python-3.8.2 foss/2020a, fosscuda/2020a
20.11 -AmberTools-21.3 foss/2020b, fosscuda/2020b
22.0 -AmberTools-22.3 foss/2021b
22.0 -AmberTools-22.3-CUDA-11.4.1 foss/2021b
22.4 -AmberTools-22.5-CUDA-11.7.0 foss/2022a

AmberMini

A stripped-down set of just antechamber, sqm, and tleap.

homepage: https://github.com/choderalab/ambermini

version toolchain
16.16.0 intel/2017b, intel/2020a

AmberTools

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

homepage: https://ambermd.org/

version versionsuffix toolchain
17 intel/2017b, intel/2018a
17 -Python-2.7.14 foss/2018a
20 -Python-3.8.2 intel/2020a
21 foss/2021a, intel/2021b
21.12 foss/2021b
22.3 foss/2021b

AMD-LibM

AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.

homepage: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/

version toolchain
3.2.2 GCC/7.3.0-2.30
3.6.0-4 GCC/9.3.0

AMD-RNG

AMD Random Number Generator Library is a pseudorandom number generator library.

homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/

version toolchain
1.0 GCC/7.3.0-2.30
2.2-4 GCC/9.3.0

AMD-SecureRNG

The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation.

homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/

version toolchain
1.0 GCC/7.3.0-2.30
2.2-4 GCC/9.3.0

AMD-uProf

AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance.

homepage: https://developer.amd.com/amd-uprof/

version toolchain
3.4.502 system
3.5.671 system
4.1.424 system

AMICA

Code for AMICA: Adaptive Mixture ICA with shared components

homepage: https://github.com/sccn/amica

version toolchain
2024.1.19 intel/2023a

AMOS

The AMOS consortium is committed to the development of open-source whole genome assembly software

homepage: http://amos.sourceforge.net

version toolchain
3.1.0 foss/2018b, foss/2021b, foss/2023a

AMPHORA2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

homepage: https://github.com/wu-lab-uva/AMPHORA2

version versionsuffix toolchain
20190730 -Java-13-pthreads-avx2 gompi/2020b

AMPL-MP

An open-source library for mathematical programming.

homepage: https://github.com/ampl/mp

version toolchain
3.1.0 GCCcore/6.4.0

amplimap

amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing (NGS) experiments with PCR-based amplicons or capture-based enrichment systems.

homepage: https://amplimap.readthedocs.io/en/latest/

version versionsuffix toolchain
0.4.16 -Python-3.6.6 foss/2018b

AMPtk

AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.

homepage: https://amptk.readthedocs.io

version toolchain
1.5.4 foss/2021b

AMRFinderPlus

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

version toolchain
3.11.18 gompi/2021b, gompi/2022b

AmrPlusPlus

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

version toolchain
2.0-20200114 GCC/8.3.0

AMS

The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.

homepage: https://www.scm.com/amsterdam-modeling-suite/

version versionsuffix toolchain
2020.102 -intelmpi iimpi/2020b
2022.102 -intelmpi iimpi/2021b
2023.101 -intelmpi iimpi/2022a
2023.104 -intelmpi iimpi/2022b

Anaconda2

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

homepage: https://www.anaconda.com

version toolchain
4.0.0 system
4.2.0 system
4.4.0 system
5.0.1 system
5.1.0 system
5.3.0 system
2018.12 system
2019.03 system
2019.07 system
2019.10 system

Anaconda3

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

homepage: https://www.anaconda.com

version toolchain
4.0.0 system
4.2.0 system
4.4.0 system
5.0.1 system
5.1.0 system
5.3.0 system
2018.12 system
2019.03 system
2019.07 system
2019.10 system
2020.02 system
2020.07 system
2020.11 system
2021.05 system
2021.11 system
2022.05 system
2022.10 system
2023.03-1 system
2023.07-2 system
2023.09-0 system
2024.02-1 system

anadama2

AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to create reproducible workflows and execute them efficiently.

homepage: http://huttenhower.sph.harvard.edu/anadama2

version toolchain
0.10.0 foss/2022a

aNCI

Non-covalent interaction (NCI) for MD trajectories

homepage: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html

version toolchain
2.0 iccifort/2019.5.281

andi

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

homepage: https://github.com/evolbioinf/andi/

version toolchain
0.13 foss/2018b

ANGEL

ANGEL: Robust Open Reading Frame prediction

homepage: https://github.com/PacificBiosciences/ANGEL

version versionsuffix toolchain
3.0 -Python-3.7.2 foss/2019a

angsd

Program for analysing NGS data.

homepage: http://www.popgen.dk/angsd

version toolchain
0.910 foss/2016a
0.921 foss/2018a
0.925 foss/2018b
0.933 GCC/8.3.0, iccifort/2019.5.281
0.935 GCC/10.2.0
0.940 GCC/11.2.0, GCC/12.3.0

ANIcalculator

This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.

homepage: https://ani.jgi.doe.gov/html/home.php

version toolchain
1.0 GCCcore/10.3.0, GCCcore/11.3.0

anndata

anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray

homepage: https://github.com/scverse/anndata

version toolchain
0.8.0 foss/2022a
0.9.2 foss/2021a
0.10.5.post1 foss/2023a

Annif

Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums.

homepage: https://github.com/NatLibFi/Annif

version versionsuffix toolchain
0.40.0 -Python-3.7.2 foss/2019a, intel/2019a

Annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. Annocript also gives information about the longest ORF and the non-coding potential using external software. Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology and sequence features.

homepage: https://github.com/frankMusacchia/Annocript

version toolchain
2.0 foss/2022a

annovar

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

homepage: http://annovar.openbioinformatics.org/en/latest/

version versionsuffix toolchain
2016Feb01 -Perl-5.22.1 foss/2016a
20191024 -Perl-5.28.1 GCCcore/8.2.0
20200607 -Perl-5.34.0 GCCcore/11.2.0

ANSYS

ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.

homepage: https://www.ansys.com

version toolchain
15.0 system
2022R2 system
2023R1 system

ANSYS_CFD

ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.

homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics

version toolchain
16.2 system
17.0 system

ant

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.

homepage: http://ant.apache.org/

version versionsuffix toolchain
1.8.4 -Java-1.7.0_10 system
1.8.4 -Java-1.7.0_21 system
1.9.0 -Java-1.7.0_15 system
1.9.0 -Java-1.7.0_21 system
1.9.3 -Java-1.7.0_60 system
1.9.3 -Java-1.7.0_79 system
1.9.6 -Java-1.7.0_75 system
1.9.6 -Java-1.7.0_79 system
1.9.6 -Java-1.7.0_80 system
1.9.6 -Java-1.8.0_66 system
1.9.6 -Java-1.8.0_72 system
1.9.6 -Java-1.8.0_77 system
1.9.7 -Java-1.8.0_92 system
1.10.0 -Java-1.8.0_112 system
1.10.1 -Java-1.8 system
1.10.1 -Java-1.8.0_121 system
1.10.1 -Java-1.8.0_144 system
1.10.1 -Java-1.8.0_152 system
1.10.1 -Java-1.8.0_162 system
1.10.5 -Java-1.8 system
1.10.6 -Java-1.8 system
1.10.7 -Java-11 system
1.10.8 -Java-11 system
1.10.9 -Java-11 system
1.10.11 -Java-11 system
1.10.11 -Java-13 system
1.10.12 -Java-11 system
1.10.12 -Java-17 system
1.10.14 -Java-11 system
1.10.14 -Java-21 system

ANTIC

Antic is an algebraic number theory library.

homepage: https://github.com/flintlib/antic

version toolchain
0.2.5 gfbf/2022a

antiSMASH

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

homepage: https://github.com/antismash/antismash

version versionsuffix toolchain
5.1.2 -Python-3.7.4 foss/2019b
5.2.0 foss/2020b
6.0.1 foss/2020b

ANTLR

ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.

homepage: http://www.antlr2.org/

version versionsuffix toolchain
2.7.7 GCCcore/7.3.0, GCCcore/8.2.0, foss/2017b, foss/2018b, foss/2019a, intel/2017b
2.7.7 -Java-11 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0
2.7.7 -Python-2.7.11 foss/2016a
2.7.7 -Python-2.7.13 intel/2017a
2.7.7 -Python-2.7.14 foss/2018a, intel/2017b
2.7.7 -Python-3.6.4 intel/2018a

ANTs

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/

version versionsuffix toolchain
2.2.0 -Python-2.7.12 foss/2016b
2.3.0 -Python-2.7.14 foss/2017b, intel/2017b
2.3.1 -Python-3.6.6 foss/2018b
2.3.2 -Python-3.7.4 foss/2019b
2.3.5 foss/2021a
2.5.0 foss/2022b

anvio

An analysis and visualization platform for 'omics data.

homepage: https://merenlab.org/software/anvio/

version versionsuffix toolchain
6.1 -Python-3.7.4 intel/2019b
8 foss/2022b

any2fasta

Convert various sequence formats to FASTA

homepage: https://github.com/tseemann/any2fasta

version versionsuffix toolchain
0.4.2 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.4.2 -Perl-5.28.1 GCCcore/8.2.0

AOCC

AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

homepage: https://developer.amd.com/amd-aocc/

version toolchain
2.3.0 GCCcore/10.2.0, GCCcore/9.3.0
3.0.0 GCCcore/10.2.0, GCCcore/10.3.0
3.1.0 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
3.2.0 GCCcore/11.2.0, GCCcore/11.3.0
4.0.0 GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

AOFlagger

The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.

homepage: https://aoflagger.readthedocs.io/

version toolchain
3.4.0 foss/2022a, foss/2023b

AOMP

AMD fork of LLVM, setup for OpenMP offloading to Accelerators

homepage: https://github.com/ROCm-Developer-Tools/aomp

version toolchain
13.0-2 GCCcore/10.2.0, gcccuda/2020a

APBS

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

version versionsuffix toolchain
1.4 -linux-static-x86_64 system

apex

A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch

homepage: https://github.com/nvidia/apex

version versionsuffix toolchain
20200325 -Python-3.7.4 fosscuda/2019b
20210420 fosscuda/2020b

APR

Apache Portable Runtime (APR) libraries.

homepage: https://apr.apache.org/

version toolchain
1.6.3 GCCcore/6.4.0, GCCcore/7.3.0, iomkl/2018a
1.7.0 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.2.0, GCCcore/9.3.0
1.7.4 GCCcore/12.3.0

APR-util

Apache Portable Runtime (APR) util libraries.

homepage: https://apr.apache.org/

version toolchain
1.6.1 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/9.3.0, iomkl/2018a
1.6.3 GCCcore/12.3.0

AptaSUITE

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments

homepage: https://drivenbyentropy.github.io/

version versionsuffix toolchain
0.9.4 -Java-11 system

ARAGORN

a program to detect tRNA genes and tmRNA genes in nucleotide sequences

homepage: http://www.ansikte.se/ARAGORN/

version toolchain
1.2.38 foss/2016b, iccifort/2019.5.281
1.2.41 foss/2021b

Arb

Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.

homepage: https://arblib.org/

version toolchain
2.16.0 GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, iccifort/2018.3.222-GCC-7.3.0-2.30
2.17.0 GCC/8.3.0
2.19.0 GCC/10.3.0
2.22.1 foss/2021b
2.23.0 gfbf/2022a

Arcade-Learning-Environment

The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE.

homepage: https://github.com/mgbellemare/Arcade-Learning-Environment

version toolchain
0.7.3 foss/2021b
0.8.1 foss/2022a

arcasHLA

arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.

homepage: https://github.com/RabadanLab/arcasHLA

version versionsuffix toolchain
0.2.0 -Python-3.7.4 foss/2019b

ARCH

Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance).

homepage: https://pypi.org/project/arch

version versionsuffix toolchain
4.5.0 -Python-3.6.4 intel/2018a

Archive-Zip

Provide an interface to ZIP archive files.

homepage: https://metacpan.org/pod/Archive::Zip

version toolchain
1.68 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0

ArchR

ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data.

