List of supported software

EasyBuild 4.4.1 supports 2388 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

3to2

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/8.2.0-2.31.1, intel/2018b

A

ABAQUS - ABINIT - ABRA2 - ABRicate - ABySS - ack - ACT - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - AFNI - AGFusion - aiohttp - ALADIN - Albacore - ALFA - alleleCount - Allinea - ALLPATHS-LG - almosthere - Alpha - ALPS - alsa-lib - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMOS - AMPHORA2 - AMPL-MP - amplimap - AmrPlusPlus - Anaconda2 - Anaconda3 - aNCI - angsd - Annif - annovar - ANSYS - ANSYS_CFD - ant - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - AOMP - APBS - apex - APR - APR-util - ARAGORN - Arb - arcasHLA - ARCH - Archive-Zip - archspec - ARGoS - argtable - Arlequin - Armadillo - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - arrow - ART - artic-ncov2019 - ArviZ - ARWEN - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - ATSAS - attr - attrdict - augur - AUGUSTUS - Autoconf - Autoconf-archive - AutoDock - AutoDock_Vina - AutoGrid - Automake - AutoMap - autopep8 - Autotools - awscli

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

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		intel/2020a
9.4.1		foss/2020b, intel/2020a, intel/2020b

ABRA2

Assembly Based ReAligner

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

version	toolchain
2.22	iccifort/2019.5.281
2.23	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

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

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

ACT

ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format.

homepage: https://sanger-pathogens.github.io/Artemis/ACT/

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

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/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/%/(github_account)s/%(namelower)s

version	toolchain
2.2.0	foss/2016b
2.2.2	foss/2018b
2.3.1	foss/2018b

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

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	-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: http://software.genetics.ucla.edu/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

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

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

aiohttp

” Async http client/server framework

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

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

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

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

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

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

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

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

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

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: http://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

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

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

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

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

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

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

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

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

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

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

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: http://www.ansys.com

version	toolchain
15.0	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

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

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/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

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

any2fasta

Convert various sequence formats to FASTA

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

version	versionsuffix	toolchain
0.4.2		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 12.0

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

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/8.2.0, GCCcore/9.3.0

APR-util

Apache Portable Runtime (APR) util libraries.

homepage: http://apr.apache.org/

version	toolchain
1.6.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/9.3.0, iomkl/2018a

ARAGORN

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

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

version	toolchain
1.2.38	foss/2016b, iccifort/2019.5.281

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

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

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

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

argtable

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

homepage: http://argtable.sourceforge.net/

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

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

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

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

Arrow

Apache Arrow is 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		fosscuda/2020b, intel/2020b
0.17.1	-Python-3.8.2	foss/2020a, intel/2020a

arrow

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

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

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

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

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

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

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

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

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

astropy

The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.

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		intelcuda/2020b

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

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

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/9.3.0

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

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

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

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

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, 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

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

AutoDock_Vina

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

homepage: http://vina.scripps.edu/index.html

version	versionsuffix	toolchain
1.1.2	_linux_x86	system

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

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

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

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

B

Bader - BAGEL - bam-readcount - BAMM - BamM - BAMSurgeon - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bat - BatMeth2 - BayesAss - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - BCEL - BCFtools - bcgTree - bcl2fastq2 - bcolz - BDBag - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - BEEF - behave - BerkeleyGW - BFAST - BFC - bgen - bgen-reader - bibtexparser - BiG-SCAPE - BinSanity - binutils - Bio-DB-HTS - Bio-EUtilities - Bio-SamTools - bioawk - biobambam2 - biomart-perl - BioPerl - BioPP - Biopython - BioServices - BirdNET - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Blosc - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - Bonito - Bonmin - Bonnie++ - Boost - Boost.Python - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - BRAKER - BreakDancer - breseq - Brotli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - BUFRLIB - buildenv - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2

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

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

bam-readcount

Count DNA sequence reads in BAM files

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

version	toolchain
0.8.0	GCC/9.3.0, foss/2018b

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/2016b

BamM

BamM is a c library, wrapped in python, that parses BAM files

homepage: http://ecogenomics.github.io/BamM/

version	versionsuffix	toolchain
1.7.3	-Python-2.7.12	foss/2016b
1.7.3	-Python-2.7.14	foss/2018a

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

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

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

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

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

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

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

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

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

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: http://www.evolution.reading.ac.uk/BayesTraitsV1.html

version	versionsuffix	toolchain
1.0-linux32		system
2.0	-Beta-Linux64	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	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
1.1.0	GCCcore/8.3.0
2.0.0	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

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: http://doc.in2p3.fr/bbftp/

version	toolchain
3.2.1	intel/2016a

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		iccifort/2020.1.217
38.90		GCC/10.2.0, GCC/9.3.0

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

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/9.3.0

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

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/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

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

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/8.2.0-2.31.1, GCC/9.3.0, gcccuda/2019b

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: http://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

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

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

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, iccifort/2020.4.304

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

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

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

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

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

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

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

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
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

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	foss/2018b

biobambam2

Tools for processing BAM files

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

version	toolchain
2.0.87	intel/2018a

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

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
1.78		foss/2020b, fosscuda/2020b, intel/2020b
1.78	-Python-3.8.2	foss/2020a, intel/2020a

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: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

version	toolchain
0.19.0	intel/2017b
0.20.1	foss/2018b, intel/2018b

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/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/9.4.0, 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

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, iimpi/2019a, iimpi/2019b
2.10.1		gompi/2020a, iimpi/2020a
2.11.0		gompi/2019b, gompi/2020a, gompi/2020b

BLAT

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

homepage: http://genome.ucsc.edu/FAQ/FAQblat.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

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

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		GCCcore/10.3.0
1.2	-amd	GCC/7.3.0-2.30
2.2	-amd	GCCcore/9.3.0
3.0	-amd	GCCcore/10.3.0

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/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

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

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

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

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

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++

Bonnie++-1.97: Enhanced performance Test of Filesystem I/O

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

version	toolchain
1.97	foss/2016a

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

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

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

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

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: http://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

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

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

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

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

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

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/8.3.0

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

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

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

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 <this module name>

homepage: None

version	toolchain
default	FCC/4.5.0, Fujitsu/21.05, foss/2017b, foss/2018b, foss/2019b, foss/2020a, foss/2020b, fosscuda/2019b, fosscuda/2020a, fosscuda/2020b, intel/2016b, intel/2017a, intel/2019b, intel/2020a, intel/2020b, intelcuda/2019b, intelcuda/2020a, intelcuda/2020b

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
5.0.0		foss/2020b
5.1.2		foss/2020b

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

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/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/2018a, intel/2018b

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

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/8.3.0, GCCcore/9.3.0

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

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/8.3.0, GCCcore/9.3.0

C

C3D - cadaver - CaDiCaL - Caffe - cairo - cairomm - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - Cargo - carputils - Cartopy - CaSpER - CastXML - Catch2 - CatMAP - causallift - causalml - CaVEMan - CAVIAR - Cbc - CBLAS - ccache - CCfits - CCL - cclib - cctools - CD-HIT - CDAT - cdbfasta - cddlib - cDNA_Cupcake - CDO - cdsapi - cell2location - CellMix - CellRanger - CellRanger-ARC - CellRanger-ATAC - Centrifuge - Cereal - CESM-deps - CFDEMcoupling - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - CHARMM - charmm - CHASE - Check - check - CheckM - Cheetah - CheMPS2 - CHERAB - chewBBACA - chi2comb - Chimera - ChimPipe - Chromaprint - cicero - CIF2Cell - CIRCexplorer - CIRCexplorer2 - Circos - CIRI - cisTEM - CITE-seq-Count - Clang - Clang-Python-bindings - CLAPACK - CLHEP - CLISP - ClonalFrameML - CLooG - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CNT-ILP - CNVkit - CNVnator - CoCoALib - code-server - CODEX2 - CoinUtils - Commet - CompareM - COMSOL - Con3F - CONCOCT - configparser - configurable-http-proxy - ConnectomeWorkbench - Control-FREEC - CoordgenLibs - Coot - core-counter - Coreutils - corner - coverage - cowsay - CP2K - CPB - CPLEX - CppUnit - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CRF++ - CRISPResso2 - CrossMap - CrossTalkZ - CRPropa - cryoDRGN - CryptoMiniSat - CSB - CSBDeep - cscope - csvkit - ctags - ctffind - Cube - CubeGUI - CubeLib - CubeWriter - CUDA - CUDAcore - cuDNN - Cufflinks - CUnit - CuPy - cURL - custodian - cutadapt - cuTENSOR - CVS - CVXOPT - CVXPY - cysignals - Cython - cytoolz - cytosim - cyvcf2

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

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/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

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

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

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

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

Cargo

The Rust package manager

homepage: https://crates.io/

version	toolchain
0.13.0	foss/2016b

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

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

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

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

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

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

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

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

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

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/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

cddlib

An efficient implementation of the Double Description Method

homepage: https://github.com/cddlib/cddlib

version	toolchain
0.94i	GCCcore/8.2.0
0.94j	GCCcore/8.3.0

cDNA_Cupcake

cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.

homepage: https://github.com/Magdoll/cDNA_Cupcake

version	versionsuffix	toolchain
5.8	-Python-2.7.14	intel/2018a

CDO

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

homepage: https://code.zmaw.de/projects/cdo

version	toolchain
1.7.2	intel/2016b
1.8.1	intel/2017a
1.9.1	intel/2017b
1.9.2	intel/2017b
1.9.5	intel/2018a, intel/2018b, iomkl/2018b
1.9.8	intel/2019b
1.9.10	gompi/2020b

cdsapi

Climate Data Store API

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

version	versionsuffix	toolchain
0.1.4		foss/2019a
0.1.4	-Python-3.6.6	foss/2018b
0.3.0		GCCcore/9.3.0

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

homepage: https://github.com/BayraktarLab/cell2location/

version	toolchain
0.05-alpha	fosscuda/2020b

CellMix

A Comprehensive Toolbox for Gene Expression Deconvolution

homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix

version	versionsuffix	toolchain
1.6.2	-R-3.5.1	foss/2018b

CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

version	toolchain
3.0.0	system
3.0.2	system
3.1.0	system
4.0.0	system
5.0.0	system
5.0.1	system
6.0.0	system
6.0.1	system

CellRanger-ARC

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression.

homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

version	toolchain
1.0.1	system
2.0.0	system

CellRanger-ATAC

Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac

version	toolchain
1.2.0	system
2.0.0	system

Centrifuge

Classifier for metagenomic sequences

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

version	toolchain
1.0.3	foss/2018b
1.0.4-beta	foss/2018b, gompi/2020a

Cereal

cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.