homepage: https://www.archrproject.com

version versionsuffix toolchain
1.0.1 -R-4.1.2 foss/2021b
1.0.2 -R-4.3.2 foss/2023a

archspec

A library for detecting, labeling, and reasoning about microarchitectures

homepage: https://github.com/archspec/archspec

version versionsuffix toolchain
0.1.0 -Python-3.7.4 GCCcore/8.3.0
0.1.0 -Python-3.8.2 GCCcore/9.3.0
0.1.2 GCCcore/10.2.0, GCCcore/10.3.0
0.1.3 GCCcore/11.2.0
0.1.4 GCCcore/11.3.0
0.2.0 GCCcore/12.2.0
0.2.1 GCCcore/12.3.0
0.2.2 GCCcore/13.2.0

AreTomo2

AreTomo2, a multi-GPU accelerated software package that fully automates motion- corrected marker-free tomographic alignment and reconstruction, now includes robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single package. AreTomo2 is part of our endeavor to build a fully-automated high- throughput processing pipeline that enables real-time reconstruction of tomograms in parallel with tomographic data collection. It strives to be fast and accurate, as well as provides for easy integration into subtomogram processing workflows by generating IMod compatible files containing alignment and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also be used for on-the-fly reconstruction of tomograms and CTF estimation in parallel with tilt series collection, enabling real-time assessment of sample quality and adjustment of collection parameters

homepage: https://github.com/czimaginginstitute/AreTomo2

version versionsuffix toolchain
1.0.0 -CUDA-12.1.1 GCCcore/12.3.0

ARGoS

A parallel, multi-engine simulator for heterogeneous swarm robotics

homepage: http://www.argos-sim.info

version versionsuffix toolchain
3.0.0-beta53 -Lua-5.2.4 foss/2018b
3.0.0-beta59 GCC/11.2.0

argtable

Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

homepage: https://argtable.sourceforge.io/

version toolchain
2.13 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016b, foss/2018b, intel/2018a, intel/2018b

aria2

aria2 is a lightweight multi-protocol & multi-source command-line download utility.

homepage: https://aria2.github.io

version toolchain
1.35.0 GCCcore/10.3.0
1.36.0 GCCcore/11.3.0

Arlequin

Arlequin: An Integrated Software for Population Genetics Data Analysis

homepage: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html

version toolchain
3.5.2.2 foss/2019b

Armadillo

Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.

homepage: https://arma.sourceforge.net/

version versionsuffix toolchain
7.600.2 -Python-2.7.12 foss/2016b
7.800.0 -Python-2.7.12 intel/2016b
7.950.1 -Python-2.7.12 intel/2016b
8.300.1 foss/2017b, intel/2017b
8.400.0 foss/2018a
9.600.5 foss/2018b
9.700.2 foss/2019a
9.880.1 foss/2020a
9.900.1 foss/2019b, foss/2020a
10.5.3 foss/2020b
10.7.5 foss/2021a
11.4.3 foss/2022a, foss/2022b
12.6.2 foss/2023a
12.8.0 foss/2023b

arosics

AROSICS is a python package to perform automatic subpixel co-registration of two satellite image datasets based on an image matching approach working in the frequency domain, combined with a multistage workflow for effective detection of false-positives.

homepage: https://github.com/GFZ/arosics

version toolchain
1.7.6 foss/2021a

ARPACK++

Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems.

homepage: https://github.com/m-reuter/arpackpp

version toolchain
2018.03.26 foss/2017b

arpack-ng

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

homepage: https://github.com/opencollab/arpack-ng

version toolchain
3.3.0 foss/2016a, intel/2016a
3.4.0 foss/2016b, foss/2017a, intel/2016b, intel/2017a
3.5.0 foss/2017b, foss/2018a, foss/2018b, intel/2017a, intel/2017b
3.6.2 intel/2018a
3.7.0 foss/2019a, foss/2019b, foss/2020a, intel/2019b, intel/2020a
3.8.0 foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2022b
3.9.0 foss/2023a, foss/2023b
3.9.1 foss/2023b

ArrayFire

ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.

homepage: https://arrayfire.com/

version versionsuffix toolchain
3.6.4 foss/2018b
3.6.4 -CUDA-9.2.88 foss/2018b

Arriba

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.

homepage: https://github.com/suhrig/arriba

version toolchain
1.1.0 foss/2018b
2.1.0 GCC/10.2.0, GCC/10.3.0
2.2.1 GCC/11.2.0
2.3.0 GCC/11.2.0
2.4.0 GCC/12.2.0

Arrow

Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.

homepage: https://arrow.apache.org

version versionsuffix toolchain
0.7.1 -Python-3.6.3 intel/2017b
0.12.0 -Python-2.7.15 foss/2018b, intel/2018b
0.12.0 -Python-3.6.6 intel/2018b
0.16.0 -Python-3.7.4 foss/2019b, intel/2019b
0.17.1 foss/2020b, fosscuda/2020b, intel/2020b
0.17.1 -Python-3.8.2 foss/2020a, intel/2020a
6.0.0 foss/2021a, foss/2021b
6.0.1 foss/2021a
8.0.0 foss/2021a, foss/2021b, foss/2022.05, foss/2022a
11.0.0 gfbf/2022b
14.0.1 gfbf/2023a

arrow-R

R interface to the Apache Arrow C++ library

homepage: https://cran.r-project.org/web/packages/arrow

version versionsuffix toolchain
0.17.1 -R-4.0.0 foss/2020a
6.0.0.2 -R-4.1.0 foss/2021a
6.0.0.2 -R-4.1.2 foss/2021b
6.0.0.2 -R-4.2.0 foss/2021b
8.0.0 -R-4.2.1 foss/2022a
11.0.0.3 -R-4.2.2 foss/2022b
14.0.0.2 -R-4.3.2 foss/2023a

ART

ART is a set of simulation tools to generate synthetic next-generation sequencing reads

homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

version toolchain
2016.06.05 GCCcore/6.4.0, intel/2016b

Artemis

The Artemis Software is a set of software tools for genome browsing and annotation. It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter.

homepage: http://sanger-pathogens.github.io/Artemis/

version versionsuffix toolchain
18.0.2 -Java-11 system
18.0.3 -Java-11 system
18.2.0 -Java-11 system

artic-ncov2019

Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus.

homepage: https://github.com/artic-network/artic-ncov2019

version versionsuffix toolchain
2020.04.13 -Python-3.6.6 foss/2018b
2021.06.24 foss/2020b

ARTS

ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors.

homepage: http://www.radiativetransfer.org/

version toolchain
2.2.64 gompi/2019a

ArviZ

Exploratory analysis of Bayesian models with Python

homepage: https://github.com/arviz-devs/arviz

version versionsuffix toolchain
0.7.0 -Python-3.7.4 foss/2019b, intel/2019b
0.11.1 intel/2020b
0.11.4 foss/2021b, intel/2021b
0.12.1 foss/2021a, foss/2022a, intel/2022a
0.16.1 foss/2023a

ARWEN

ARWEN, tRNA detection in metazoan mitochondrial sequences

homepage: http://mbio-serv2.mbioekol.lu.se/ARWEN

version toolchain
1.2.3 GCCcore/7.3.0

ASAP

ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.

homepage: https://computationalpathologygroup.github.io/ASAP/

version versionsuffix toolchain
2.0 -CUDA-11.3.1 foss/2021a
2.1 foss/2022a

ASAP3

ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE).

homepage: https://wiki.fysik.dtu.dk/asap/

version versionsuffix toolchain
3.10.7 -Python-3.5.2 foss/2016b
3.10.7 -Python-3.6.2 foss/2017b
3.10.8 -Python-3.5.2 foss/2016b
3.10.8 -Python-3.6.2 foss/2017b
3.10.8 -Python-3.6.3 foss/2017b
3.10.10 -Python-3.6.6 foss/2018b, intel/2018b, iomkl/2018b
3.11.10 -Python-3.7.2 foss/2019a, intel/2019a
3.12.2 -ASE-3.21.1 foss/2020b, intel/2020b
3.12.7 -ASE-3.21.1 foss/2020b, intel/2020b
3.13.2 foss/2023a
3.13.3 foss/2023a, intel/2023a

ASCAT

ASCAT is a method to derive copy number profiles of tumor cells, accounting for normal cell admixture and tumor aneuploidy.

homepage: https://github.com/VanLoo-lab/ascat

version versionsuffix toolchain
3.1.2 -R-4.2.1 foss/2022a
3.1.2 -R-4.2.2 foss/2022b

ASE

ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.

homepage: https://wiki.fysik.dtu.dk/ase/

version versionsuffix toolchain
3.9.1.4567 -Python-2.7.11 intel/2016a
3.10.0 -Python-2.7.11 intel/2016.02-GCC-4.9
3.11.0 -Python-2.7.12 intel/2016b
3.13.0 -Python-2.7.12 foss/2016b
3.13.0 -Python-2.7.13 intel/2017a
3.15.0 -Python-2.7.12 foss/2016b
3.15.0 -Python-2.7.14 intel/2017b
3.15.0 -Python-3.5.2 foss/2016b
3.15.0 -Python-3.6.2 foss/2017b
3.15.0 -Python-3.6.3 foss/2017b
3.16.2 -Python-3.6.4 iomkl/2018.02, iomkl/2018a
3.16.2 -Python-3.6.6 foss/2018b, intel/2018b, iomkl/2018b
3.17.0 -Python-3.6.6 foss/2018b, intel/2018b, iomkl/2018b
3.17.0 -Python-3.7.2 foss/2019a, intel/2019a
3.18.0 -Python-3.6.6 foss/2018b, intel/2018b
3.18.0 -Python-3.7.2 foss/2019a, intel/2019a
3.19.0 -Python-3.6.6 foss/2018b, intel/2018b
3.19.0 -Python-3.7.4 foss/2019b, fosscuda/2019b, intel/2019b
3.19.0 -Python-3.8.2 foss/2020a, intel/2020a
3.20.1 foss/2020b, fosscuda/2020b, intel/2020b
3.20.1 -Python-3.7.4 foss/2019b, intel/2019b
3.20.1 -Python-3.8.2 intel/2020a
3.21.1 foss/2020b, fosscuda/2020b, intel/2020b
3.21.1 -Python-3.8.2 foss/2020a
3.22.0 foss/2020b, foss/2021a, fosscuda/2020b, intel/2020b, intel/2021a
3.22.1 foss/2021b, foss/2022a, gfbf/2022b, gfbf/2023a, gomkl/2021a, iimkl/2023a, intel/2021b, intel/2022a

ASF-SearchAPI

asf_search is a Python module for performing searches of the ASF catalog. In addition, it offers baseline functionality and download support.

homepage: https://docs.asf.alaska.edu/

version toolchain
6.5.0 foss/2022a

ASHS

Automatic Segmentation of Hippocampal Subfields (ASHS)

homepage: https://sites.google.com/site/hipposubfields/home

version toolchain
rev103_20140612 system

Aspera-CLI

IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

homepage: https://asperasoft.com

version versionsuffix toolchain
3.7.2 .354.010c3b8 system
3.9.0 .1326.6985b21 system
3.9.6 .1467.159c5b1 system

Aspera-Connect

Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.

homepage: http://downloads.asperasoft.com/connect2/

version toolchain
3.6.1 system
3.9.6 system

assimp

Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.

homepage: https://github.com/assimp/assimp

version toolchain
5.0.1 GCCcore/8.3.0
5.2.5 GCCcore/12.3.0
5.3.1 GCCcore/13.2.0

Assimulo

Assimulo is a simulation package for solving ordinary differential equations.

homepage: https://jmodelica.org/assimulo/

version versionsuffix toolchain
2.9 -Python-2.7.15 intel/2018b

ASTRID

ASTRID-2 is a method for estimating species trees from gene trees.

homepage: https://github.com/pranjalv123/ASTRID

version toolchain
2.2.1 gompi/2019a

astro-tulips

tulips creates diagrams of the structure and evolution of stars. It creates plots and movies based on output from the MESA stellar evolution code

homepage: https://astro-tulips.readthedocs.io/en/latest/installation.html

version toolchain
1.0.1 foss/2022a

astropy

The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion.

homepage: https://www.astropy.org/

version versionsuffix toolchain
2.0.12 -Python-2.7.15 foss/2018b, intel/2018b
2.0.14 foss/2019a
4.0.1 -Python-3.7.4 foss/2019b
4.0.1 -Python-3.8.2 foss/2020a, intel/2020a
4.2.1 foss/2020b, intel/2020b, intelcuda/2020b
4.3.1 foss/2021a, foss/2021b, intel/2021a
5.0.4 foss/2021a
5.1.1 foss/2022a
5.2.2 gfbf/2022b

at-spi2-atk

AT-SPI 2 toolkit bridge

homepage: https://wiki.gnome.org/Accessibility

version toolchain
2.26.3 fosscuda/2018b
2.32.0 GCCcore/8.2.0
2.34.1 GCCcore/8.3.0
2.34.2 GCCcore/9.3.0
2.38.0 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

at-spi2-core

Assistive Technology Service Provider Interface.

homepage: https://wiki.gnome.org/Accessibility

version toolchain
2.26.3 fosscuda/2018b
2.32.0 GCCcore/8.2.0
2.34.0 GCCcore/8.3.0
2.36.0 GCCcore/9.3.0
2.38.0 GCCcore/10.2.0
2.40.2 GCCcore/10.3.0
2.40.3 GCCcore/11.2.0
2.44.1 GCCcore/11.3.0
2.46.0 GCCcore/12.2.0
2.49.91 GCCcore/12.3.0
2.50.0 GCCcore/13.2.0

ATAT

The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools

homepage: https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/

version toolchain
3.36 GCCcore/9.3.0

ATK

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

homepage: https://developer.gnome.org/atk/

version toolchain
2.18.0 intel/2016a
2.20.0 foss/2016a, intel/2016a
2.22.0 foss/2016b, intel/2016b
2.26.0 intel/2017a
2.26.1 foss/2018b, intel/2017b
2.27.1 foss/2017b, intel/2017b
2.28.1 foss/2018a, foss/2018b, fosscuda/2018b, intel/2018a
2.32.0 GCCcore/8.2.0
2.34.1 GCCcore/8.3.0
2.36.0 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
2.38.0 GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

ATLAS

ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.

homepage: http://math-atlas.sourceforge.net

version versionsuffix toolchain
3.10.2 -LAPACK-3.6.1 GCC/5.4.0-2.26

atomate

atomate has implementations of FireWorks workflows for Materials Science.

homepage: https://pythonhosted.org/atomate/

version versionsuffix toolchain
0.4.4 -Python-2.7.13 intel/2017a

AtomPAW

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

version toolchain
4.1.0.5 intel/2018b
4.1.0.6 intel/2018b

atools

Tools to make using job arrays a lot more convenient.

homepage: https://github.com/gjbex/atools

version versionsuffix toolchain
1.4.2 -Python-2.7.12 intel/2016b
1.4.6 -Python-2.7.16 GCCcore/8.3.0
1.4.8 -Python-2.7.18 GCCcore/10.3.0, GCCcore/11.2.0
1.5.1 GCCcore/11.2.0, GCCcore/12.3.0, GCCcore/13.2.0

atropos

Atropos is tool for specific, sensitive, and speedy trimming of NGS reads.

homepage: https://atropos.readthedocs.io

version versionsuffix toolchain
1.1.21 -Python-3.6.6 intel/2018b

ATSAS

ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.

homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

version versionsuffix toolchain
2.5.1-1 .el6.x86_64 system
2.5.1-1 .sl5.x86_64 system
2.7.1-1 .el7.x86_64 system

attr

Commands for Manipulating Filesystem Extended Attributes

homepage: https://savannah.nongnu.org/projects/attr

version toolchain
2.4.47 GCCcore/8.2.0
2.4.48 GCCcore/9.3.0
2.5.1 GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

attrdict

AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.

homepage: https://github.com/bcj/AttrDict

version versionsuffix toolchain
2.0.1 -Python-3.7.4 GCCcore/8.3.0

attrdict3

AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.

homepage: https://github.com/pirofti/AttrDict3

version toolchain
2.0.2 GCCcore/11.2.0, GCCcore/11.3.0

augur

Pipeline components for real-time phylodynamic analysis

homepage: https://github.com/nextstrain/augur

version versionsuffix toolchain
7.0.2 -Python-3.7.4 intel/2019b

AUGUSTUS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

homepage: https://bioinf.uni-greifswald.de/augustus/

version versionsuffix toolchain
3.2.3 -Python-2.7.13 intel/2017a
3.3 foss/2018a
3.3.2 intel/2019a
3.3.2 -Python-2.7.13 intel/2017a
3.3.2 -Python-2.7.14 foss/2017b, intel/2017b
3.3.2 -Python-2.7.15 intel/2018b
3.3.3 foss/2019b, intel/2019b
3.4.0 foss/2020a, foss/2020b, foss/2021a, foss/2021b
3.5.0 foss/2022a, foss/2022b

Austin

Austin is a Python frame stack sampler for CPython written in pure C.

homepage: https://github.com/P403n1x87/austin

version toolchain
3.2.0 GCCcore/11.2.0, system

AUTO-07p

AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.

homepage: https://github.com/auto-07p

version toolchain
0.9.3 foss/2021a

Autoconf

Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.

homepage: https://www.gnu.org/software/autoconf/

version toolchain
2.68 foss/2016b
2.69 GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/10.2.0, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.71 FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Autoconf-archive

The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software.

homepage: https://www.gnu.org/software/autoconf-archive

version toolchain
2019.01.06 GCC/8.2.0-2.31.1
2021.02.19 GCCcore/10.2.0
2023.02.20 GCCcore/11.3.0

AutoDock

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: http://autodock.scripps.edu/

version toolchain
4.2.5.1 GCC/5.2.0
4.2.6 GCC/10.3.0

AutoDock-GPU

OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

homepage: https://github.com/ccsb-scripps/AutoDock-GPU

version versionsuffix toolchain
1.5.3 -CUDA-11.3.1 GCC/10.3.0
1.5.3 -CUDA-11.7.0 GCC/11.3.0

AutoDock-Vina

AutoDock Vina is an open-source program for doing molecular docking.

homepage: https://vina.scripps.edu/

version versionsuffix toolchain
1.1.2 -linux_x86 system
1.2.3 foss/2021a, foss/2021b

AutoDockSuite

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://autodock.scripps.edu/

version toolchain
4.2.6 GCCcore/8.3.0

AutoGeneS

AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples.

homepage: https://github.com/theislab/AutoGeneS

version toolchain
1.0.4 foss/2020b

AutoGrid

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: http://autodock.scripps.edu/

version toolchain
4.2.5.1 GCC/5.2.0

Automake

Automake: GNU Standards-compliant Makefile generator

homepage: https://www.gnu.org/software/automake/automake.html

version toolchain
1.11.3 foss/2016b
1.14 GCC/4.8.2, intel/2016a
1.14.1 GCC/4.8.2
1.15 GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.15.1 GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.3.0
1.16.1 GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0
1.16.2 GCCcore/10.2.0
1.16.3 FCC/4.5.0, GCCcore/10.3.0
1.16.4 GCCcore/11.2.0
1.16.5 GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.

homepage: https://github.com/mquinodo/AutoMap

version versionsuffix toolchain
1.0 -20200324 foss/2019b

autopep8

A tool that automatically formats Python code to conform to the PEP 8 style guide.

homepage: https://github.com/hhatto/autopep8

version versionsuffix toolchain
1.4.4 -Python-3.6.4 intel/2018a
2.0.4 foss/2022a

Autotools

This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

homepage: https://autotools.io

version toolchain
20150119 GCC/4.9.2
20150215 GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
20170619 GCCcore/6.4.0, GCCcore/7.2.0
20180311 GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0
20200321 GCCcore/10.2.0
20210128 FCC/4.5.0, GCCcore/10.3.0
20210726 GCCcore/11.2.0
20220317 GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Avogadro2

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

homepage: https://two.avogadro.cc/index.html

version versionsuffix toolchain
1.97.0 -linux-x86_64 system

avro-cpp

C++ implementation of Avro data serialization system.

homepage: https://avro.apache.org

version toolchain
1.11.1 GCC/11.2.0

awscli

Universal Command Line Environment for AWS

homepage: https://pypi.python.org/pypi/awscli

version versionsuffix toolchain
1.11.1 -Python-2.7.12 intel/2016b
1.11.56 -Python-2.7.12 foss/2016b
1.16.290 -Python-3.6.6 foss/2018b
1.17.7 -Python-3.7.4 GCCcore/8.3.0
1.18.89 -Python-3.8.2 GCCcore/9.3.0
2.0.55 -Python-3.8.2 GCCcore/9.3.0
2.11.21 GCCcore/11.3.0
2.15.2 GCCcore/12.2.0

Ax

Ax is an accessible, general-purpose platform for understanding, managing, deploying, and automating adaptive experiments. Adaptive experimentation is the machine-learning guided process of iteratively exploring a (possibly infinite) parameter space in order to identify optimal configurations in a resource-efficient manner. Ax currently supports Bayesian optimization and bandit optimization as exploration strategies. Bayesian optimization in Ax is powered by BoTorch, a modern library for Bayesian optimization research built on PyTorch.

homepage: https://ax.dev/

version toolchain
0.3.3 foss/2022a

axel

Lightweight CLI download accelerator

homepage: https://github.com/axel-download-accelerator/axel

version toolchain
2.17.9 GCCcore/8.3.0, GCCcore/9.3.0

B

BA3-SNPS-autotune - BabelStream - babl - Bader - BAGEL - BAli-Phy - bam-readcount - Bambi - bamFilters - BAMM - BAMSurgeon - bamtofastq - BamTools - BamUtil - Bandage - barrnap - basemap - bases2fastq - Bash - bashplotlib - bat - batchgenerators - BatMeth2 - BayesAss - BayesAss3-SNPs - BayeScan - BayeScEnv - BayesPrism - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - bcbio-gff - BCEL - BCFtools - bcgTree - bcl-convert - bcl2fastq2 - bcolz - bcrypt - BDBag - Beagle - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - BEEF - behave - bench - BerkeleyGW - BFAST - BFC - BGC-Bayesian-genomic-clines - BgeeCall - BgeeDB - bgen - bgen-reader - BiasAdjustCXX - bibtexparser - BiG-SCAPE - BigDFT - BinSanity - binutils - Bio-DB-HTS - Bio-EUtilities - Bio-SamTools - Bio-SearchIO-hmmer - bioawk - biobakery-workflows - biobambam2 - biogeme - biom-format - biomart-perl - BioPerl - BioPP - Biopython - BioServices - BirdNET - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Block - Blosc - Blosc2 - BLT - bmtagger - BMTK - bnpy - BOINC - bokeh - BoltzTraP - BoltzTraP2 - Bonito - Bonmin - Bonnie++ - Boost - Boost.MPI - Boost.Python - Boost.Python-NumPy - boost_histogram - BOPTEST - boto3 - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - Braindecode - BRAKER - BreakDancer - breseq - BRiAl - Brotli - Brotli-python - Brunsli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - btllib - BuDDy - BUFRLIB - build - buildenv - buildingspy - Bullet - BUSCO - BUStools - BWA - bwa-mem2 - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2

BA3-SNPS-autotune

This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS.

homepage: https://github.com/stevemussmann/BA3-SNPS-autotune

version toolchain
2.1.2 GCC/11.3.0

BabelStream

STREAM, for lots of devices written in many programming models

homepage: https://uob-hpc.github.io/BabelStream

version versionsuffix toolchain
3.4 -omp GCC/11.2.0

babl

babl is pixel encoding and color space conversion engine in C

homepage: https://www.gegl.org/babl

version toolchain
0.1.86 GCCcore/10.3.0

Bader

A fast algorithm for doing Bader's analysis on a charge density grid.

homepage: http://theory.cm.utexas.edu/henkelman/code/bader/

version toolchain
1.02 intel/2018a
1.03 intel/2018b
1.04 GCC/11.2.0, iccifort/2020.4.304

BAGEL

BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program.

homepage: http://www.nubakery.org

version toolchain
1.1.1 intel/2016b
1.2.2 foss/2021a, foss/2023a

BAli-Phy

BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.

homepage: http://www.bali-phy.org/

version toolchain
3.6.0 system

bam-readcount

Count DNA sequence reads in BAM files

homepage: https://github.com/genome/bam-readcount

version toolchain
0.8.0 GCC/11.2.0, GCC/9.3.0, foss/2018b
1.0.1 GCC/12.2.0

Bambi

Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines.

homepage: https://bambinos.github.io/bambi

version toolchain
0.7.1 foss/2021b, intel/2021b

bamFilters

A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage.