homepage: https://uscilab.github.io/cereal/

version	toolchain
1.3.0	system

CESM-deps

CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth’s past, present, and future climate states.

homepage: https://www.cesm.ucar.edu/models/cesm2/

version	toolchain
2	foss/2018b, intel/2018b, iomkl/2018b

CFDEMcoupling

CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework.

homepage: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework

version	toolchain
3.8.0	foss/2018a

CFITSIO

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

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

version	toolchain
3.38	foss/2016a, intel/2016a
3.41	GCCcore/5.4.0, GCCcore/6.3.0, intel/2016b
3.42	GCCcore/6.4.0, intel/2017b
3.45	GCCcore/7.3.0, intel/2018b
3.47	GCCcore/8.2.0, GCCcore/8.3.0
3.48	GCCcore/9.3.0

cftime

Time-handling functionality from netcdf4-python

homepage: https://github.com/Unidata/cftime

version	versionsuffix	toolchain
1.0.0	-Python-3.6.4	intel/2018a
1.0.0b1	-Python-3.6.2	foss/2017b
1.0.1	-Python-2.7.15	intel/2018b
1.0.1	-Python-3.6.6	foss/2018b, intel/2018b

CGAL

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.

homepage: https://www.cgal.org/

version	versionsuffix	toolchain
4.8	-Python-2.7.11	foss/2016a, intel/2016a
4.8.1		foss/2016b, intel/2016b
4.8.1	-Python-2.7.12	foss/2016b, intel/2016b
4.9	-Python-2.7.12	intel/2016b
4.9	-Python-2.7.13	intel/2017a
4.11	-Python-2.7.13	intel/2017a
4.11	-Python-2.7.14	foss/2017b, intel/2017b
4.11	-Python-3.6.3	foss/2017b, intel/2017b
4.11.1	-Python-2.7.14	foss/2018a, intel/2018a
4.11.1	-Python-2.7.15	foss/2018b
4.11.1	-Python-3.6.4	foss/2018a
4.11.1	-Python-3.6.6	foss/2018b
4.14	-Python-3.7.2	foss/2019a, intel/2019a
4.14.1	-Python-3.7.4	foss/2019b, intel/2019b
4.14.3	-Python-3.8.2	gompi/2020a, iimpi/2020a
5.2		gompi/2020b

cget

Cmake package retrieval. This can be used to download and install cmake packages

homepage: https://cget.readthedocs.io/en/latest/index.html

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

Cgl

The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.

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

version	toolchain
0.60.2	foss/2018b

CGmapTools

Command-line Toolset for Bisulfite Sequencing Data Analysis

homepage: https://cgmaptools.github.io/

version	toolchain
0.1.2	intel/2019b

CGNS

The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.

homepage: https://cgns.github.io/

version	toolchain
3.3.1	foss/2016b
4.1.0	intelcuda/2019b

CharLS

CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios.

homepage: https://github.com/team-charls/charls

version	toolchain
2.0.0	GCCcore/6.4.0, GCCcore/7.3.0
2.1.0	GCCcore/8.2.0, GCCcore/8.3.0

CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems.

homepage: http://www.charmm.org

version	toolchain
37b2	foss/2016a, intel/2016a

charmm

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements.

homepage: http://www.charmm.org

version	toolchain
43b2	foss/2017b, intel/2017b

CHASE

Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.

homepage: http://people.duke.edu/~asallen/Software.html

version	toolchain
20130626	system

Check

Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

homepage: https://libcheck.github.io/check/

version	toolchain
0.15.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0

check

Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

homepage: https://libcheck.github.io/check/

version	toolchain
0.12.0	GCCcore/6.4.0

CheckM

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

homepage: https://github.com/Ecogenomics/CheckM

version	versionsuffix	toolchain
1.0.13	-Python-2.7.14	foss/2017b, intel/2017b
1.0.13	-Python-2.7.15	foss/2018b
1.0.13	-Python-3.6.3	foss/2017b, intel/2017b
1.0.18	-Python-2.7.15	foss/2019a
1.0.18	-Python-2.7.18	foss/2020b
1.1.2	-Python-3.7.4	foss/2019b, intel/2019b
1.1.3	-Python-3.8.2	intel/2020a

Cheetah

Cheetah is an open source template engine and code generation tool.

homepage: https://cheetahtemplate.org

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

CheMPS2

CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.

homepage: https://github.com/SebWouters/CheMPS2

version	toolchain
1.6	intel/2016a
1.7-rc2	intel/2016a
1.7.1	intel/2016a
1.7.2	intel/2016a
1.8	intel/2016b
1.8.8	intel/2018b
1.8.9	foss/2018b, foss/2019a, intel/2018b, intel/2019a, intel/2019b

CHERAB

CHERAB is a python library for forward modelling diagnostics based on spectroscopic plasma emission.

homepage: https://cherab.github.io/documentation/index.html

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

chewBBACA

chewBBACA stands for “BSR-Based Allele Calling Algorithm”. chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.

homepage: https://github.com/B-UMMI/chewBBACA

version	versionsuffix	toolchain
2.5.5	-Python-3.8.2	intel/2020a

chi2comb

Cumulative density function of linear combinations of independent chi-square random variables and a standard Normal distribution. As of now, this is basically a repackaging of the davies function implemented in the CompQuadForm library for R.

homepage: https://github.com/limix/chi2comb

version	toolchain
0.0.3	GCCcore/7.3.0

Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

homepage: https://www.cgl.ucsf.edu/chimera/

version	versionsuffix	toolchain
1.10	-linux_x86_64	system

ChimPipe

ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.

homepage: https://chimpipe.readthedocs.org/

version	versionsuffix	toolchain
0.9.5		foss/2018b
0.9.5	-Python-2.7.12	foss/2016b

Chromaprint

Chromaprint is the core component of the AcoustID project. It’s a client-side library that implements a custom algorithm for extracting fingerprints from any audio source.

homepage: https://acoustid.org/chromaprint

version	toolchain
1.4.3	GCCcore/8.2.0

cicero

Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments.

homepage: https://cole-trapnell-lab.github.io/cicero-release

version	versionsuffix	toolchain
1.3.4.11	-R-4.0.3-Monocle3	foss/2020b

CIF2Cell

CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files.

homepage: https://sourceforge.net/projects/cif2cell

version	versionsuffix	toolchain
1.2.10	-Python-2.7.16	GCCcore/8.3.0

CIRCexplorer

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

homepage: https://circexplorer2.readthedocs.io/

version	versionsuffix	toolchain
1.1.10	-Python-2.7.14	intel/2017b

CIRCexplorer2

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

homepage: http://circexplorer2.readthedocs.io/

version	versionsuffix	toolchain
2.3.2	-Python-2.7.14	intel/2017b
2.3.3	-Python-2.7.14	intel/2018a
2.3.8	-Python-2.7.18	foss/2020b

Circos

Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

homepage: http://www.circos.ca/

version	versionsuffix	toolchain
0.69-5	-Perl-5.24.0	foss/2016b
0.69-6	-Perl-5.26.1	GCCcore/6.4.0
0.69-6	-Perl-5.28.0	GCCcore/7.3.0
0.69-9		GCCcore/9.3.0

CIRI

CircRNA Identifier. A de novo circular RNA identification tool

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

version	versionsuffix	toolchain
2.0.6	-Perl-5.26.0	intel/2017b

cisTEM

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

homepage: https://cistem.org/

version	toolchain
1.0.0-beta	foss/2018a

CITE-seq-Count

A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.

homepage: https://github.com/Hoohm/CITE-seq-Count

version	versionsuffix	toolchain
1.4.3	-Python-3.6.6	foss/2018b
1.4.3	-Python-3.7.4	foss/2019b

Clang

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.

homepage: https://clang.llvm.org/

version	versionsuffix	toolchain
3.3		GCC/4.8.1
3.4		GCC/4.8.2
3.4.1		GCC/4.8.2
3.4.2		GCC/4.8.2
3.6.0		GCC/4.9.2
3.6.1		GCC/4.9.2
3.7.0		GNU/4.9.3-2.25
3.7.1		GCC/4.9.3-2.25, foss/2016a
3.8.0		GCC/4.9.3-2.25
3.8.1		GCC/5.4.0-2.26, foss/2016b
5.0.0		GCC/6.4.0-2.28
5.0.1		GCC/6.4.0-2.28
6.0.1		GCC/6.4.0-2.28, GCC/7.3.0-2.30
7.0.0		GCC/6.4.0-2.28
7.0.1		GCC/7.3.0-2.30
8.0.0		GCCcore/8.2.0
8.0.0	-CUDA-10.1.105	GCCcore/8.2.0
8.0.1	-CUDA-10.1.105	GCC/8.2.0-2.31.1
8.0.1	-CUDA-10.1.243	GCC/8.3.0
9.0.1		GCCcore/8.3.0
9.0.1	-CUDA-10.1.243	GCC/8.3.0
10.0.0		GCCcore/8.3.0, GCCcore/9.3.0
10.0.1		GCCcore/9.3.0
11.0.0		GCCcore/9.3.0
11.0.1		GCCcore/10.2.0, gcccuda/2020b

Clang-Python-bindings

Python bindings for libclang

homepage: https://clang.llvm.org

version	versionsuffix	toolchain
8.0.0	-Python-2.7.15	GCCcore/8.2.0
10.0.1	-Python-3.8.2	GCCcore/9.3.0

CLAPACK

C version of LAPACK

homepage: http://www.netlib.org/clapack

version	toolchain
3.2.1	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2017a

CLHEP

The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.

homepage: https://proj-clhep.web.cern.ch/proj-clhep/

version	toolchain
2.1.1.0	intel/2016a
2.1.3.1	intel/2016a
2.2.0.8	intel/2016a
2.3.1.1	intel/2016a
2.3.4.3	foss/2017b, intel/2017b
2.4.0.0	intel/2017b
2.4.1.0	foss/2017b, foss/2018b, intel/2017b, intel/2018b
2.4.1.3	foss/2019b, foss/2020a
2.4.4.0	GCC/10.2.0

CLISP

Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.

homepage: https://clisp.sourceforge.io/

version	toolchain
2.49	GCCcore/6.4.0, GCCcore/9.3.0

ClonalFrameML

Efficient Inference of Recombination in Whole Bacterial Genomes

homepage: https://github.com/xavierdidelot/ClonalFrameML

version	toolchain
1.11	foss/2016b

CLooG

CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN…) that reaches each integral point of one or more parameterized polyhedra. CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code.

homepage: http://www.bastoul.net/cloog/index.php

version	toolchain
0.18.1	GCC/4.8.2

Clp

Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.