homepage: https://github.com/institut-de-genomique/bamFilters

version toolchain
2022-06-30 GCC/11.3.0

BAMM

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/

version toolchain
2.5.0 foss/2022a

BAMSurgeon

Tools for adding mutations to existing .bam files, used for testing mutation callers

homepage: https://github.com/adamewing/bamsurgeon

version versionsuffix toolchain
1.2 -Python-2.7.16 GCC/8.3.0

bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.

homepage: https://github.com/10XGenomics/bamtofastq

version toolchain
1.4.0 GCCcore/10.3.0

BamTools

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

homepage: https://github.com/pezmaster31/bamtools

version toolchain
2.4.0 foss/2016b
2.4.1 intel/2017a
2.5.0 foss/2016b, intel/2017b
2.5.1 GCC/10.2.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, iccifort/2020.4.304, intel/2017b, intel/2018b
2.5.2 GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0

BamUtil

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

version toolchain
1.0.13 intel/2016b
1.0.14 intel/2018a

Bandage

Bandage is a program for visualising de novo assembly graphs

homepage: http://rrwick.github.io/Bandage

version versionsuffix toolchain
0.8.1 _Centos system
0.8.1 _Ubuntu system
0.9.0 GCCcore/11.2.0, GCCcore/11.3.0

barrnap

Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.

homepage: https://github.com/tseemann/barrnap

version toolchain
0.9 GCC/8.2.0-2.31.1, foss/2018b, gompi/2020b, gompi/2021b, gompi/2022a

basemap

The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python

homepage: https://matplotlib.org/basemap/

version versionsuffix toolchain
1.0.7 -Python-2.7.13 intel/2017a
1.0.7 -Python-3.6.3 intel/2017b
1.0.7 -Python-3.6.4 intel/2018a
1.2.0 -Python-3.6.6 intel/2018b
1.2.2 -Python-3.8.2 foss/2020a
1.3.6 foss/2022a
1.3.9 foss/2023a

bases2fastq

Bases2Fastq Software demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. The Element AVITI™ System records base calls, which are the main output of a sequencing run, with associated quality scores (Q-scores) in bases files. Bases files must be converted into the FASTQ file format for secondary analysis. To generate QC reports, also load BeautifulSoup and bokeh.

homepage: https://docs.elembio.io/docs/bases2fastq

version toolchain
1.5.1 system

Bash

Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).

homepage: http://www.gnu.org/software/bash

version toolchain
4.3 GCC/4.9.2

bashplotlib

bashplotlib is a python package and command line tool for making basic plots in the terminal. It's a quick way to visualize data when you don't have a GUI.

homepage: https://github.com/glamp/bashplotlib

version toolchain
0.6.5 GCCcore/10.3.0

bat

The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark

homepage: https://pypi.python.org/pypi/bat

version versionsuffix toolchain
0.3.3 -Python-3.6.3 intel/2017b

batchgenerators

Data augmentation toolkit developed at the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) to suit all our deep learning data augmentation needs.

homepage: https://github.com/MIC-DKFZ/batchgenerators

version toolchain
0.25 foss/2021a

BatMeth2

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

homepage: https://github.com/GuoliangLi-HZAU/BatMeth2

version toolchain
2.1 foss/2019b

BayesAss

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

homepage: http://www.rannala.org/?page_id=245

version toolchain
3.0.4 foss/2016a

BayesAss3-SNPs

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols.

homepage: https://github.com/stevemussmann/BayesAss3-SNPs

version toolchain
1.1 GCC/11.3.0

BayeScan

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/

version toolchain
2.1 foss/2016a, foss/2018a, intel/2018a

BayeScEnv

BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.

homepage: https://github.com/devillemereuil/bayescenv

version toolchain
1.1 GCC/8.3.0, foss/2016a, iccifort/2019.5.281

BayesPrism

Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

homepage: https://github.com/Danko-Lab/BayesPrism

version versionsuffix toolchain
2.0 -R-4.2.1 foss/2022a

BayesTraits

BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

homepage: https://github.com/AndrewPMeade/BayesTraits-Public

version versionsuffix toolchain
1.0-linux32 system
2.0 -Beta-Linux64 system
3.0.2 -Linux system

Bazel

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/

version versionsuffix toolchain
0.4.4 system
0.7.0 GCCcore/6.4.0
0.10.0 GCCcore/6.4.0
0.11.0 GCCcore/6.4.0
0.11.1 GCCcore/6.4.0
0.12.0 GCCcore/6.4.0
0.16.0 GCCcore/6.4.0, GCCcore/7.3.0
0.18.0 GCCcore/7.3.0
0.20.0 GCCcore/7.3.0, GCCcore/8.2.0
0.25.2 GCCcore/8.2.0
0.26.1 GCCcore/8.2.0, GCCcore/8.3.0
0.29.1 GCCcore/8.2.0, GCCcore/8.3.0
0.29.1 -Java-1.8 GCCcore/9.3.0
1.1.0 GCCcore/8.3.0
2.0.0 GCCcore/10.2.0, GCCcore/8.3.0
3.4.1 GCCcore/8.3.0
3.6.0 GCCcore/9.3.0
3.7.1 GCCcore/8.3.0
3.7.2 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0
4.2.2 GCCcore/11.2.0
5.1.1 GCCcore/11.3.0
6.3.1 GCCcore/12.2.0, GCCcore/12.3.0

bbcp

BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp

homepage: http://www.slac.stanford.edu/~abh/bbcp/

version versionsuffix toolchain
12.01.30.00.0 -amd64_linux26 system

bbFTP

bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface

homepage: https://software.in2p3.fr/bbftp/

version toolchain
3.2.1 GCCcore/9.3.0, intel/2016a, system

BBMap

BBMap short read aligner, and other bioinformatic tools.

homepage: https://sourceforge.net/projects/bbmap/

version versionsuffix toolchain
36.62 -Java-1.8.0_112 intel/2016b
37.93 foss/2018a, intel/2018a
38.26 foss/2018b
38.50b GCC/8.2.0-2.31.1
38.76 GCC/8.2.0-2.31.1
38.79 GCC/8.3.0
38.87 GCC/8.2.0-2.31.1, iccifort/2020.1.217
38.90 GCC/10.2.0, GCC/9.3.0
38.96 GCC/10.3.0
38.98 GCC/11.2.0
39.01 GCC/11.3.0, GCC/12.2.0

bc

bc is an arbitrary precision numeric processing language.

homepage: https://www.gnu.org/software/bc/

version toolchain
1.06.95 GCC/4.8.2

BCALM

de Bruijn graph compaction in low memory

homepage: https://github.com/GATB/bcalm

version toolchain
2.2.0 foss/2018a

bcbio-gff

Read and write Generic Feature Format (GFF) with Biopython integration.

homepage: https://github.com/chapmanb/bcbb/tree/master/gff

version versionsuffix toolchain
0.6.6 -Python-3.8.2 foss/2020a
0.6.7 foss/2021a
0.7.0 foss/2020b, foss/2022a, foss/2022b

BCEL

The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class).

homepage: https://commons.apache.org/proper/commons-bcel/

version versionsuffix toolchain
5.2 -Java-1.8 system
6.5.0 -Java-1.8 system

BCFtools

Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

homepage: http://www.htslib.org/

version toolchain
1.3 foss/2016a, intel/2016a
1.3.1 foss/2016b
1.6 foss/2016b, foss/2017b, intel/2017b
1.8 GCC/6.4.0-2.28
1.9 foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
1.10.2 GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281
1.11 GCC/10.2.0
1.12 GCC/10.2.0, GCC/10.3.0, GCC/9.3.0
1.14 GCC/11.2.0
1.15.1 GCC/11.3.0
1.17 GCC/12.2.0
1.18 GCC/12.3.0

bcgTree

Automatized phylogenetic tree building from bacterial core genomes.

homepage: https://github.com/molbiodiv/bcgTree

version versionsuffix toolchain
1.0.10 -Perl-5.26.1 intel/2018a
1.1.0 -Perl-5.28.0 intel/2018b

bcl-convert

The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.

homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html

version versionsuffix toolchain
4.0.3-2 el7.x86_64 system

bcl2fastq2

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

version versionsuffix toolchain
2.19.1 -Python-2.7.12 foss/2016b
2.20.0 GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/8.3.0, GCC/9.3.0, foss/2018b, intel/2019a
2.20.0 -Python-2.7.12 foss/2016b
2.20.0 -Python-2.7.14 intel/2017b

bcolz

bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.

homepage: https://bcolz.blosc.org/en/latest/

version versionsuffix toolchain
1.1.1 -Python-2.7.13 foss/2017a
1.2.1 foss/2020b
1.2.1 -Python-3.8.2 foss/2020a

bcrypt

Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)

homepage: https://github.com/pyca/bcrypt/

version toolchain
4.0.1 GCCcore/12.3.0

BDBag

The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles.

homepage: https://github.com/fair-research/bdbag

version versionsuffix toolchain
1.4.1 -Python-2.7.14 intel/2018a
1.4.1 -Python-3.6.4 intel/2018a
1.6.3 intel/2021b

Beagle

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

homepage: https://faculty.washington.edu/browning/beagle/beagle.html

version versionsuffix toolchain
5.4.22Jul22.46e -Java-11 system

beagle-lib

beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

homepage: https://github.com/beagle-dev/beagle-lib

version versionsuffix toolchain
2.1.2 foss/2016a, foss/2017a
3.0.1 foss/2018a, intel/2018a
3.0.2 foss/2018b
3.0.2 -CUDA-9.2.88 foss/2018b
3.1.2 GCC/10.2.0, GCC/10.3.0, GCC/8.2.0-2.31.1, GCC/9.3.0, gcccuda/2019b, iccifort/2019.1.144-GCC-8.2.0-2.31.1
4.0.0 GCC/11.3.0

Beast

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

homepage: https://beast2.org

version toolchain
1.8.4 system
1.10.1 intel/2018a
1.10.4 GCC/10.2.0, GCC/8.2.0-2.31.1
2.4.0 foss/2016a
2.4.7 foss/2017a
2.5.0 foss/2018a
2.5.1 foss/2018b
2.5.2 GCC/8.2.0-2.31.1
2.6.3 gcccuda/2019b
2.6.4 GCC/10.2.0
2.6.7 GCC/10.3.0
2.7.3 GCC/11.3.0

BeautifulSoup

Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.

homepage: https://www.crummy.com/software/BeautifulSoup

version versionsuffix toolchain
4.6.0 -Python-3.6.3 intel/2017b
4.6.3 -Python-3.6.4 intel/2018a
4.7.1 -Python-3.6.6 intel/2018b
4.8.0 GCCcore/8.2.0
4.9.1 GCCcore/8.3.0
4.9.1 -Python-3.8.2 GCCcore/9.3.0
4.9.3 GCCcore/10.2.0
4.10.0 GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
4.11.1 GCCcore/12.2.0
4.12.2 GCCcore/12.3.0, GCCcore/13.2.0

BEDOPS

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

homepage: http://bedops.readthedocs.io/en/latest/index.html

version toolchain
2.4.1 GCC/4.8.4
2.4.2 GCC/4.8.2
2.4.20 system
2.4.26 system
2.4.30 foss/2016b
2.4.32 foss/2018a, intel/2018a
2.4.35 foss/2018b
2.4.41 foss/2021b

BEDTools

BEDTools: a powerful toolset for genome arithmetic. 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://bedtools.readthedocs.io/

version toolchain
2.25.0 foss/2016a
2.26.0 GCCcore/6.4.0, foss/2016a, intel/2016b, intel/2017a, intel/2017b
2.27.1 GCCcore/6.4.0, foss/2016b, foss/2018b, intel/2017a, intel/2018a
2.28.0 GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.29.2 GCC/8.3.0, GCC/9.3.0
2.30.0 GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, iccifort/2020.4.304
2.31.0 GCC/12.3.0

BEEF

BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.

homepage: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software

version toolchain
0.1.1 iccifort/2019.5.281, iccifort/2020.4.304

behave

behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project.

homepage: http://pythonhosted.org/behave

version versionsuffix toolchain
1.2.5 -Python-2.7.12 foss/2016b
1.2.6 -Python-3.6.4 intel/2018a

bench

Tools to accurately benchmark and analyze execution times for R expressions.