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

version	toolchain
1.17.3	foss/2018b

Clustal-Omega

Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms

homepage: http://www.clustal.org/omega/

version	toolchain
1.2.0	foss/2016b
1.2.4	GCC/8.3.0, foss/2018b, intel/2018a, intel/2018b

ClustalW2

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

homepage: https://www.ebi.ac.uk/Tools/msa/clustalw2/

version	toolchain
2.1	foss/2016b, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2017b, intel/2018b, intel/2020a

Cluster-Buster

Cluster-Buster: Finding dense clusters of motifs in DNA sequences

homepage: https://github.com/weng-lab/cluster-buster/

version	toolchain
20160106	intel/2016a

ClusterShell

ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.

homepage: https://cea-hpc.github.io/clustershell/

version	toolchain
1.7.3	system

CMake

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

homepage: https://www.cmake.org

version	toolchain
2.8.11	GCC/4.8.1
2.8.12	GCC/4.8.1, GCC/4.8.2
3.0.0	GCC/4.8.3
3.1.0	GCC/4.9.2
3.1.3	GCC/4.9.2, system
3.2.1	GCC/4.9.2, GNU/4.9.3-2.25
3.3.1	system
3.3.2	GNU/4.9.3-2.25, gimkl/2.11.5
3.4.1	GCC/4.9.2, GCCcore/4.9.3, foss/2016a, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
3.4.3	foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a
3.5.1	intel/2016a
3.5.2	GCC/4.9.3-2.25, foss/2016a, foss/2016b, intel/2016a, intel/2016b, system
3.6.1	GCC/5.4.0-2.26, GCCcore/4.9.3, foss/2016b, intel/2016b, system
3.6.2	GCCcore/5.4.0, foss/2016b, intel/2016b
3.7.1	GCCcore/5.4.0, GCCcore/6.2.0, foss/2016b, intel/2016b
3.7.2	GCCcore/6.3.0, foss/2016b, intel/2016b
3.8.0	GCCcore/6.3.0
3.8.1	GCCcore/6.3.0
3.8.2	GCCcore/6.3.0
3.9.1	GCCcore/6.3.0, GCCcore/6.4.0, system
3.9.4	GCCcore/6.4.0
3.9.5	GCCcore/6.4.0
3.9.6	system
3.10.0	GCCcore/6.4.0
3.10.1	GCCcore/6.4.0
3.10.2	GCCcore/6.4.0, GCCcore/7.2.0
3.10.3	GCCcore/6.4.0, GCCcore/7.2.0
3.11.1	GCCcore/6.4.0
3.11.4	GCCcore/6.4.0, GCCcore/7.3.0
3.12.1	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, system
3.13.3	GCCcore/8.2.0
3.15.1	system
3.15.3	GCCcore/8.3.0
3.16.4	GCCcore/9.3.0
3.18.4	GCCcore/10.2.0, system
3.20.1	GCCcore/10.3.0

CNT-ILP

Integer Linear Program for the Copy-Number Tree Problem

homepage: https://compbio.cs.brown.edu/projects/cnt-ilp/

version	toolchain
20171031	GCC/8.2.0-2.31.1

CNVkit

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

homepage: https://github.com/etal/cnvkit

version	versionsuffix	toolchain
0.9.2	-Python-2.7.14	intel/2017b
0.9.3	-Python-3.6.4	intel/2018a
0.9.6	-Python-3.7.2-R-3.6.0	foss/2019a
0.9.8	-R-4.0.3	foss/2020b

CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

homepage: https://github.com/abyzovlab/CNVnator

version	toolchain
0.3.3	foss/2016b

CoCoALib

CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra.

homepage: http://cocoa.dima.unige.it/cocoalib

version	toolchain
0.99601	GCC/8.2.0-2.31.1
0.99700	GCC/8.3.0

code-server

Run VS Code on any machine anywhere and access it in the browser.

homepage: https://github.com/cdr/code-server

version	toolchain
3.7.3	system

CODEX2

Full-spectrum copy number variation detection by high-throughput DNA sequencing

homepage: https://github.com/yuchaojiang/CODEX2

version	versionsuffix	toolchain
20180227	-R-3.4.3	intel/2017b

CoinUtils

CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.

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

version	toolchain
2.11.3	GCCcore/7.3.0, foss/2018b

Commet

COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.

homepage: https://colibread.inria.fr/software/commet/

version	versionsuffix	toolchain
20150415	-Python-2.7.11	foss/2016a

CompareM

A toolbox for comparative genomics.

homepage: https://github.com/dparks1134/CompareM

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

COMSOL

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.

homepage: https://www.comsol.com

version	toolchain
5.4.0.225	system

Con3F

Con3F is a Python package to read, manipulate and convert force field files

homepage: https://github.ugent.be/CMM/con3f

version	versionsuffix	toolchain
1.0-20190329	-Python-3.7.2	intel/2019a

CONCOCT

Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

homepage: https://concoct.readthedocs.io

version	versionsuffix	toolchain
1.0.0	-Python-2.7.14	foss/2017b
1.0.0	-Python-2.7.15	foss/2018b
1.0.0	-Python-3.6.3	foss/2017b
1.1.0	-Python-2.7.15	foss/2019a
1.1.0	-Python-2.7.18	foss/2020b

configparser

configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5

homepage: https://docs.python.org/3/library/configparser.html

version	versionsuffix	toolchain
3.5.0	-Python-2.7.11	foss/2016a
3.5.0	-Python-2.7.12	foss/2016b, intel/2016b
3.5.0	-Python-3.5.2	intel/2016b
3.5.0	-Python-3.6.3	intel/2017b

configurable-http-proxy

HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.

homepage: https://github.com/jupyterhub/configurable-http-proxy

version	versionsuffix	toolchain
1.3.0	-nodejs-4.4.7	foss/2016a
3.1.1	-nodejs-8.9.4	foss/2017a
4.2.1		GCCcore/10.2.0

ConnectomeWorkbench

Connectome Workbench is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

homepage: https://www.humanconnectome.org/software/connectome-workbench

version	versionsuffix	toolchain
1.2.2		system
1.3.2		GCCcore/8.2.0, foss/2017b, intel/2017b
1.4.2	-rh_linux64	system

Control-FREEC

Copy number and genotype annotation from whole genome and whole exome sequencing data.

homepage: https://github.com/BoevaLab/FREEC

version	toolchain
11.5	GCC/7.3.0-2.30, GCC/8.2.0-2.31.1

CoordgenLibs

Schrodinger-developed 2D Coordinate Generation

homepage: https://github.com/schrodinger/coordgenlibs

version	toolchain
1.3.2	gompi/2019a, iimpi/2019a

Coot

Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot

version	versionsuffix	toolchain
0.8.1	-binary-Linux-x86_64-rhel-6-python-gtk2	system

core-counter

Tool to check available cores and OMP threads

homepage: https://github.com/gjbex/core-counter

version	toolchain
1.1.1	system

Coreutils

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

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

version	toolchain
8.23	GCC/4.9.2
8.27	GCCcore/5.4.0
8.29	GCCcore/6.4.0
8.32	GCCcore/8.3.0, GCCcore/9.3.0

corner

Make some beautiful corner plots.

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

version	versionsuffix	toolchain
2.0.1	-Python-2.7.15	foss/2019a
2.0.1	-Python-3.7.2	foss/2019a

coverage

Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.

homepage: https://coverage.readthedocs.io

version	versionsuffix	toolchain
4.5.1	-Python-2.7.14	intel/2017b

cowsay

Configurable talking characters in ASCII art

homepage: https://github.com/tnalpgge/rank-amateur-cowsay

version	toolchain
3.04	system

CP2K

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

homepage: https://www.cp2k.org/

version	versionsuffix	toolchain
3.0		intel/2016a, intel/2016b, intel/2017b, intel/2018a
3.0	-psmp	intel/2016b
4.1		intel/2016b
4.1	-psmp	foss/2016b
5.1		foss/2018a, intel/2017b, intel/2018a, intel/2020a
6.1		foss/2019a, intel/2018a, intel/2020a
7.1		foss/2020b, intel/2020a, intel/2020b
7.1	-psmp	foss/2020b
8.1		foss/2020b

CPB

CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene in order to discover genes that function in a common biological process. In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives with a nonparametric filtering scheme. In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information.

homepage: http://tda.gatech.edu/software/cpb/index.html

version	versionsuffix	toolchain
11-4-2011	-Python-2.7.13	foss/2017a

CPLEX

IBM ILOG CPLEX Optimizer’s mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.

homepage: https://www.ibm.com/analytics/cplex-optimizer

version	versionsuffix	toolchain
12.9		GCCcore/8.2.0
12.10	-Python-3.7.4	GCCcore/8.3.0

CppUnit

CppUnit is the C++ port of the famous JUnit framework for unit testing.

homepage: https://freedesktop.org/wiki/Software/cppunit/

version	toolchain
1.12.1	GCCcore/6.4.0, GCCcore/7.3.0, foss/2016a
1.15.1	GCCcore/8.3.0, GCCcore/9.3.0

cram

Cram is a functional testing framework for command line applications.

homepage: https://bitheap.org/cram

version	toolchain
0.7	GCCcore/8.2.0

cramtools

CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.

homepage: https://github.com/enasequence/cramtools/

version	versionsuffix	toolchain
2.0	-Java-1.7.0_80	system
3.0	-Java-1.7.0_80	system

CrayCCE

Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayGNU

Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayIntel

Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayPGI

Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

crb-blast

Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.

homepage: https://github.com/cboursnell/crb-blast

version	versionsuffix	toolchain
0.6.9		intel/2017a
0.6.9	-Ruby-2.6.1	foss/2018b

CRF++

CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking.

homepage: https://taku910.github.io/crfpp/

version	toolchain
0.58	iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b

CRISPResso2

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

homepage: https://github.com/pinellolab/CRISPResso2

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

CrossMap

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF.

homepage: http://crossmap.sourceforge.net

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

CrossTalkZ

CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.

homepage: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/

version	toolchain
1.4	foss/2016a

CRPropa

CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment.

homepage: https://crpropa.desy.de

version	versionsuffix	toolchain
3.1.5	-Python-3.7.2	foss/2019a
3.1.6	-Python-3.8.2	foss/2020a

cryoDRGN

cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

homepage: https://cb.csail.mit.edu/cb/cryodrgn/

version	toolchain
0.3.2	fosscuda/2020b

CryptoMiniSat

CryptoMiniSat is an advanced SAT solver

homepage: https://github.com/msoos/cryptominisat

version	versionsuffix	toolchain
5.0.1	-Python-2.7.12	intel/2016b

CSB

Computational Structural Biology Toolbox CSB is a python library and application framework, which can be used to solve problems in the field of structural bioinformatics. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components: 1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. 2. Application framework - console applications (“protocols”), which consume objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works.

homepage: https://github.com/csb-toolbox

version	toolchain
1.2.5	foss/2020b

CSBDeep

CSBDeep is a toolbox for Content-aware Image Restoration (CARE).

homepage: https://csbdeep.bioimagecomputing.com/

version	versionsuffix	toolchain
0.4.1	-Python-3.7.2	foss/2019a, fosscuda/2019a

cscope

Cscope is a developer’s tool for browsing source code.

homepage: http://cscope.sourceforge.net/

version	toolchain
15.9	system

csvkit

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

homepage: https://github.com/wireservice/csvkit

version	versionsuffix	toolchain
1.0.4		GCCcore/8.2.0
1.0.5	-Python-3.7.4	GCCcore/8.3.0

ctags

Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.

homepage: http://ctags.sourceforge.net/

version	toolchain
5.8	system

ctffind

Program for finding CTFs of electron micrographs.

homepage: https://grigoriefflab.umassmed.edu/ctffind4

version	toolchain
4.1.13	foss/2019a, fosscuda/2019a, fosscuda/2019b
4.1.14	foss/2019b, fosscuda/2019b, fosscuda/2020b

Cube

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.

homepage: http://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.3.4	foss/2016a

CubeGUI

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.4	GCCcore/8.2.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0

CubeLib

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.4	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0

CubeWriter

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.3	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0

CUDA

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

homepage: https://developer.nvidia.com/cuda-toolkit

version	toolchain
5.5.22	GCC/4.8.2, system
6.0.37	system
6.5.14	system
7.0.28	system
7.5.18	GCC/4.9.4-2.25, iccifort/2016.3.210-GCC-4.9.3-2.25, system
8.0.44	GCC/5.4.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26, system
8.0.61	system
8.0.61_375.26	GCC/5.4.0-2.26
9.0.176	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28, system
9.1.85	GCC/6.4.0-2.28, system
9.2.88	GCC/6.4.0-2.28, GCC/7.3.0-2.30, system
9.2.148.1	system
10.0.130	system
10.1.105	GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1, system
10.1.168	system
10.1.243	GCC/8.3.0, iccifort/2019.5.281, system
10.2.89	GCC/8.3.0
11.0.2	GCC/9.3.0, iccifort/2020.1.217
11.1.1	GCC/10.2.0, iccifort/2020.4.304

CUDAcore

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

homepage: https://developer.nvidia.com/cuda-toolkit

version	toolchain
11.0.2	system
11.1.1	system
11.2.1	system
11.2.2	system
11.3.0	system
11.3.1	system

cuDNN

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

homepage: https://developer.nvidia.com/cudnn

version	versionsuffix	toolchain
4.0		system
5.0	-CUDA-7.5.18	system
5.0-rc		system
5.1	-CUDA-8.0.44	system
6.0	-CUDA-8.0.61	system
6.0.21	-CUDA-7.5.18	system
6.0.21	-CUDA-8.0.44	system
7.0.2	-CUDA-9.0.176	system
7.0.5	-CUDA-8.0.44	system
7.0.5	-CUDA-9.0.176	system
7.0.5	-CUDA-9.1.85	system
7.0.5.15		fosscuda/2017b, fosscuda/2018a, intelcuda/2017b
7.1.4.18		fosscuda/2018b
7.4.2.24		gcccuda/2019a
7.4.2.24	-CUDA-10.0.130	system
7.5.0.56	-CUDA-10.0.130	system
7.6.2.24	-CUDA-10.1.243	system
7.6.4.38		gcccuda/2019a, gcccuda/2019b
7.6.4.38	-CUDA-10.0.130	system
8.0.4.30	-CUDA-11.0.2	system
8.0.4.30	-CUDA-11.1.1	system
8.0.5.39	-CUDA-11.1.1	system
8.1.0.77	-CUDA-11.2.1	system
8.1.1.33	-CUDA-11.2.1	system
8.2.1.32	-CUDA-11.3.1	system

Cufflinks

Transcript assembly, differential expression, and differential regulation for RNA-Seq

homepage: http://cole-trapnell-lab.github.io/cufflinks/

version	toolchain
2.2.1	foss/2016a, foss/2016b, foss/2018b, gompi/2019b, intel/2017b, intel/2018a
20190706	GCC/10.2.0, gompi/2019a

CUnit

Automated testing framework for C.

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

version	toolchain
2.1-3	GCCcore/6.4.0

CuPy

CuPy is an open-source array library accelerated with NVIDIA CUDA.

homepage: https://cupy.dev

version	versionsuffix	toolchain
8.2.0	-Python-3.7.4	fosscuda/2019b
8.5.0		fosscuda/2020b

cURL

libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.

homepage: https://curl.haxx.se

version	toolchain
7.33.0	GCC/4.8.2
7.34.0	GCC/4.8.2
7.40.0	GCC/4.9.2
7.46.0	iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
7.47.0	foss/2016a, intel/2016.02-GCC-4.9, intel/2016a
7.49.1	GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b
7.52.1	gimkl/2017a, intel/2016b
7.53.1	GCCcore/6.3.0
7.54.0	GCCcore/6.3.0
7.55.1	GCCcore/6.4.0
7.56.0	GCCcore/6.4.0
7.56.1	GCCcore/6.4.0
7.58.0	GCCcore/6.4.0
7.59.0	GCCcore/6.4.0
7.60.0	GCCcore/7.2.0, GCCcore/7.3.0
7.63.0	GCCcore/8.2.0
7.66.0	GCCcore/8.3.0
7.69.1	GCCcore/9.3.0
7.72.0	GCCcore/10.2.0
7.76.0	GCCcore/10.3.0

custodian

A simple JIT job management framework in Python.

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

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

cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

homepage: https://opensource.scilifelab.se/projects/cutadapt/

version	versionsuffix	toolchain
1.9.1	-Python-2.7.11	foss/2016a
1.9.1	-Python-2.7.12	foss/2016b
1.14	-Python-2.7.13	foss/2017a, intel/2017a
1.15	-Python-3.5.2	foss/2016b
1.16	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
1.16	-Python-3.6.3	foss/2017b, intel/2017b
1.16	-Python-3.6.4	foss/2018a, intel/2018a
1.18		GCCcore/8.2.0, GCCcore/8.3.0
1.18	-Python-2.7.15	foss/2018b
1.18	-Python-2.7.18	GCC/10.2.0
1.18	-Python-3.6.6	foss/2018b, intel/2018b
2.1	-Python-3.6.6	foss/2018b
2.7	-Python-3.7.4	GCCcore/8.3.0
2.8	-Python-3.7.4	GCCcore/8.3.0
2.10	-Python-3.7.4	GCCcore/8.3.0
2.10	-Python-3.8.2	GCCcore/9.3.0

cuTENSOR

The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.

homepage: https://developer.nvidia.com/cutensor

version	versionsuffix	toolchain
1.2.2.5		gcccuda/2019b
1.2.2.5	-CUDA-11.1.1	system

CVS

CVS is a version control system, an important component of Source Configuration Management (SCM).

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

version	toolchain
1.11.23	GCC/4.8.2, GCCcore/4.9.3, GCCcore/6.4.0

CVXOPT

CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python’s extensive standard library and on the strengths of Python as a high-level programming language.

homepage: https://cvxopt.org

version	versionsuffix	toolchain
1.1.9	-Python-2.7.13	intel/2017a
1.2.1	-Python-3.6.4	intel/2018a
1.2.3		foss/2019a
1.2.4	-Python-3.7.4	intel/2019b
1.2.6		foss/2020b

CVXPY

CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers.

homepage: https://www.cvxpy.org/

version	versionsuffix	toolchain
1.0.24		foss/2019a
1.0.28	-Python-3.7.4	foss/2019b

cysignals

The cysignals package provides mechanisms to handle interrupts (and other signals and errors) in Cython code.

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

version	versionsuffix	toolchain
1.10.2	-Python-2.7.14	foss/2017b, intel/2017b
1.10.2	-Python-3.6.3	foss/2017b, intel/2017b

Cython

Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).

homepage: https://cython.org/

version	versionsuffix	toolchain
0.23.4	-Python-2.7.10	gimkl/2.11.5
0.24.1	-Python-2.7.11	foss/2016a
0.25.2	-Python-2.7.12	foss/2016b
0.25.2	-Python-3.6.4	intel/2018a
0.27.3	-Python-2.7.15	GCCcore/8.2.0
0.29.10	-Python-2.7.14	foss/2017b, intel/2017b
0.29.10	-Python-3.6.3	foss/2017b, intel/2017b
0.29.22		GCCcore/10.2.0

cytoolz

Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.

homepage: https://github.com/pytoolz/cytoolz

version	versionsuffix	toolchain
0.10.1	-Python-3.6.6	foss/2018b
0.10.1	-Python-3.7.2	GCCcore/8.2.0

cytosim

Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).

homepage: https://github.com/nedelec/cytosim

version	versionsuffix	toolchain
20190117	-mkl	gomkl/2019a

cyvcf2

cython + htslib == fast VCF and BCF processing

homepage: https://github.com/brentp/cyvcf2

version	versionsuffix	toolchain
0.10.10	-Python-3.6.6	foss/2018b
0.11.5		foss/2019a, intel/2019a

D

dadi - dagitty - Dalton - damageproto - dammit - DANPOS2 - DAS_Tool - dask - datamash - davix - DB - DB_File - DBD-mysql - DBG2OLC - DBus - dbus-glib - dcm2niix - DCMTK - dd - deal.II - deap - decona - deconf - DeconICA - deepdiff - DeepSurv - deepTools - Delly - DeMixT - DendroPy - destiny - detonate - DFA - DFT-D3 - DFTB+ - dftd3-lib - DIAL - DIAMOND - dicom2nifti - DicomBrowser - Diffutils - dijitso - dill - DIRAC - distributed - DL_POLY_4 - DL_POLY_Classic - dm-reverb - dm-tree - DMCfun - DMTCP - DOLFIN - Doris - DosageConvertor - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - Drake - DROP - dropEst - DSA - dSFMT - DSRC - Dsuite - dtcmp - dtcwt - dxpy

dadi

∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum.

homepage: https://bitbucket.org/gutenkunstlab/dadi

version	versionsuffix	toolchain
1.7.0	-Python-2.7.12	intel/2016b

dagitty

A port of the web-based software ‘DAGitty’, available at <http://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.