homepage: https://cran.r-project.org/web/packages/bench/index.html

version versionsuffix toolchain
1.1.2 -R-4.2.1 foss/2022a

BerkeleyGW

The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.

homepage: https://www.berkeleygw.org

version versionsuffix toolchain
1.0.6 intel/2016.02-GCC-4.9
1.1-beta2 intel/2016.02-GCC-4.9
1.2.0 intel/2017a, intel/2018a
2.0.0 foss/2017b, foss/2018b, intel/2017b, intel/2018a
2.1.0 -Python-3.7.4 foss/2019b, intel/2019b
3.0.1 foss/2020b, foss/2021a
3.1.0 foss/2022a, intel/2022a
4.0 foss/2022a

BFAST

BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: 1) Speed: enables billions of short reads to be mapped quickly. 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. 3) An easy way to measurably tune accuracy at the expense of speed.

homepage: http://bfast.sourceforge.net/

version toolchain
0.7.0a foss/2016b

BFC

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

homepage: https://github.com/lh3/bfc

version toolchain
1 foss/2018a

BGC-Bayesian-genomic-clines

Collection of code for Bayesian genomic cline analyses.

homepage: https://github.com/zgompert/BGC-Bayesian-genomic-clines

version toolchain
1.03 gompi/2021a

BgeeCall

Automatic RNA-Seq present/absent gene expression calls generation

homepage: https://github.com/BgeeDB/BgeeCall

version versionsuffix toolchain
1.16.0 -R-%(rver)s foss/2021a

BgeeDB

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology.

homepage: https://github.com/BgeeDB/BgeeDB_R

version versionsuffix toolchain
2.26.0 -R-%(rver)s foss/2021a

bgen

A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.

homepage: https://github.com/limix/bgen

version toolchain
3.0.2 GCCcore/7.3.0
3.0.3 GCCcore/9.3.0
4.1.3 GCCcore/10.2.0

bgen-reader

A bgen file format reader. This python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats.

homepage: https://github.com/limix/bgen-reader-py

version versionsuffix toolchain
3.0.2 -Python-3.6.6 foss/2018b

BiasAdjustCXX

BiasAdjustCXX command-line tool for the application of fast and efficient bias corrections in climatic research

homepage: https://biasadjustcxx.readthedocs.io/en/latest/

version toolchain
1.9.1 gompi/2021b

bibtexparser

Bibtex parser in Python 2.7 and 3.x

homepage: https://github.com/sciunto-org/python-bibtexparser

version toolchain
1.1.0 GCCcore/8.2.0

BiG-SCAPE

BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.

homepage: https://bigscape-corason.secondarymetabolites.org/index.html

version versionsuffix toolchain
1.0.1 -Python-3.7.4 intel/2019b
1.1.5 foss/2022a

BigDFT

BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-suite is a set of different packages to run bigdft.

homepage: https://gitlab.com/l_sim/bigdft-suite

version toolchain
1.9.1 foss/2021b

BinSanity

BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.

homepage: https://github.com/edgraham/BinSanity/wiki

version versionsuffix toolchain
0.3.5 -Python-3.7.4 foss/2019b

binutils

binutils: GNU binary utilities

homepage: https://directory.fsf.org/project/binutils/

version toolchain
2.25 GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, system
2.25.1 system
2.26 GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.3.0, system
2.27 GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, system
2.28 GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, system
2.29 GCCcore/7.2.0, GCCcore/system, system
2.30 GCCcore/7.3.0, GCCcore/8.1.0, system
2.31.1 GCCcore/7.4.0, GCCcore/8.2.0, system
2.32 GCCcore/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, system
2.34 GCCcore/10.1.0, GCCcore/9.3.0, system
2.35 GCCcore/10.2.0, system
2.36.1 FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/8.4.0, GCCcore/9.4.0, system
2.37 GCCcore/11.2.0, system
2.38 GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/9.5.0, system
2.39 GCCcore/12.2.0, system
2.40 GCCcore/11.4.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Bio-DB-HTS

Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

homepage: https://metacpan.org/release/Bio-DB-HTS

version versionsuffix toolchain
2.11 -Perl-5.26.0 foss/2017b, intel/2017b
2.11 -Perl-5.26.1 intel/2018a
2.11 -Perl-5.28.0 foss/2018b
3.01 GCC/10.2.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0
3.01 -Perl-5.28.1 GCC/8.2.0-2.31.1

Bio-EUtilities

BioPerl low-level API for retrieving and storing data from NCBI eUtils

homepage: https://github.com/bioperl/bio-eutilities

version toolchain
1.76 GCCcore/8.3.0

Bio-SamTools

This is a Perl interface to the SAMtools sequence alignment interface.

homepage: http://search.cpan.org/~lds/Bio-SamTools/

version versionsuffix toolchain
1.43 -Perl-5.24.1 intel/2017a

Bio-SearchIO-hmmer

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

version toolchain
1.7.3 GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

bioawk

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

homepage: https://github.com/lh3/bioawk

version toolchain
1.0 GCC/10.3.0, GCC/11.2.0, foss/2018b

biobakery-workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment.

homepage: http://huttenhower.sph.harvard.edu/biobakery_workflows

version toolchain
3.1 foss/2022a

biobambam2

Tools for processing BAM files

homepage: https://github.com/gt1/biobambam2

version toolchain
2.0.87 GCC/11.3.0, intel/2018a
2.0.185 GCC/12.3.0

biogeme

Biogeme is a open source Python package designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.

homepage: https://pypi.python.org/pypi/biogeme

version toolchain
3.1.2 foss/2021a
3.2.6 foss/2022a
3.2.8 foss/2021a
3.2.10 foss/2022a

biom-format

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.

homepage: https://biom-format.org

version versionsuffix toolchain
2.1.10 -Python-3.8.2 foss/2020a
2.1.12 foss/2021b
2.1.14 foss/2022a
2.1.15 foss/2022b

biomart-perl

The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts.

homepage: https://useast.ensembl.org/info/data/biomart/biomart_perl_api.html

version versionsuffix toolchain
0.7_e6db561 -Perl-5.26.0 GCCcore/6.4.0

BioPerl

Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.

homepage: https://bioperl.org/

version versionsuffix toolchain
1.6.924 -Perl-5.20.3 intel/2016a
1.6.924 -Perl-5.22.1 foss/2016a
1.7.0 -Perl-5.24.0 foss/2016b
1.7.1 -Perl-5.24.0 intel/2016b
1.7.1 -Perl-5.24.1 intel/2017a
1.7.2 GCCcore/8.3.0
1.7.2 -Perl-5.26.0 foss/2017b, intel/2017b
1.7.2 -Perl-5.26.1 intel/2018a
1.7.2 -Perl-5.28.0 foss/2018b, intel/2018b
1.7.2 -Perl-5.28.1 GCCcore/8.2.0
1.7.7 GCCcore/9.3.0
1.7.8 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

BioPP

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

version toolchain
2.4.1 GCC/8.2.0-2.31.1, GCC/9.3.0

Biopython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

homepage: https://www.biopython.org

version versionsuffix toolchain
1.65 -Python-2.7.11 foss/2016a
1.68 -Python-2.7.12 foss/2016b, intel/2016b
1.68 -Python-3.5.2 foss/2016b, intel/2016b
1.70 -Python-2.7.13 foss/2017a
1.70 -Python-2.7.14 foss/2017b, intel/2017b
1.70 -Python-3.6.1 intel/2017a
1.70 -Python-3.6.3 foss/2017b, intel/2017b
1.71 -Python-2.7.14 intel/2018a
1.71 -Python-3.6.4 foss/2018a, intel/2018a
1.72 -Python-2.7.15 foss/2018b, intel/2018b
1.72 -Python-3.6.6 foss/2018b
1.73 foss/2019a, fosscuda/2019a, intel/2019a
1.73 -Python-3.6.6 foss/2018b
1.74 foss/2019a
1.75 -Python-2.7.16 foss/2019b
1.75 -Python-3.7.4 foss/2019b, fosscuda/2019b, intel/2019b
1.76 -Python-2.7.18 foss/2020b, foss/2021b
1.78 foss/2020b, fosscuda/2020b, intel/2020b
1.78 -Python-3.8.2 foss/2020a, intel/2020a
1.79 foss/2021a, foss/2021b, foss/2022a, intel/2021b
1.81 foss/2022b
1.83 foss/2023a

BioServices

Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).

homepage: https://bioservices.readthedocs.io/

version versionsuffix toolchain
1.7.9 -Python-3.8.2 foss/2020a

BirdNET

BirdNET is a research platform that aims at recognizing birds by sound at scale. We support various hardware and operating systems such as Arduino microcontrollers, the Raspberry Pi, smartphones, web browsers, workstation PCs, and even cloud services. BirdNET is a citizen science platform as well as an analysis software for extremely large collections of audio. BirdNET aims to provide innovative tools for conservationists, biologists, and birders alike.

homepage: https://birdnet.cornell.edu/

version versionsuffix toolchain
20201214 -Python-3.7.4 fosscuda/2019b

biscuit

Utilities to help analyze bisulfite-treated sequence data

homepage: https://github.com/zwdzwd/biscuit

version toolchain
0.1.4 foss/2016a

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

homepage: https://www.bioinformatics.babraham.ac.uk/projects/bismark/

version toolchain
0.19.0 intel/2017b
0.20.1 foss/2018b, intel/2018b
0.23.1 foss/2021b
0.24.0 GCC/11.3.0
0.24.1 GCC/12.2.0

Bison

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

version toolchain
2.7 GCC/4.8.1, GCC/4.8.4, GCCcore/6.3.0, GCCcore/6.4.0, system
3.0.2 GCC/4.8.2
3.0.3 GCC/4.9.2
3.0.4 GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-2.25, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.1.0, GCCcore/system, GNU/4.9.3-2.25, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
3.0.5 GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/system, system
3.2.2 GCCcore/7.4.0
3.3.2 GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/8.4.0, GCCcore/9.1.0, GCCcore/9.2.0, system
3.5.2 system
3.5.3 GCCcore/10.2.0, GCCcore/9.3.0, system
3.6.1 GCCcore/10.1.0
3.7.1 GCCcore/10.2.0, system
3.7.6 FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/11.2.0, GCCcore/9.4.0, system
3.8.2 GCCcore/11.3.0, GCCcore/11.4.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/9.5.0, system

bitarray

bitarray provides an object type which efficiently represents an array of booleans

homepage: https://github.com/ilanschnell/bitarray

version versionsuffix toolchain
0.8.3 -Python-2.7.15 intel/2018b
0.8.3 -Python-3.6.6 intel/2018b
1.2.1 -Python-3.7.4 foss/2019b
1.5.3 -Python-2.7.16 GCC/8.3.0

BLACS

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/

version toolchain
1.1 gmvapich2/2016a

BLASR

The PacBio® long read aligner

homepage: https://github.com/PacificBiosciences/blasr

version toolchain
2.2 intel/2016b
5.3.3 gompi/2019a
20170330 intel/2017a

blasr_libcpp

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

version toolchain
20170426 intel/2017a

BLAST

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

homepage: http://blast.ncbi.nlm.nih.gov/

version versionsuffix toolchain
2.2.26 -Linux_x86_64 system
2.8.1 -Linux_x86_64 system
2.10.0 -Linux_x86_64 system
2.10.1 -Linux_x86_64 system
2.11.0 -Linux_x86_64 system

BLAST+

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

homepage: https://blast.ncbi.nlm.nih.gov/

version versionsuffix toolchain
2.2.31 system
2.3.0 -Python-2.7.11 foss/2016a
2.6.0 -Python-2.7.12 foss/2016b
2.6.0 -Python-2.7.13 foss/2017a, intel/2017a
2.6.0 -Python-2.7.14 intel/2017b
2.7.1 foss/2018a, foss/2018b, intel/2018a, intel/2018b
2.7.1 -Python-2.7.14 intel/2017b
2.8.1 foss/2018b
2.9.0 gompi/2019a, gompi/2019b, gompi/2021b, iimpi/2019a, iimpi/2019b
2.10.1 gompi/2020a, iimpi/2020a
2.11.0 gompi/2019b, gompi/2020a, gompi/2020b, gompi/2021a
2.12.0 gompi/2021b
2.13.0 gompi/2022a
2.14.0 gompi/2022b
2.14.1 gompi/2023a