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

version	versionsuffix	toolchain
0.2-2	-R-3.5.1	foss/2018b

Dalton

The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html.

homepage: https://daltonprogram.org/

version	versionsuffix	toolchain
2016	-i8	intel/2017b

damageproto

X protocol and ancillary headers for xinerama

homepage: http://www.freedesktop.org/wiki/Software/xlibs

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

dammit

dammit is a simple de novo transcriptome annotator. It was born out of the observations that annotation is mundane and annoying, all the individual pieces of the process exist already, and the existing solutions are overly complicated or rely on crappy non-free software.

homepage: http://www.camillescott.org/dammit/

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

DANPOS2

A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2

homepage: https://sites.google.com/site/danposdoc

version	versionsuffix	toolchain
2.2.2	-Python-2.7.12	foss/2016b

DAS_Tool

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

homepage: https://github.com/cmks/DAS_Tool

version	versionsuffix	toolchain
1.1.1	-R-3.5.1-Python-2.7.15	foss/2018b

dask

Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.

homepage: https://dask.org/

version	versionsuffix	toolchain
0.8.2	-Python-2.7.11	intel/2016a
0.8.2	-Python-3.5.1	intel/2016a
0.11.0	-Python-2.7.11	foss/2016a
0.11.0	-Python-2.7.12	intel/2016b
0.11.0	-Python-3.5.2	intel/2016b
0.12.0	-Python-2.7.12	intel/2016b
0.12.0	-Python-3.5.2	foss/2016b, intel/2016b
0.16.0	-Python-2.7.14	foss/2017b, intel/2017b
0.16.0	-Python-3.6.3	foss/2017b, intel/2017b
0.17.0	-Python-2.7.13	foss/2017a, intel/2017a
0.17.0	-Python-3.6.1	intel/2017a
0.17.2	-Python-3.6.4	foss/2018a, intel/2018a
0.19.4	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
1.0.0	-Python-3.6.6	foss/2018b, intel/2018b
1.1.4	-Python-2.7.15	fosscuda/2018b
2.3.0	-Python-3.7.2	foss/2019a
2.8.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
2.18.1	-Python-3.8.2	foss/2020a, intel/2020a
2021.2.0		foss/2020b, fosscuda/2020b, intel/2020b

datamash

GNU datamash performs basic numeric, textual and statistical operations on input data files

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

version	toolchain
1.3	foss/2018a
1.5	GCCcore/10.2.0, GCCcore/7.3.0, GCCcore/8.3.0

davix

The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols.

homepage: https://dmc.web.cern.ch/projects/davix/home

version	toolchain
0.6.6	intel/2017a
0.7.5	GCCcore/8.3.0

DB

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

homepage: http://www.oracle.com/technetwork/products/berkeleydb

version	toolchain
4.8.30	intel/2016a
6.2.23	foss/2016a
6.2.32	GCCcore/6.4.0, intel/2017a
18.1.25	GCCcore/7.3.0
18.1.32	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
18.1.40	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0

DB_File

Perl5 access to Berkeley DB version 1.x.

homepage: https://perldoc.perl.org/DB_File.html

version	versionsuffix	toolchain
1.835		GCCcore/9.3.0
1.835	-Perl-5.20.3	intel/2016a
1.835	-Perl-5.22.1	foss/2016a
1.855		GCCcore/10.2.0

DBD-mysql

Perl binding for MySQL

homepage: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm

version	versionsuffix	toolchain
4.032	-Perl-5.22.2	intel/2016a
4.033	-Perl-5.24.0	intel/2016b
4.042	-Perl-5.24.1	intel/2017a
4.046	-Perl-5.26.0	foss/2017b, intel/2017b
4.046	-Perl-5.26.1	intel/2018a
4.048	-Perl-5.28.0	foss/2018b
4.050		GCC/10.2.0
4.050	-Perl-5.28.1	foss/2019a

DBG2OLC

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

homepage: https://github.com/yechengxi/DBG2OLC

version	toolchain
20170208	intel/2016b, intel/2017a
20180221	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28

DBus

D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a “single instance” application or daemon, and to launch applications and daemons on demand when their services are needed.

homepage: http://dbus.freedesktop.org/

version	toolchain
1.10.8	foss/2016a, intel/2016a
1.10.12	intel/2016b
1.10.20	GCCcore/6.4.0
1.11.20	intel/2017a
1.13.0	intel/2017b
1.13.6	GCCcore/6.4.0, GCCcore/7.3.0
1.13.8	GCCcore/8.2.0
1.13.12	GCCcore/8.3.0, GCCcore/9.3.0
1.13.18	GCCcore/10.2.0, GCCcore/10.3.0

dbus-glib

D-Bus is a message bus system, a simple way for applications to talk to one another.

homepage: http://dbus.freedesktop.org/doc/dbus-glib

version	toolchain
0.106	foss/2016a, intel/2016a
0.108	intel/2016b, intel/2017a
0.110	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, intel/2017b

dcm2niix

dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.

homepage: https://github.com/rordenlab/dcm2niix

version	toolchain
1.0.20180622	GCCcore/6.4.0, GCCcore/7.3.0
1.0.20190902	GCCcore/7.3.0, GCCcore/8.2.0
1.0.20200331	GCCcore/8.3.0
1.0.20201102	GCCcore/8.3.0

DCMTK

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

homepage: https://dicom.offis.de/dcmtk

version	toolchain
3.6.3	GCCcore/7.3.0
3.6.5	GCCcore/8.2.0, GCCcore/8.3.0

dd

dd is a package for working with binary decision diagrams that includes both a pure Python implementation and Cython bindings to C libraries (CUDD, Sylvan, BuDDy). The Python and Cython modules implement the same API, so the same user code runs with both. All the standard operations on BDDs are available, including dynamic variable reordering using sifting, garbage collection, dump/load from files, plotting, and a parser of quantified Boolean expressions. This module includes bindings for: CUDD v3.0.0, Sylvan v1.0.0

homepage: https://github.com/tulip-control/dd

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

deal.II

deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.

homepage: https://www.dealii.org

version	toolchain
9.1.1	intel/2019a

deap

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent.

homepage: http://deap.readthedocs.org/en/master/

version	versionsuffix	toolchain
0.9.2	-Python-2.7.12	intel/2016b

decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads

homepage: https://github.com/Saskia-Oosterbroek/decona

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

deconf

decomposition (deconfounding) of OMICS datasets in heterogeneous tissues

homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/

version	versionsuffix	toolchain
1.0.1	-R-3.5.1	foss/2018b

DeconICA

Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is an R package for identifying immune-related signals in transcriptome through deconvolution or unsupervised source separation methods.

homepage: https://urszulaczerwinska.github.io/DeconICA

version	versionsuffix	toolchain
0.1.0	-R-3.5.1	foss/2018b

deepdiff

DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.

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

version	versionsuffix	toolchain
3.3.0	-Python-2.7.15	intel/2018b
3.3.0	-Python-3.6.6	foss/2018b, intel/2018b
4.0.6	-Python-3.7.2	GCCcore/8.2.0
5.0.2	-Python-3.7.4	GCCcore/8.3.0

DeepSurv

DeepSurv is a deep learning approach to survival analysis.

homepage: https://github.com/jaredleekatzman/DeepSurv

version	versionsuffix	toolchain
2.0.0-20180922	-Python-3.6.6	fosscuda/2018b

deepTools

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

homepage: https://deeptools.readthedocs.io/

version	versionsuffix	toolchain
2.5.4	-Python-3.6.3	intel/2017b
3.3.1	-Python-3.6.6	foss/2018b
3.3.1	-Python-3.7.4	intel/2019b
3.3.1	-Python-3.8.2	foss/2020a

Delly

Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.

homepage: https://github.com/dellytools/delly/

version	versionsuffix	toolchain
0.7.8	-linux_x86_64	system
0.8.7		gompi/2020b

DeMixT

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.

homepage: https://bioinformatics.mdanderson.org/main/DeMixT

version	versionsuffix	toolchain
0.2.1	-R-3.5.1	foss/2018b

DendroPy

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

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

version	versionsuffix	toolchain
4.4.0		GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2019a
4.4.0	-Python-2.7.15	intel/2018b
4.5.2		GCCcore/10.2.0
4.5.2	-Python-2.7.18	GCCcore/10.2.0

destiny

R packages to create and plot diffusion maps.

homepage: https://bioconductor.org/packages/destiny

version	versionsuffix	toolchain
2.5.6	-R-3.4.0	intel/2017a

detonate

DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

homepage: http://deweylab.biostat.wisc.edu/detonate/

version	toolchain
1.11	intel/2017b

DFA

Python library for modeling DFAs, Moore Machines, and Transition Systems.

homepage: https://github.com/mvcisback/dfa

version	versionsuffix	toolchain
0.3.4	-Python-3.8.2	GCCcore/9.3.0
2.1.2		GCCcore/10.2.0

DFT-D3

DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.

homepage: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english

version	toolchain
3.2.0	GCC/8.3.0, intel/2019a

DFTB+

DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.

homepage: https://www.dftb-plus.info

version	versionsuffix	toolchain
1.3.1		intel/2017a
17.1	-Python-2.7.14	intel/2017b
19.1	-Python-2.7.16	foss/2019b
19.1	-Python-2.7.16-mpi	foss/2019b

dftd3-lib

This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.

homepage: https://github.com/dftbplus/dftd3-lib

version	toolchain
0.9	GCC/8.3.0

DIAL

DIAL (De novo Identification of Alleles) is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate in genotyping assays.

homepage: http://www.bx.psu.edu/miller_lab/

version	toolchain
2011.06.06	foss/2016a

DIAMOND

Accelerated BLAST compatible local sequence aligner

homepage: https://github.com/bbuchfink/diamond

version	toolchain
0.9.22	foss/2018a, foss/2018b, intel/2018a, intel/2018b
0.9.24	iccifort/2019.1.144-GCC-8.2.0-2.31.1
0.9.30	GCC/8.3.0, iccifort/2019.5.281
0.9.36	GCC/9.3.0
2.0.4	GCC/9.3.0
2.0.6	GCC/7.3.0-2.30
2.0.7	GCC/10.2.0

dicom2nifti

Python library for converting dicom files to nifti

homepage: https://github.com/icometrix/dicom2nifti

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

DicomBrowser

DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once.

homepage: http://nrg.wustl.edu/software/dicom-browser/

version	versionsuffix	toolchain
1.7.0b5	-Java-1.7.0_80	system

Diffutils

Diffutils: GNU diff utilities - find the differences between files

homepage: http://www.gnu.org/software/diffutils/diffutils.html

version	toolchain
3.3	GCC/4.8.2

dijitso

dijitso is a Python module for distributed just-in-time shared library building.

homepage: https://bitbucket.org/fenics-project/dijitso

version	versionsuffix	toolchain
2019.1.0	-Python-3.7.4	foss/2019b

dill

dill extends python’s pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.