BLAT

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

version toolchain
3.5 GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2016b, foss/2018b, intel/2016b, intel/2017a
3.7 GCC/10.3.0, GCC/11.2.0, GCC/11.3.0

Blender

Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

homepage: https://www.blender.org/

version versionsuffix toolchain
2.77a -Python-3.5.2 intel/2016b
2.79 -Python-3.6.1 intel/2017a
2.79b -Python-3.6.6 intel/2018b
2.79b -Python-3.6.6-CUDA-9.2.88 foss/2018b
2.81 -Python-3.7.4 foss/2019b, intel/2019b
3.0.0 -linux-x64 system
3.1.2 -linux-x64 system
3.2.2 -linux-x64 system
3.3.1 -linux-x86_64-CUDA-11.7.0 system
3.4.1 -linux-x86_64-CUDA-11.7.0 system
3.5.0 -linux-x86_64-CUDA-11.7.0 system
3.6.5 -linux-x86_64-CUDA-12.1.1 system
4.0.1 -linux-x86_64-CUDA-12.1.1 system

BLIS

AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

homepage: https://developer.amd.com/amd-cpu-libraries/blas-library/

version versionsuffix toolchain
0.3.2 GCC/7.3.0-2.30
0.6.0 GCC/8.3.0-2.32
0.8.0 GCCcore/10.2.0, GCCcore/9.3.0
0.8.1 GCC/10.3.0, GCC/11.2.0, GCCcore/10.3.0
0.9.0 GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, GCC/13.2.0, intel-compilers/2022.1.0
1.2 -amd GCC/7.3.0-2.30
2.2 -amd GCCcore/9.3.0
3.0 -amd GCCcore/10.3.0
3.0.1 -amd GCC/11.2.0, GCCcore/10.2.0, GCCcore/10.3.0
3.1 -amd GCCcore/11.2.0

Blitz++

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

version toolchain
0.10 GCCcore/6.4.0, foss/2016a
1.0.2 GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/9.3.0

BlobTools

A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.

homepage: https://blobtools.readme.io/docs

version versionsuffix toolchain
20180528 -Python-2.7.15 foss/2018b

Block

Block implements the density matrix renormalization group (DMRG) algorithm for quantum chemistry.

homepage: https://sanshar.github.io/Block/

version toolchain
1.5.3-20200525 foss/2022a, foss/2022b

Blosc

Blosc, an extremely fast, multi-threaded, meta-compressor library

homepage: https://www.blosc.org/

version toolchain
1.11.1 intel/2016b
1.12.1 GCCcore/6.4.0, foss/2016b, foss/2017a, intel/2017a
1.14.2 GCCcore/6.4.0, foss/2016a
1.14.4 GCCcore/7.3.0
1.17.0 GCCcore/8.2.0
1.17.1 GCCcore/8.3.0, GCCcore/9.3.0
1.21.0 GCCcore/10.2.0, GCCcore/10.3.0
1.21.1 GCCcore/11.2.0
1.21.3 GCCcore/11.3.0, GCCcore/12.2.0
1.21.5 GCCcore/12.3.0, GCCcore/13.2.0

Blosc2

Blosc, an extremely fast, multi-threaded, meta-compressor library

homepage: https://www.blosc.org/

version toolchain
2.0.3 GCCcore/10.2.0
2.0.4 GCCcore/10.3.0
2.4.3 GCCcore/11.2.0, GCCcore/11.3.0
2.6.1 GCCcore/11.3.0
2.8.0 GCCcore/12.2.0, GCCcore/12.3.0
2.13.2 GCCcore/13.2.0

BLT

BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, and miscellaneous commands.

homepage: http://blt.sourceforge.net/

version toolchain
20181223 GCCcore/11.2.0

bmtagger

Best Match Tagger for removing human reads from metagenomics datasets

homepage: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/

version toolchain
3.101 foss/2018b, gompi/2019a, gompi/2020b

BMTK

The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models.

homepage: https://alleninstitute.github.io/bmtk/index.html

version toolchain
1.0.8 foss/2021a

bnpy

Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts.

homepage: https://github.com/bnpy/bnpy

version versionsuffix toolchain
0.1.6 -Python-2.7.15 foss/2018b

BOINC

BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others.

homepage: https://boinc.berkeley.edu

version versionsuffix toolchain
7.2.42 -client GCC/4.8.2

bokeh

Statistical and novel interactive HTML plots for Python

homepage: https://github.com/bokeh/bokeh

version versionsuffix toolchain
0.12.3 -Python-2.7.12 intel/2016b
0.12.3 -Python-3.5.2 intel/2016b
0.12.15 -Python-3.6.4 intel/2018a
1.0.4 -Python-3.6.6 foss/2018b, intel/2018b
1.3.4 -Python-3.7.2 foss/2019a
1.4.0 -Python-3.7.4 foss/2019b, fosscuda/2019b, intel/2019b
2.0.2 -Python-3.8.2 foss/2020a, intel/2020a
2.2.3 foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
2.4.1 foss/2021a
2.4.2 foss/2021b
2.4.3 foss/2022a
3.2.1 foss/2022b
3.2.2 foss/2023a

BoltzTraP

Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients.

homepage: http://www.icams.de/content/departments/cmat/boltztrap/

version toolchain
1.2.5 intel/2016a

BoltzTraP2

BoltzTraP2 provides a numerically stable and efficient method for obtaining analytic representations of electronic bands based on density-functional-theory results for relatively sparse grids. It achieves this goal by using smoothed Fourier interpolation.

homepage: https://www.boltztrap.org

version toolchain
22.12.1 foss/2022a

Bonito

Convolution Basecaller for Oxford Nanopore Reads

homepage: https://github.com/nanoporetech/bonito

version versionsuffix toolchain
0.1.0 -Python-3.7.4 foss/2019b, fosscuda/2019b
0.1.4 -Python-3.7.4 fosscuda/2019b
0.2.0 -Python-3.7.4 fosscuda/2019b
0.2.2 -Python-3.7.4 fosscuda/2019b
0.3.2 -Python-3.7.4 fosscuda/2019b
0.3.5 -Python-3.7.4 fosscuda/2019b
0.3.8 fosscuda/2020b
0.4.0 fosscuda/2020b

Bonmin

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

homepage: https://coin-or.github.io/Ipopt

version toolchain
1.8.7 intel/2019a

Bonnie++

Enhanced performance Test of Filesystem I/O

homepage: https://www.coker.com.au/bonnie++

version toolchain
1.97 foss/2016a
2.00a GCC/10.3.0

Boost

Boost provides free peer-reviewed portable C++ source libraries.

homepage: https://www.boost.org/

version versionsuffix toolchain
1.54.0 -Python-2.7.12 foss/2016b
1.55.0 system
1.55.0 -Python-2.7.11 foss/2016a
1.57.0 -Python-2.7.10 gimkl/2.11.5
1.58.0 intel/2017a
1.58.0 -Python-2.7.11 foss/2016a, intel/2016a
1.58.0 -serial GCC/4.9.2
1.59.0 -Python-2.7.11 foss/2016a, intel/2016a
1.60.0 foss/2016a, intel/2016a
1.60.0 -Python-2.7.11 foss/2016a, intel/2016a
1.60.0 -Python-3.5.1 foss/2016a
1.61.0 foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.61.0 -Python-2.7.11 foss/2016a, intel/2016a
1.61.0 -Python-2.7.12 foss/2016b, intel/2016b
1.61.0 -Python-3.5.1 foss/2016a
1.62.0 -Python-2.7.12 intel/2016b
1.63.0 foss/2017a
1.63.0 -Python-2.7.12 foss/2016b, intel/2016b
1.63.0 -Python-2.7.13 foss/2017a, intel/2017a
1.63.0 -Python-2.7.14 foss/2018a, intel/2017b
1.63.0 -Python-3.5.2 foss/2016b
1.64.0 gompi/2019a, gompic/2019a, intel/2017a
1.64.0 -Python-2.7.13 intel/2017a
1.65.0 -Python-2.7.13 intel/2017a
1.65.1 foss/2017a, foss/2017b, intel/2017a, intel/2017b
1.65.1 -Python-2.7.13 intel/2017a
1.65.1 -Python-2.7.14 foss/2017b, intel/2017b
1.65.1 -Python-3.6.3 foss/2017b, intel/2017b
1.66.0 foss/2018a, intel/2017b, intel/2018.01, intel/2018a
1.66.0 -Python-2.7.14 foss/2018a, intel/2017b, intel/2018a
1.66.0 -Python-3.6.3 intel/2018.01
1.66.0 -Python-3.6.4 foss/2018a, intel/2018a
1.66.0 -no_mpi GCCcore/6.4.0
1.67.0 foss/2018b, fosscuda/2018b, intel/2018a, intel/2018b
1.67.0 -Python-2.7.14 foss/2018a
1.68.0 -Python-2.7.15 foss/2018b, intel/2018b
1.68.0 -Python-3.6.6 foss/2018b, intel/2018b
1.69.0 intel/2019.01
1.70.0 gompi/2019a, gompic/2019a, iimpi/2019a, iimpic/2019a
1.71.0 gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b
1.72.0 gompi/2020a, gompic/2020a, iimpi/2020a
1.72.0 -no_mpi GCCcore/9.3.0
1.74.0 GCC/10.2.0, iccifort/2020.4.304
1.75.0 GCC/11.2.0
1.76.0 GCC/10.3.0, intel-compilers/2021.2.0
1.77.0 GCC/11.2.0, intel-compilers/2021.4.0
1.79.0 GCC/11.2.0, GCC/11.3.0
1.81.0 GCC/12.2.0
1.82.0 GCC/12.3.0
1.83.0 GCC/13.2.0

Boost.MPI

Boost provides free peer-reviewed portable C++ source libraries.

homepage: https://www.boost.org/

version toolchain
1.76.0 gompi/2021a
1.77.0 gompi/2021b
1.79.0 gompi/2022a, gompi/2022b
1.81.0 gompi/2022b
1.82.0 gompi/2023a

Boost.Python

Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.

homepage: https://boostorg.github.io/python

version versionsuffix toolchain
1.64.0 gompi/2019a, gompic/2019a
1.65.1 -Python-2.7.14 foss/2017b, intel/2017b
1.66.0 -Python-2.7.14 intel/2018a
1.66.0 -Python-3.6.4 foss/2018a, intel/2018a
1.67.0 -Python-2.7.15 foss/2018b, fosscuda/2018b, intel/2018b
1.67.0 -Python-3.6.6 foss/2018b, intel/2018b
1.70.0 gompi/2019a, gompic/2019a, iimpi/2019a, iimpic/2019a
1.71.0 gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b
1.72.0 gompi/2020a, gompic/2020a, iimpi/2020a
1.74.0 GCC/10.2.0
1.76.0 GCC/10.3.0
1.77.0 GCC/11.2.0
1.79.0 GCC/11.3.0
1.83.0 GCC/13.2.0

Boost.Python-NumPy

Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.

homepage: https://boostorg.github.io/python

version toolchain
1.79.0 foss/2022a

boost_histogram

Boost-histogram is a Python package providing Python bindings for Boost.Histogram.

homepage: https://boost-histogram.readthedocs.io

version toolchain
1.2.1 foss/2021a

BOPTEST

This repository contains code for the Building Optimization Performance Test framework (BOPTEST) that is being developed as part of the IBPSA Project 1.

homepage: https://ibpsa.github.io/project1-boptest/

version toolchain
0.3.0 system

boto3

Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2.

homepage: https://github.com/boto/boto3

version toolchain
1.20.13 GCCcore/10.3.0, GCCcore/11.2.0
1.26.37 GCCcore/11.3.0
1.26.163 GCCcore/12.2.0
1.28.70 GCCcore/12.3.0

Bottleneck

Fast NumPy array functions written in C

homepage: https://kwgoodman.github.io/bottleneck-doc

version versionsuffix toolchain
1.2.1 -Python-3.6.4 intel/2018a
1.3.2 -Python-3.8.2 foss/2020a
1.3.6 foss/2022a
1.3.7 foss/2022a

Bowtie

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

version toolchain
1.1.2 GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, intel/2016b, intel/2017a, intel/2018a
1.2.1.1 foss/2016b, intel/2017b
1.2.2 foss/2018b, intel/2017b, intel/2018a
1.2.3 GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
1.3.0 GCC/10.2.0, GCC/9.3.0
1.3.1 GCC/10.3.0, GCC/11.2.0, GCC/11.3.0

Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

homepage: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

version toolchain
2.2.8 foss/2016a
2.2.9 foss/2016a, intel/2016b
2.3.2 foss/2016b, foss/2017a, intel/2017a
2.3.3.1 intel/2017b
2.3.4 intel/2017b
2.3.4.1 foss/2017b, intel/2017b, intel/2018a
2.3.4.2 foss/2018b, intel/2018b
2.3.4.3 foss/2017b
2.3.5.1 GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
2.4.1 GCC/9.3.0
2.4.2 GCC/10.2.0, GCC/9.3.0
2.4.4 GCC/10.3.0, GCC/11.2.0
2.4.5 GCC/11.3.0
2.5.1 GCC/10.3.0, GCC/12.2.0, GCC/12.3.0

Bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

homepage: http://docs.bpipe.org/

version toolchain
0.9.9.2 intel/2017a

bpp

The aim of this project is to implement a versatile high-performance version of the BPP software.

homepage: https://github.com/bpp/bpp

version toolchain
4.3.8 GCC/8.3.0
4.4.0 GCC/10.3.0

bpytop

Resource monitor that shows usage and stats for processor, memory, disks, network and processes.

homepage: https://github.com/aristocratos/bpytop/

version toolchain
1.0.60 GCCcore/10.2.0
1.0.67 GCCcore/10.3.0

Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length.

homepage: https://ccb.jhu.edu/software/bracken/

version toolchain
2.6.0 GCCcore/9.3.0
2.6.2 GCCcore/11.2.0
2.7 GCCcore/11.2.0
2.9 GCCcore/10.3.0

Braindecode

Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain data with deep learning models. It includes dataset fetchers, data preprocessing and visualization tools, as well as implementations of several deep learning architectures and data augmentations for analysis of EEG, ECoG and MEG.

homepage: https://braindecode.org/

version versionsuffix toolchain
0.7 -PyTorch-1.10.0 foss/2021a
0.7 -PyTorch-1.10.0-CUDA-11.3.1 foss/2021a
0.8.1 -PyTorch-2.1.2 foss/2023a

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

homepage: https://github.com/Gaius-Augustus/BRAKER

version versionsuffix toolchain
2.1.2 intel/2019a
2.1.5 -Python-3.7.4 intel/2019b
2.1.6 foss/2021b, foss/2022a

BreakDancer

BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads

homepage: http://gmt.genome.wustl.edu/packages/breakdancer

version toolchain
1.4.5 intel/2017a

breseq

breseq is a computational pipeline for the analysis of short-read re-sequencing data

homepage: https://barricklab.org/breseq

version versionsuffix toolchain
0.35.0 -R-3.6.0 intel/2019a
0.35.4 -R-4.0.0 foss/2020a
0.36.1 foss/2021b
0.38.1 foss/2022a

BRiAl

BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.

homepage: https://github.com/BRiAl/BRiAl

version toolchain
1.2.12 GCC/11.3.0

Brotli

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

version toolchain
1.0.9 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0
1.1.0 GCCcore/13.2.0

Brotli-python

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

version toolchain
1.0.9 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0
1.1.0 GCCcore/13.2.0

Brunsli

Brunsli is a lossless JPEG repacking library.

homepage: https://github.com/google/brunsli/

version toolchain
0.1 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

bsddb3

bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.

homepage: https://pypi.org/project/bsddb3/

version versionsuffix toolchain
6.2.6 GCCcore/8.2.0
6.2.6 -Python-2.7.15 fosscuda/2018b
6.2.9 GCCcore/10.2.0, GCCcore/11.3.0

BSMAPz

Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.

homepage: https://github.com/zyndagj/BSMAPz

version versionsuffix toolchain
1.1.1 -Python-2.7.16 intel/2019b

Bsoft

Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.

homepage: https://lsbr.niams.nih.gov/bsoft/

version toolchain
2.0.2 foss/2017b
2.0.7 GCC/9.3.0

BSseeker2

BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.

homepage: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2

version versionsuffix toolchain
2.1.8 -Python-2.7.16 GCC/8.3.0, iccifort/2019.5.281

btllib

Bioinformatics Technology Lab common code library

homepage: https://github.com/bcgsc/btllib

version toolchain
1.7.0 GCC/12.3.0

BuDDy

A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more.

homepage: http://buddy.sourceforge.net/

version toolchain
2.4 GCCcore/10.2.0

BUFRLIB

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

version toolchain
11.3.0.2 iccifort/2020.1.217

build

A simple, correct Python build frontend.

homepage: https://github.com/pypa/build

version toolchain
0.10.0 foss/2022a, foss/2022b
1.0.3 foss/2023a, foss/2023b

buildenv

This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show

homepage:

version versionsuffix toolchain
default FCC/4.5.0, Fujitsu/21.05, foss/2017b, foss/2018b, foss/2019b, foss/2020a, foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2022b, foss/2023a, foss/2023b, fosscuda/2019b, fosscuda/2020a, fosscuda/2020b, intel/2016b, intel/2017a, intel/2019b, intel/2020a, intel/2020b, intel/2021a, intel/2021b, intel/2022a, intel/2022b, intel/2023a, intel/2023b, intelcuda/2019b, intelcuda/2020a, intelcuda/2020b, nvompi/2022.07
default -CUDA-11.3.1 foss/2021a
default -CUDA-11.4.1 foss/2021b
default -CUDA-11.7.0 foss/2022a
default -CUDA-12.0.0 foss/2022b
default -CUDA-12.1.1 foss/2023a

buildingspy

Python modules for automating Modelica simulations and for running unit test for the Buildings library

homepage: https://simulationresearch.lbl.gov/modelica/buildingspy

version toolchain
4.0.0 foss/2022a

Bullet

Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics.

homepage: http://bulletphysics.org/

version toolchain
2.83.7 foss/2016a, intel/2016a

BUSCO

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

homepage: https://busco.ezlab.org/

version versionsuffix toolchain
1.22 -Python-2.7.13 intel/2017a
2.0.1 -Python-2.7.13 intel/2017a
3.0.2 -Python-2.7.15 intel/2018b
4.0.5 -Python-3.7.4 foss/2019b
4.0.6 foss/2020b
5.0.0 foss/2020b
5.1.2 foss/2020b
5.4.2 foss/2021a
5.4.3 foss/2021b
5.4.5 foss/2022a
5.4.7 foss/2022b

BUStools

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.

homepage: https://github.com/BUStools/bustools

version toolchain
0.40.0 GCCcore/9.3.0, foss/2018b
0.43.1 GCCcore/11.3.0

BWA

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

homepage: http://bio-bwa.sourceforge.net/

version toolchain
0.7.12 foss/2016b
0.7.13 foss/2016a, intel/2016a
0.7.15 GCCcore/5.4.0, GCCcore/6.4.0, foss/2016a, foss/2016b, intel/2016b, intel/2017a
0.7.16a foss/2016b, intel/2017a
0.7.17 GCC/10.2.0, GCC/10.3.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, iccifort/2020.4.304, intel/2017b, intel/2018a, intel/2018b
0.7.17-20220923 GCCcore/12.3.0

bwa-mem2

The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.

homepage: https://github.com/bwa-mem2/bwa-mem2

version toolchain
2.2.1 intel-compilers/2023.1.0

bwa-meth

Fast and accurante alignment of BS-Seq reads.

homepage: https://github.com/brentp/bwa-meth

version toolchain
0.2.2 iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
0.2.6 GCC/11.3.0

bwakit

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.

homepage: https://github.com/lh3/bwa/tree/master/bwakit

version versionsuffix toolchain
0.7.15 _x64-linux system

bwidget

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

version toolchain
1.9.13 GCCcore/8.2.0
1.9.14 GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.9.15 GCCcore/11.2.0, GCCcore/11.3.0

BWISE

de Bruijn Workflow using Integral information of Short pair End reads

homepage: https://github.com/Malfoy/BWISE

version versionsuffix toolchain
20180820 -Python-3.6.4 foss/2018a

bx-python

The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

homepage: https://github.com/bxlab/bx-python

version versionsuffix toolchain
0.7.4 -Python-2.7.12 foss/2016b
0.7.4 -Python-2.7.13 intel/2017a
0.8.1 -Python-2.7.14 intel/2018a
0.8.2 -Python-3.6.6 foss/2018b
0.8.4 foss/2019a
0.8.8 -Python-3.7.4 foss/2019b
0.8.9 -Python-3.8.2 foss/2020a
0.8.11 foss/2021a
0.8.13 foss/2021b
0.9.0 foss/2022a
0.10.0 foss/2023a

BXH_XCEDE_TOOLS

A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.

homepage: http://www.nitrc.org/projects/bxh_xcede_tools/

version toolchain
1.11.1 system

byacc

Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.

homepage: http://invisible-island.net/byacc/byacc.html

version toolchain
20160324 intel/2016a
20160606 foss/2016b, intel/2016b
20170709 GCCcore/6.4.0

byobu

Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer

homepage: https://byobu.org

version toolchain
5.133 GCC/8.3.0

bzip2

bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

homepage: https://sourceware.org/bzip2

version toolchain
1.0.6 GCC/4.8.1, GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.0.8 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/8.3.0, GCCcore/9.3.0, system

C

c-ares - C3D - cadaver - CaDiCaL - CAFE5 - Caffe - cairo - cairomm - Calcam - CalculiX-CrunchiX - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - captum - Cargo - Carma - carputils - Cartopy - CASA - casacore - Casanovo - CaSpER - CASPR - CASTEP - castor - CastXML - CAT-BAT - CatBoost - Catch2 - category_encoders - CatLearn - CatMAP - causallift - causalml - CaVEMan - CAVIAR - Cbc - CBLAS - ccache - CCfits - CCL - cclib - cctbx-base - cctools - CD-HIT - CDAT - cdbfasta - CDBtools - cddlib - CDFlib - cDNA_Cupcake - CDO - cdo-bindings - cdsapi - cell2location - CellBender - CellChat - CellMix - CellOracle - Cellpose - CellRanger - CellRanger-ARC - CellRanger-ATAC - CellRank - CellTypist - CENSO - centerline - Centrifuge - Cereal - CESM-deps - CFDEMcoupling - cffi - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - CHASE - Check - CheckM - CheckM-Database - Cheetah - Chemaxon-Marvin - chemprop - CheMPS2 - CHERAB - chewBBACA - chi2comb - Chimera - ChimPipe - ChIPseeker - Chromaprint - cicero - CIF2Cell - cimfomfa - CIRCexplorer - CIRCexplorer2 - Circlator - Circos - Circuitscape - CIRI - CIRI-long - CIRIquant - cisTEM - CITE-seq-Count - Clair3 - Clang - Clang-AOMP - Clang-Python-bindings - CLAPACK - Clarabel.rs - CLEAR - CLEASE - CLHEP - CliMetLab - CLIP - cliquer - CLISP - ClonalFrameML - CLooG - CloudCompare - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CMAverse - CmdStanR - cmocean - CMSeq - CNT-ILP - CNVkit - CNVnator - Co-phylog - COBRApy - CoCoALib - CodAn - code-cli - code-server - CODEX2 - CodingQuarry - Cogent - Coin - CoinUtils - ColabFold - colossalai - Commet - CompareM - Compress-Raw-Zlib - COMSOL - Con3F - conan - CONCOCT - Concorde - ConcurrentVersionsSystem - configparser - configurable-http-proxy - CONN - connected-components-3d - ConnectomeWorkbench - contextily - Control-FREEC - cooler - CoordgenLibs - Coot - CopyKAT - core-counter - Coreutils - corner - CoSymLib - coverage - cowsay - CP2K - CPB - CPC2 - cpio - CPLEX - CPMD - CPPE - CppHeaderParser - CppUnit - cppy - cppyy - cppzmq - cpu_features - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CREST - CRF++ - CRISPR-DAV - CRISPResso2 - cromwell - crossguid - CrossMap - CrossTalkZ - CRPropa - Crumble - cryoCARE - cryoDRGN - cryptography - CryptoMiniSat - CrystFEL - CSB - CSBDeep - CSBLAST - cscope - csvkit - ctags - ctffind - CTPL - Cube - CubeGUI - CubeLib - CubeWriter - CuCLARK - CUDA - CUDA-Samples - CUDAcompat - CUDAcore - CUDD - cuDNN - Cufflinks - CUnit - CuPy - cURL - cuSPARSELt - custodian - cutadapt - cuTENSOR - cuteSV - CUTLASS - CVglasso - CVXOPT - CVXPY - CWIPI - cwltool - cxxopts - cysignals - Cython - cython-blis - cytoolz - Cytoscape - cytosim - cyvcf2

c-ares

c-ares is a C library for asynchronous DNS requests (including name resolves)

homepage: https://c-ares.org/

version toolchain
1.17.2 GCCcore/10.2.0, GCCcore/10.3.0
1.18.1 GCCcore/11.2.0, GCCcore/11.3.0
1.19.1 GCCcore/12.3.0
1.27.0 GCCcore/13.2.0