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

version	toolchain
0.3.0	GCCcore/8.2.0
0.3.3	GCCcore/10.2.0, GCCcore/8.3.0
0.3.4	GCCcore/10.3.0

DIRAC

DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations

homepage: http://www.diracprogram.org

version	versionsuffix	toolchain
19.0	-Python-2.7.18-int64	intel/2020a
19.0	-Python-2.7.18-mpi-int64	intel/2020a

distributed

Dask.distributed is a lightweight library for distributed computing in Python. It extends both the concurrent.futures and dask APIs to moderate sized clusters.

homepage: https://distributed.readthedocs.io/

version	versionsuffix	toolchain
1.14.3	-Python-2.7.12	intel/2016b
1.14.3	-Python-3.5.2	intel/2016b
1.21.6	-Python-3.6.4	intel/2018a

DL_POLY_4

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software

homepage: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx

version	toolchain
5.0.0	foss/2020b, intel/2020b

DL_POLY_Classic

DL_POLY Classic is a freely available molecular dynamics program developed from the DL_POLY_2 package. This version does not install the java gui.

homepage: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/

version	versionsuffix	toolchain
1.9		intel/2016b
1.9	-PLUMED-2.2.3	intel/2016b
1.10		foss/2019b, intel/2019b

dm-reverb

Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues.

homepage: https://github.com/deepmind/reverb

version	toolchain
0.2.0	foss/2020b

dm-tree

dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each “leaf” preserving the overall structure.

homepage: https://github.com/deepmind/tree

version	toolchain
0.1.1	GCCcore/8.3.0
0.1.5	GCCcore/10.2.0

DMCfun

Diffusion Model of Conflict (DMC) in Reaction Time Tasks

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

version	versionsuffix	toolchain
1.3.0	-R-3.6.2	foss/2019b

DMTCP

DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications.

homepage: http://dmtcp.sourceforge.net/index.html

version	toolchain
2.4.5	system
2.5.0	foss/2016a
2.5.1	system
2.5.2	GCCcore/8.3.0, foss/2016b, foss/2018b
2.6.0	GCCcore/8.2.0, GCCcore/9.3.0

DOLFIN

DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.

homepage: https://bitbucket.org/fenics-project/dolfin

version	versionsuffix	toolchain
2018.1.0.post1	-Python-3.6.4	foss/2018a
2019.1.0.post0	-Python-3.7.4	foss/2019b

Doris

Delft object-oriented radar interferometric software

homepage: http://doris.tudelft.nl/

version	toolchain
4.02	intel/2017a
4.04beta4	foss/2018a, intel/2017a
4.06beta2	intel/2017a

DosageConvertor

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in the input files and may NOT work for non-Minimac3/4 VCF files.

homepage: http://genome.sph.umich.edu/wiki/DosageConvertor

version	toolchain
1.0.4	GCC/10.2.0

dotNET-Core-Runtime

.NET is a free, cross-platform, open source developer platform for building many different types of applications.

homepage: https://www.microsoft.com/net/

version	toolchain
2.0.7	GCCcore/6.4.0

dotNET-SDK

.NET is a free, cross-platform, open source developer platform for building many different types of applications.

homepage: https://www.microsoft.com/net/

version	versionsuffix	toolchain
3.1.300	-linux-x64	system

double-conversion

Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.

homepage: https://github.com/google/double-conversion

version	toolchain
3.0.3	foss/2018a
3.1.4	GCCcore/8.2.0, GCCcore/8.3.0
3.1.5	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0

DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

homepage: https://github.com/chris-mcginnis-ucsf/DoubletFinder

version	versionsuffix	toolchain
2.0.3	-R-4.0.0	foss/2020a

Doxygen

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

homepage: https://www.doxygen.org

version	toolchain
1.8.9.1	GCC/4.9.2
1.8.10	GNU/4.9.3-2.25, intel/2016.02-GCC-4.9
1.8.11	GCC/4.9.2, GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
1.8.13	GCCcore/6.3.0, GCCcore/6.4.0, gimkl/2017a
1.8.14	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0
1.8.15	GCCcore/8.2.0
1.8.16	GCCcore/8.3.0
1.8.17	GCCcore/9.3.0
1.8.20	GCCcore/10.2.0
1.9.1	GCCcore/10.3.0

Drake

Drake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies.

homepage: https://github.com/Factual/drake

version	versionsuffix	toolchain
1.0.3	-Java-1.8	system

DROP

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

homepage: https://gagneurlab-drop.readthedocs.io

version	versionsuffix	toolchain
1.0.3	-R-4.0.3	foss/2020b

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

homepage: https://github.com/hms-dbmi/dropEst

version	versionsuffix	toolchain
0.7.1	-R-3.4.3	intel/2017b

DSA

Digital Sorting Algorithm

homepage: https://github.com/zhandong/DSA

version	versionsuffix	toolchain
1.0	-R-3.5.1	foss/2018b

dSFMT

Double precision SIMD-oriented Fast Mersenne Twister.

homepage: https://github.com/MersenneTwister-Lab/dSFMT

version	toolchain
2.2.5	GCCcore/10.2.0

DSRC

DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.

homepage: http://sun.aei.polsl.pl/dsrc

version	versionsuffix	toolchain
2.0rc	-linux-64-bit	system

Dsuite

Fast calculation of the ABBA-BABA statistics across many populations/species

homepage: https://github.com/millanek/Dsuite

version	toolchain
20190713	iccifort/2019.1.144-GCC-8.2.0-2.31.1

dtcmp

Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI.

homepage: https://github.com/llnl/dtcmp

version	toolchain
1.1.0	gompi/2019a, gompi/2020a, iimpi/2019a, iimpi/2020a

dtcwt

Dual-Tree Complex Wavelet Transform library for Python

homepage: https://github.com/rjw57/dtcwt

version	versionsuffix	toolchain
0.12.0	-Python-2.7.15	foss/2018b
0.12.0	-Python-3.7.4	intel/2019b

dxpy

DNAnexus Platform API bindings for Python

homepage: http://autodoc.dnanexus.com/

version	versionsuffix	toolchain
0.266.1	-Python-2.7.14	intel/2018a

E

E-ANTIC - ea-utils - earthengine-api - EasyBuild - EasyQC - ecCodes - eccodes-python - ED2 - edlib - EggLib - eggnog-mapper - Eigen - EIGENSOFT - elastix - elfutils - Elk - ELPA - ELPH - ELSI - Emacs - EMAN2 - EMBOSS - emcee - EMU - enaBrowserTool - enchant - EnsEMBLCoreAPI - entrypoints - EPD - EPIC - EricScript - ESMF - ESMPy - ESMValTool - eSpeak-NG - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - ExifTool - exiv2 - Exonerate - expat - expect - eXpress - Extrae

E-ANTIC

E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons.

homepage: https://github.com/videlec/e-antic

version	toolchain
0.1.2	GCC/8.2.0-2.31.1
0.1.5	GCC/8.3.0

ea-utils

Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

homepage: http://expressionanalysis.github.io/ea-utils/

version	toolchain
1.04.807	foss/2016a, foss/2016b, intel/2016b

earthengine-api

Python and JavaScript bindings for calling the Earth Engine API

homepage: https://github.com/google/earthengine-api

version	versionsuffix	toolchain
0.1.143	-Python-2.7.14	intel/2018a

EasyBuild

EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.

homepage: https://easybuilders.github.io/easybuild

version	toolchain
1.0.0	system
1.0.1	system
1.0.2	system
1.1.0	system
1.2.0	system
1.3.0	system
1.4.0	system
1.5.0	system
1.6.0	system
1.7.0	system
1.8.0	system
1.8.1	system
1.8.2	system
1.9.0	system
1.10.0	system
1.11.0	system
1.11.1	system
1.12.0	system
1.12.1	system
1.13.0	system
1.14.0	system
1.15.0	system
1.15.1	system
1.15.2	system
1.16.0	system
1.16.1	system
1.16.2	system
2.0.0	system
2.1.0	system
2.1.1	system
2.2.0	system
2.3.0	system
2.4.0	system
2.5.0	system
2.6.0	system
2.7.0	system
2.8.0	system
2.8.1	system
2.8.2	system
2.9.0	system
3.0.0	system
3.0.1	system
3.0.2	system
3.1.0	system
3.1.1	system
3.1.2	system
3.2.0	system
3.2.1	system
3.3.0	system
3.3.1	system
3.4.0	system
3.4.1	system
3.5.0	system
3.5.1	system
3.5.2	system
3.5.3	system
3.6.0	system
3.6.1	system
3.6.2	system
3.7.0	system
3.7.1	system
3.8.0	system
3.8.1	system
3.9.0	system
3.9.1	system
3.9.2	system
3.9.3	system
3.9.4	system
4.0.0	system
4.0.1	system
4.1.0	system
4.1.1	system
4.1.2	system
4.2.0	system
4.2.1	system
4.2.2	system
4.3.0	system
4.3.1	system
4.3.2	system
4.3.3	system
4.3.4	system
4.4.0	system

EasyQC

EasyQC is an R-package that provides advanced functionality to (1) perform file-level QC of single genome-wide association (GWA) data-sets (2) conduct quality control across several GWA data-sets (meta-level QC) (3) simplify data-handling of large-scale GWA data-sets.

homepage: http://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/

version	versionsuffix	toolchain
9.2	-R-3.3.1	intel/2016b

ecCodes

ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).

homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home

version	versionsuffix	toolchain
2.7.3		intel/2018a
2.7.3	-Python-2.7.14	intel/2017b
2.8.2		intel/2018a
2.9.2		intel/2018b, iomkl/2018b
2.12.5		gompi/2019a
2.15.0		gompi/2019b, iimpi/2019b
2.17.0		foss/2018b, gompi/2019b
2.18.0		gompi/2020a
2.20.0		gompi/2020b

eccodes-python

Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library.

homepage: https://github.com/ecmwf/eccodes-python

version	versionsuffix	toolchain
1.0.0	-Python-3.7.4	foss/2019b
1.0.0	-Python-3.8.2	foss/2020a
1.1.0		foss/2020b

ED2

The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry

homepage: https://github.com/EDmodel/ED2

version	versionsuffix	toolchain
20170201		intel/2017a
20170201	-serial	intel/2017a

edlib

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.

homepage: https://martinsos.github.io/edlib

version	versionsuffix	toolchain
1.3.8.post1	-Python-3.7.4	GCC/8.3.0, iccifort/2019.5.281
1.3.8.post1	-Python-3.8.2	GCC/9.3.0
1.3.8.post2	-Python-3.8.2	iccifort/2020.1.217

EggLib

EggLib is a C++/Python library and program package for evolutionary genetics and genomics.

homepage: http://egglib.sourceforge.net/

version	toolchain
2.1.10	intel/2016a

eggnog-mapper

EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

homepage: https://github.com/eggnogdb/eggnog-mapper

version	versionsuffix	toolchain
1.0.3	-Python-2.7.14	intel/2018a
2.1.4		foss/2020b

Eigen

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

homepage: https://eigen.tuxfamily.org

version	toolchain
3.2.3	foss/2016a, foss/2016b
3.2.5	system
3.2.6	system
3.2.7	foss/2016a, intel/2016a
3.2.8	foss/2016a, intel/2016a, system
3.2.9	foss/2016b, intel/2016b
3.2.10	intel/2016b
3.3.2	foss/2016b, intel/2016b
3.3.3	GCCcore/6.3.0, intel/2016b
3.3.4	system
3.3.5	system
3.3.7	GCCcore/9.3.0, system
3.3.8	GCCcore/10.2.0
3.3.9	GCCcore/10.3.0

EIGENSOFT

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

homepage: http://www.hsph.harvard.edu/alkes-price/software/

version	toolchain
6.0.1	foss/2016a
6.1.1	foss/2016a
6.1.4	foss/2016b
7.2.1	foss/2018b, foss/2019a, foss/2019b, intel/2019a

elastix

elastix: a toolbox for rigid and nonrigid registration of images.

homepage: http://elastix.isi.uu.nl/

version	toolchain
4.9.0	foss/2018a

elfutils

The elfutils project provides libraries and tools for ELF files and DWARF data.

homepage: https://elfutils.org/

version	toolchain
0.182	GCCcore/9.3.0
0.183	GCCcore/10.2.0
0.185	GCCcore/10.3.0, GCCcore/8.2.0, GCCcore/8.3.0

Elk

An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.

homepage: http://elk.sourceforge.net/

version	toolchain
4.0.15	intel/2016b
4.3.6	intel/2017a
6.3.2	intel/2019b
7.0.12	foss/2020b

ELPA

Eigenvalue SoLvers for Petaflop-Applications .

homepage: https://elpa.rzg.mpg.de

version	toolchain
2015.02.002	foss/2018a, gimkl/2017a, intel/2018a
2016.05.004	intel/2016b, intel/2017a
2016.11.001.pre	foss/2018b, intel/2018b
2017.11.001	foss/2018b, intel/2018a, intel/2018b
2018.05.001	foss/2018b, intel/2018b
2018.11.001	intel/2019a
2019.11.001	foss/2019b, foss/2020a, intel/2019b, intel/2020a, iomkl/2019b
2020.05.001	intel/2020a
2020.11.001	foss/2020b, intel/2020b
2021.05.001	foss/2021a, intel/2021a

ELPH

ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

homepage: http://ccb.jhu.edu/software/ELPH/index.shtml

version	toolchain
1.0.1	foss/2018b

ELSI

ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.

homepage: https://wordpress.elsi-interchange.org/

version	versionsuffix	toolchain
2.5.0		intel/2019b
2.5.0	-PEXSI	intel/2019b

Emacs

GNU Emacs is an extensible, customizable text editor–and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.

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

version	versionsuffix	toolchain
24.3		GCC/4.8.3
24.3	-bare	GCC/4.8.3
24.4		GCC/4.9.2
24.5		GCC/4.9.3-2.25
25.1		foss/2016a
25.3		GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0
26.3		GCCcore/8.3.0
27.1		GCCcore/10.2.0, GCCcore/9.3.0

EMAN2

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

homepage: https://blake.bcm.edu/emanwiki/EMAN2

version	versionsuffix	toolchain
2.3		system
2.3	-Python-2.7.15	foss/2019a, fosscuda/2019a
2.21a	-Python-2.7.14-Boost-1.63.0	foss/2018a

EMBOSS

EMBOSS is ‘The European Molecular Biology Open Software Suite’. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

homepage: http://emboss.sourceforge.net/

version	versionsuffix	toolchain
6.6.0		GCC/8.2.0-2.31.1, foss/2016b, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2017a, intel/2018b
6.6.0	-Java-11	GCC/8.3.0
6.6.0	-Java-13	GCC/10.2.0
6.6.0	-X11-20170314	intel/2017a

emcee

Emcee is an extensible, pure-Python implementation of Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It’s designed for Bayesian parameter estimation and it’s really sweet!

homepage: https://dfm.io/emcee

version	versionsuffix	toolchain
2.2.1		foss/2019a
2.2.1	-Python-2.7.15	foss/2018b, intel/2018b
2.2.1	-Python-3.6.6	foss/2018b, intel/2018b

EMU

EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets

homepage: http://www.popgen.dk/software/index.php/EMU

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

enaBrowserTool

enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.

homepage: https://github.com/enasequence/enaBrowserTools/

version	versionsuffix	toolchain
1.5.4	-Python-3.7.2	GCCcore/8.2.0

enchant

Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.

homepage: https://abiword.github.io/enchant/

version	toolchain
1.6.1	intel/2017a

EnsEMBLCoreAPI

The Ensembl Core Perl API and SQL schema

homepage: https://www.ensembl.org/info/docs/api/index.html

version	versionsuffix	toolchain
96.0-r20190601	-Perl-5.28.1	foss/2019a

entrypoints

Entry points are a way for Python packages to advertise objects with some common interface.

homepage: https://github.com/takluyver/entrypoints

version	versionsuffix	toolchain
0.2.2	-Python-2.7.11	foss/2016a
0.2.2	-Python-2.7.12	foss/2016b, intel/2016b
0.2.2	-Python-3.5.1	foss/2016a
0.2.2	-Python-3.5.2	intel/2016b

EPD

The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.

homepage: http://www.enthought.com/products/edudownload.php

version	toolchain
7.3-2-rh5	system

EPIC

Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data.

homepage: https://gfellerlab.shinyapps.io/EPIC_1-1

version	versionsuffix	toolchain
1.1	-R-3.5.1	foss/2018b

EricScript

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

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

version	versionsuffix	toolchain
0.5.5	-R-3.4.0	intel/2017a

ESMF

The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.

homepage: https://www.earthsystemcog.org/projects/esmf/

version	versionsuffix	toolchain
6.3.0rp1		intel/2017a
6.3.0rp1	-HDF5-1.8.18	intel/2017a
7.0.0		foss/2016a
7.0.2		intel/2017b
7.1.0r		foss/2018b, foss/2019a, intel/2018a, intel/2018b, iomkl/2018b
8.0.0		foss/2019b, intel/2019b
8.0.1		foss/2020a, foss/2020b, intel/2020a, intel/2020b

ESMPy

Earth System Modeling Framework (ESMF) Python Interface

homepage: https://earthsystemmodeling.org/esmpy

version	versionsuffix	toolchain
8.0.0	-Python-3.7.4	intel/2019b
8.0.1		intel/2020b

ESMValTool

The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics and performance metrics tool for the evaluation of Earth System Models (ESMs) that allows for routine comparison of single or multiple models, either against predecessor versions or against observations.

homepage: https://www.esmvaltool.org/

version	versionsuffix	toolchain
1.1.0	-Python-2.7.14	intel/2017b

eSpeak-NG

The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.

homepage: https://github.com/espeak-ng/espeak-ng

version	toolchain
1.50	gompi/2020a

Essentia

Open-source library and tools for audio and music analysis, description and synthesis

homepage: https://essentia.upf.edu

version	versionsuffix	toolchain
2.1_beta5	-Python-2.7.15	foss/2019a

ETE

A Python framework for the analysis and visualization of trees

homepage: http://etetoolkit.org

version	versionsuffix	toolchain
3.0.0b36	-Python-2.7.12	intel/2016b
3.1.1	-Python-3.6.6	foss/2018b
3.1.2	-Python-3.8.2	foss/2020a

ETSF_IO

A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.

homepage: http://www.etsf.eu/resources/software/libraries_and_tools

version	toolchain
1.0.4	foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b

eudev

eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.

homepage: https://wiki.gentoo.org/wiki/Project:Eudev

version	toolchain
3.1.5	foss/2016a, gimkl/2.11.5, intel/2016a
3.2	GCCcore/4.9.3
3.2.2	GCCcore/6.4.0

EvidentialGene

EvidentialGene is a genome informatics project for “Evidence Directed Gene Construction for Eukaryotes”, for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.

homepage: http://arthropods.eugenes.org/EvidentialGene/

version	versionsuffix	toolchain
2018.01.01	-Perl-5.24.1	intel/2017a

evmix

evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation

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

version	versionsuffix	toolchain
2.6	-R-3.3.1	intel/2016b

ExaBayes

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters

homepage: https://cme.h-its.org/exelixis/web/software/exabayes/

version	toolchain
1.5	foss/2016b

ExifTool

Perl module (Image::ExifTool) and program (exiftool) to read EXIF information from images

homepage: https://owl.phy.queensu.ca/~phil/exiftool/

version	toolchain
12.00	GCCcore/9.3.0

exiv2

Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata.

homepage: https://exiv2.org

version	toolchain
0.27.4	GCCcore/10.3.0

Exonerate

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

version	toolchain
2.4.0	GCC/10.2.0, GCC/6.4.0-2.28, GCC/8.3.0, foss/2016a, foss/2016b, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017a

expat

Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)

homepage: https://libexpat.github.io

version	toolchain
2.1.0	GCC/4.9.2, foss/2016a, intel/2016a
2.1.1	foss/2016a, intel/2016a
2.2.0	GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, foss/2016b, gimkl/2017a, intel/2016b
2.2.4	GCCcore/6.4.0
2.2.5	GCCcore/6.4.0, GCCcore/7.3.0
2.2.6	GCCcore/8.2.0
2.2.7	GCCcore/8.3.0
2.2.9	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0

expect

Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.

homepage: https://core.tcl.tk/expect/index

version	toolchain
5.45.4	GCCcore/7.3.0, GCCcore/9.3.0

eXpress

Streaming quantification for high-throughput sequencing

homepage: https://pachterlab.github.io/eXpress

version	toolchain
1.5.1	intel/2017b

Extrae

Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.

homepage: https://www.bsc.es/computer-sciences/performance-tools

version	toolchain
3.4.1	foss/2017a
3.7.1	intel/2019a
3.8.0	gompi/2020b

F

f90cache - Faber - FabIO - faceswap - FALCON - FANN - fast5 - FASTA - fastahack - FastaIndex - FastANI - FastME - fastp - fastPHASE - fastq-pair - fastq-tools - FastQ_Screen - FastQC - fastqsplitter - FastQTL - fastqz - FastRFS - fastStructure - FastTree - FastViromeExplorer - FASTX-Toolkit - fatslim - fbm - FCC - FCM - FDS - fdstools - FDTD_Solutions - feh - FEniCS - fermi-lite - Ferret - festival - fetchMG - FFC - FFLAS-FFPACK - FFmpeg - ffmpi - ffnet - fftlib - FFTW - fgbio - FGSL - FHI-aims - FIAT - FIGARO - FigureGen - Fiji - file - filevercmp - Filtlong - find_circ - findhap - findutils - fineRADstructure - fineSTRUCTURE - Fiona - Firefox - FIRESTARTER - FireWorks - FIt-SNE - FIX - fixesproto - FLAC - FLAIR - FLANN - FLASH - Flask - flatbuffers - flatbuffers-python - FLEUR - flex - Flexbar - FlexiBLAS - FlexiDot - Flink - FLINT - FLTK - FLUENT - Flye - FMILibrary - FMRIprep - fmt - FoldX - fontconfig - fontsproto - foss - fosscuda - FoX - FPM - fpocket - fqtrim - fqzcomp - FragGeneScan - FRANz - FreeFEM - FreeFem++ - freeglut - FreeImage - FreeSASA - FreeSurfer - freetype - freetype-py - FreeXL - FriBidi - FRUIT - FRUIT_processor - FSL - FSLeyes - fsom - FTGL - Fujitsu - fullrmc - FUNWAVE-TVD - FUSE - FuSeq - FusionCatcher - futhark - futile - future - fxtract

f90cache

f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.

homepage: http://people.irisa.fr/Edouard.Canot/f90cache/

version	toolchain
0.96	system

Faber

Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail.

homepage: https://stefanseefeld.github.io/faber

version	toolchain
0.3	GCCcore/8.3.0

FabIO

FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, …), for a total of 20 different file formats (like CBF, EDF, TIFF, …) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).

homepage: http://www.silx.org

version	versionsuffix	toolchain
0.10.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.11.0		foss/2020b

faceswap

Faceswap is a tool that utilizes deep learning to recognize and swap faces in pictures and videos.

homepage: https://github.com/deepfakes/faceswap

version	versionsuffix	toolchain
20180212	-Python-3.6.3	foss/2017b

FALCON

Falcon: a set of tools for fast aligning long reads for consensus and assembly

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

version	versionsuffix	toolchain
1.8.8		intel/2017b
1.8.8	-Python-2.7.16	intel/2019b

FANN

Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.

homepage: http://leenissen.dk

version	toolchain
2.2.0	GCCcore/6.4.0, intel/2018a

fast5

A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.

homepage: http://simpsonlab.github.io/2017/02/27/packing_fast5/

version	toolchain
0.6.5	system

FASTA

The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

homepage: http://fasta.bioch.virginia.edu

version	toolchain
36.3.5e	foss/2016b

fastahack

Utilities for indexing and sequence extraction from FASTA files.

homepage: https://github.com/ekg/fastahack

version	toolchain
1.0.0	GCCcore/9.3.0

FastaIndex

FastA index (.fai) handler compatible with samtools faidx

homepage: https://github.com/lpryszcz/FastaIndex

version	versionsuffix	toolchain
0.11rc7	-Python-2.7.14	intel/2017b

FastANI

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.

homepage: https://github.com/ParBLiSS/FastANI

version	toolchain
1.1	foss/2018b, intel/2018b
1.2	GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1
1.3	iccifort/2019.5.281
1.31	iccifort/2020.1.217
1.33	GCC/10.2.0, iccifort/2020.4.304

FastME

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

homepage: http://www.atgc-montpellier.fr/fastme/

version	toolchain
2.1.5	foss/2016a
2.1.6.1	GCC/8.3.0, iccifort/2019.5.281, intel/2018a, intel/2018b

fastp

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

homepage: https://github.com/OpenGene/fastp

version	toolchain
0.19.7	foss/2018b
0.20.0	GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2019.5.281

fastPHASE

fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf

homepage: http://stephenslab.uchicago.edu/software.html#fastphase

version	toolchain
1.4.8	system

fastq-pair

Match up paired end fastq files quickly and efficiently.

homepage: https://github.com/linsalrob/fastq-pair

version	toolchain
1.0	GCCcore/8.2.0

fastq-tools

This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.

homepage: https://homes.cs.washington.edu/~dcjones/fastq-tools/

version	toolchain
0.8	foss/2016b, foss/2018b

FastQ_Screen

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

version	versionsuffix	toolchain
0.11.3	-Perl-5.24.0	foss/2016b
0.11.4	-Perl-5.24.0	foss/2016b
0.12.0	-Perl-5.26.1	intel/2018a
0.13.0	-Perl-5.28.0	foss/2018b

FastQC

FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.

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

version	versionsuffix	toolchain
0.10.1	-Java-1.7.0_80	system
0.11.2	-Java-1.7.0_60	system
0.11.3	-Java-1.7.0_80	system
0.11.4	-Java-1.8.0_66	system
0.11.4	-Java-1.8.0_74	system
0.11.5	-Java-1.7.0_80	system
0.11.5	-Java-1.8.0_144	system
0.11.5	-Java-1.8.0_74	system
0.11.7	-Java-1.8.0_162	system
0.11.8	-Java-1.8	system
0.11.8	-Java-11	system
0.11.9	-Java-1.8	system
0.11.9	-Java-11	system

fastqsplitter

Splits fastq files evenly.

homepage: https://github.com/LUMC/fastqsplitter

version	versionsuffix	toolchain
1.2.0	-Python-3.7.2	GCCcore/8.2.0

FastQTL

FastQTL is a QTL mapper

homepage: http://fastqtl.sourceforge.net/

version	toolchain
2.184	foss/2018b

fastqz

fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing machines. It is one of the compressors described in the paper: Bonfield JK, Mahoney MV (2013) Compression of FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190

homepage: http://mattmahoney.net/dc/fastqz/

version	toolchain
1.5	GCC/4.8.2

FastRFS

Fast Robinson Foulds Supertrees

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

version	toolchain
1.0-20190613	gompi/2019a

fastStructure

fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

homepage: https://rajanil.github.io/fastStructure/

version	versionsuffix	toolchain
1.0	-Python-2.7.11	foss/2016a
1.0	-Python-2.7.12	foss/2016b
1.0	-Python-2.7.13	foss/2017a
1.0	-Python-2.7.15	foss/2019a

FastTree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

homepage: http://www.microbesonline.org/fasttree/

version	toolchain
2.1.10	foss/2018b, intel/2017b, intel/2018a, intel/2018b
2.1.11	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

FastViromeExplorer

Identify the viruses/phages and their abundance in the viral metagenomics data.

homepage: https://code.vt.edu/saima5/FastViromeExplorer

version	toolchain
20180422	foss/2019b

FASTX-Toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

homepage: http://hannonlab.cshl.edu/fastx_toolkit/

version	toolchain
0.0.14	GCC/9.3.0, GCCcore/7.3.0, foss/2016a, foss/2016b, intel/2018a

fatslim

FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories.

homepage: https://github.com/FATSLiM/fatslim

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

fbm

Exact methods for simulating fractional Brownian motion and fractional Gaussian noise in Python

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

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

FCC

Fujitsu Compiler based compiler toolchain.

homepage: (none)

version	toolchain
4.5.0	system

FCM

FCM is a set of tools for managing and building source code.

homepage: http://www.metoffice.gov.uk/research/collaboration/fcm

version	toolchain
2.3.1	system

FDS

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

homepage: https://pages.nist.gov/fds-smv

version	versionsuffix	toolchain
6.0.1	-no-OFED	system
6.5.2		intel/2016b
6.5.3		intel/2017a
6.6.0		intel/2017b, intel/2018a
6.7.0		intel/2018a
6.7.4		intel/2020a
6.7.5		intel/2020a
6.7.6		intel/2020b

fdstools

Forensic DNA Sequencing Tools Tools for characterisation and filtering of PCR stutter artefacts and other systemic noise in Next Generation Sequencing data of forensic STR markers.

homepage: https://git.lumc.nl/jerryhoogenboom/fdstools

version	versionsuffix	toolchain
20160322	-Python-2.7.11	foss/2016a

FDTD_Solutions

High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.

homepage: http://www.lumerical.com/tcad-products/fdtd/

version	toolchain
8.6.2	system
8.11.337	system
8.16.982	system
8.20.1731	system

feh

feh is an X11 image viewer aimed mostly at console users. Unlike most other viewers, it does not have a fancy GUI, but simply displays images. It is controlled via commandline arguments and configurable key/mouse actions.

homepage: https://feh.finalrewind.org/

version	toolchain
2.26	GCCcore/6.4.0

FEniCS

FEniCS is a computing platform for solving partial differential equations (PDEs).

homepage: https://fenicsproject.org/

version	versionsuffix	toolchain
2019.1.0	-Python-3.7.4	foss/2019b

fermi-lite

Standalone C library for assembling Illumina short reads in small regions.

homepage: https://github.com/lh3/fermi-lite

version	toolchain
20190320	GCCcore/9.3.0

Ferret

Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

homepage: https://ferret.pmel.noaa.gov/Ferret/

version	toolchain
7.3	intel/2017b
7.5.0	foss/2019b

festival

University of Edinburgh’s Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems.

homepage: [’http://festvox.org/festival/’]

version	toolchain
2.5.0	GCCcore/9.3.0

fetchMG

The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes in an easy and accurate manner.

homepage: http://vm-lux.embl.de/~mende/fetchMG/about.html

version	toolchain
1.0	GCCcore/8.3.0, GCCcore/9.3.0

FFC

The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.

homepage: https://bitbucket.org/fenics-project/ffc

version	versionsuffix	toolchain
2018.1.0	-Python-3.6.4	foss/2018a
2019.1.0.post0	-Python-3.7.4	foss/2019b

FFLAS-FFPACK

Finite Field Linear Algebra Subroutines / Package

homepage: https://linbox-team.github.io/fflas-ffpack/

version	toolchain
2.2.0	foss/2016a

FFmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

homepage: https://www.ffmpeg.org/

version	toolchain
0.10.16	gimkl/2.11.5, intel/2016a
2.8.6	intel/2016a
2.8.7	foss/2016a, intel/2016a
3.0.2	foss/2016a, intel/2016a
3.1.3	foss/2016b, intel/2016b
3.2.4	gimkl/2017a
3.3.1	foss/2016b
3.3.4	intel/2017a
3.4	GCCcore/6.4.0
3.4.1	foss/2017b, intel/2017b
3.4.2	foss/2018a, intel/2018a
3.4.5	foss/2018b
4.0	foss/2018a, intel/2018a
4.0.1	intel/2018a
4.1	foss/2018b, fosscuda/2018b, intel/2018b
4.1.3	GCCcore/8.2.0
4.2.1	GCCcore/8.3.0
4.2.2	GCCcore/9.3.0
4.3.1	GCCcore/10.2.0
4.3.2	GCCcore/10.3.0

ffmpi

Fujitsu