C3D

Convert3D Medical Image Processing Tool

homepage: https://sourceforge.net/projects/c3d/

version toolchain
1.0.0 system

cadaver

cadaver is a command-line WebDAV client for Unix.

homepage: http://www.webdav.org/cadaver/

version toolchain
0.23.3 intel/2017a

CaDiCaL

CaDiCaL is a simplified satisfiability solver. The original goal of the development of CaDiCaL was to obtain a CDCL solver, which is easy to understand and change, while at the same time not being much slower than other state-of-the-art CDCL solvers.

homepage: https://github.com/arminbiere/cadical

version toolchain
1.3.0 GCC/9.3.0

CAFE5

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

version toolchain
5.0.0 GCC/10.2.0

Caffe

Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.

homepage: https://github.com/BVLC/caffe

version versionsuffix toolchain
1.0 -CUDA-9.1.85-Python-2.7.14 intel/2017b
1.0 -Python-2.7.13 intel/2017a
1.0 -Python-2.7.14 intel/2017b
rc3 -CUDA-7.5.18-Python-2.7.11 foss/2016a

cairo

Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

homepage: https://cairographics.org

version versionsuffix toolchain
1.14.6 foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.14.6 -GLib-2.48.0 foss/2016a, intel/2016a
1.14.8 intel/2017a
1.14.10 GCCcore/6.3.0, GCCcore/6.4.0, intel/2017b
1.14.12 GCCcore/6.4.0, GCCcore/7.3.0
1.16.0 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.17.4 GCCcore/11.3.0, GCCcore/12.2.0
1.17.8 GCCcore/12.3.0
1.18.0 GCCcore/13.2.0

cairomm

The Cairomm package provides a C++ interface to Cairo.

homepage: http://cairographics.org

version toolchain
1.12.2 GCCcore/6.4.0, GCCcore/7.3.0
1.16.2 GCC/11.3.0

Calcam

Calcam is a Python package providing tools for spatial calibration of cameras, i.e. determining the mapping between pixel coordinates in an image and real-world 3D sight lines & coordinates.

homepage: https://euratom-software.github.io/calcam

version versionsuffix toolchain
2.1.0 -Python-2.7.14 intel/2018a
2.1.0 -Python-3.6.4 intel/2018a

CalculiX-CrunchiX

A Free Software Three-Dimensional Structural Finite Element Program

homepage: http://www.calculix.de

version toolchain
2.20 foss/2021a, foss/2022b, foss/2023a

Calendrical

Calendrical module is for calendrical calculations.

homepage: https://www.funaba.org/code#calendrical

version versionsuffix toolchain
2.0.1 -Python-3.6.3 intel/2017b
2.0.2a -Python-3.6.4 intel/2018a
2.0.2a -Python-3.6.6 intel/2018b

Calib

Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing.

homepage: https://github.com/vpc-ccg/calib

version toolchain
0.3.4 GCC/9.3.0

CAMPARI

CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion.

homepage: http://campari.sourceforge.net/V4/index.html

version toolchain
4.0 intel/2020b

Cantera

Chemical kinetics, thermodynamics, and transport tool suite

homepage: https://github.com/Cantera/cantera

version versionsuffix toolchain
2.2.1 -Python-2.7.12 intel/2016b
2.3.0 -Python-2.7.12 foss/2016b, intel/2016b
2.3.0 -Python-2.7.13 intel/2017a
2.3.0 -Python-2.7.14 foss/2017b, intel/2017b, intel/2018a
2.4.0 -Python-2.7.14 intel/2018a
2.6.0 foss/2022a
3.0.0 foss/2023a

canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing

homepage: https://canu.readthedocs.io

version versionsuffix toolchain
1.4 foss/2016b
1.7 intel/2018a
1.8 -Perl-5.26.0 foss/2017b, intel/2017b
1.8 -Perl-5.28.0 foss/2018b
1.8 -Perl-5.28.1 GCCcore/8.2.0
1.9 -Java-11 GCCcore/8.3.0
2.1.1 GCCcore/10.2.0
2.1.1 -Java-11 GCCcore/9.3.0
2.2 GCC/12.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.2 -Java-11 GCCcore/10.3.0

Canvas

Copy number variant (CNV) calling from DNA sequencing data

homepage: https://github.com/Illumina/canvas

version toolchain
1.39.0.1598 system

CAP3

CAP3 assembly program

homepage: http://seq.cs.iastate.edu/

version toolchain
20071221-intel-x86 system
20071221-intel-x86_64 system
20071221-opteron system

CapnProto

Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.

homepage: https://capnproto.org

version toolchain
0.6.1 GCCcore/6.4.0
0.7.0 GCCcore/7.3.0
0.8.0 GCCcore/9.3.0
0.9.1 GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
0.10.2 GCCcore/11.3.0
0.10.3 GCCcore/12.2.0
1.0.1 GCCcore/12.3.0
1.0.1.1 GCCcore/13.2.0

captum

Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.

homepage: https://captum.ai/

version versionsuffix toolchain
0.5.0 foss/2022a
0.5.0 -CUDA-11.7.0 foss/2022a

Cargo

The Rust package manager

homepage: https://crates.io/

version toolchain
0.13.0 foss/2016b

Carma

Carma - A molecular dynamics analysis program

homepage: http://utopia.duth.gr/~glykos/Carma.html

version toolchain
2.01 foss/2019b

carputils

carputils is a Python framework for generating and running openCARP examples.

homepage: https://git.opencarp.org/openCARP/carputils

version versionsuffix toolchain
20200915 -Python-3.8.2 foss/2020a
20210513 foss/2020b

Cartopy

Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.

homepage: https://scitools.org.uk/cartopy/docs/latest/

version versionsuffix toolchain
0.18.0 -Python-3.7.4 foss/2019b
0.18.0 -Python-3.8.2 foss/2020a
0.19.0.post1 foss/2020b, intel/2020b
0.20.0 foss/2021a
0.20.3 foss/2021b, foss/2022a
0.22.0 foss/2023a

CASA

CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama Large Millimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also for other radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, and one of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA Sky Survey (VLASS).

homepage: https://casa.nrao.edu/

version versionsuffix toolchain
6.5.5-21 -py3.8 system

casacore

A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them.

homepage: https://github.com/casacore/casacore

version toolchain
3.4.0 foss/2021b
3.5.0 foss/2022a, foss/2023b

Casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

homepage: https://casanovo.readthedocs.io

version versionsuffix toolchain
3.3.0 foss/2022a
3.3.0 -CUDA-11.7.0 foss/2022a

CaSpER

CaSpER is a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data.

homepage: https://github.com/akdess/CaSpER

version toolchain
2.0 foss/2019b

CASPR

Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.

homepage: https://judithbergada.github.io/CASPR

version toolchain
20200730 foss/2022a

CASTEP

CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.

homepage: http://www.castep.org

version toolchain
21.1.1 CrayCCE/19.06, CrayGNU/19.06, foss/2019b, intel/2019b, iomkl/2019b
22.11 foss/2022a
23.1 foss/2023a

castor

Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.

homepage: https://CRAN.R-project.org/package=castor

version toolchain
1.7.11 foss/2022a

CastXML

CastXML is a C-family abstract syntax tree XML output tool.

homepage: https://github.com/CastXML/CastXML

version toolchain
0.4.3 GCCcore/8.3.0
20160617 foss/2016a
20180806 foss/2018a

CAT-BAT

Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).

homepage: https://github.com/dutilh/CAT

version toolchain
5.2.3 GCC/10.3.0

CatBoost

CatBoost is a high-performance open source library for gradient boosting on decision trees

homepage: https://catboost.ai

version toolchain
1.2 gfbf/2023a

Catch2

A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)

homepage: https://github.com/catchorg/Catch2

version toolchain
2.9.1 system
2.11.0 system
2.13.4 system
2.13.9 GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, system

category_encoders

A set of scikit-learn-style transformers for encoding categorical variables into numeric by means of different techniques.

homepage: https://github.com/scikit-learn-contrib/category_encoders

version toolchain
2.4.1 foss/2021b

CatLearn

An environment for atomistic machine learning in Python for applications in catalysis

homepage: https://catlearn.readthedocs.io

version toolchain
0.6.2 intel/2022a

CatMAP

Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening.

homepage: https://catmap.readthedocs.io

version versionsuffix toolchain
20170927 -Python-2.7.14 intel/2017b
20220519 foss/2022a

causallift

CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data

homepage: https://github.com/Minyus/causallift

version versionsuffix toolchain
1.0.6 -Python-3.8.2 foss/2020a

causalml

Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML

homepage: https://github.com/uber/causalml

version versionsuffix toolchain
0.3.0-20180610 -Python-3.7.2 foss/2019a
0.8.0-20200909 -Python-3.8.2 foss/2020a

CaVEMan

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

homepage: http://cancerit.github.io/CaVEMan/

version toolchain
1.13.2 foss/2018a

CAVIAR

CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.

homepage: https://github.com/fhormoz/caviar

version toolchain
2.2-20190419 foss/2019b

Cbc

Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.

homepage: https://github.com/coin-or/Cbc

version toolchain
2.10.3 foss/2018b
2.10.5 foss/2020b, foss/2021a, foss/2022b
2.10.11 foss/2023a

CBLAS

C interface to the BLAS

homepage: https://www.netlib.org/blas/

version toolchain
20110120 foss/2016b, intel/2019b, intel/2020a

ccache

Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again

homepage: https://ccache.dev/

version versionsuffix toolchain
3.2.5 system
3.3.1 system
3.3.3 system
3.3.4 -f90 system
3.7.11 system
4.2.1 system
4.6.1 GCCcore/11.2.0
4.6.3 GCCcore/11.3.0, system
4.7.5 system
4.8.3 system
4.9 GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

CCfits

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: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/

version toolchain
2.5 GCCcore/9.3.0

CCL

Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.

homepage: https://ccl.clozure.com/

version toolchain
1.11.5 system
1.12 GCCcore/9.3.0
1.12.1 GCCcore/10.3.0
1.12.2 GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/13.2.0

cclib

cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

homepage: https://cclib.github.io/

version versionsuffix toolchain
1.5 -Python-3.5.2 foss/2016b
1.6.3 -Python-3.8.2 foss/2020a, intel/2020a
1.7.2 foss/2021b
1.8 foss/2023a

cctbx-base

The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.

homepage: https://github.com/cctbx/cctbx_project

version toolchain
2020.8 foss/2020b, fosscuda/2020b

cctools

The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once.

homepage: https://ccl.cse.nd.edu/

version toolchain
7.0.22 GCCcore/8.3.0

CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

homepage: https://github.com/weizhongli/cdhit

version versionsuffix toolchain
4.6.4 -2015-0603 GNU/4.9.3-2.25
4.6.6 foss/2016b
4.6.8 foss/2018b, intel/2017a, intel/2018a
4.8.1 GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/8.3.0, GCC/9.3.0, foss/2018b, iccifort/2019.5.281

CDAT

CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems.

homepage: https://github.com/CDAT/cdat

version versionsuffix toolchain
8.2.1 -Python-3.8.2 foss/2020a

cdbfasta

Fasta file indexing and retrival tool

homepage: https://sourceforge.net/projects/cdbfasta

version toolchain
0.99 GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281

CDBtools

CDB (Constant DataBase) indexing and retrieval tools for FASTA files

homepage: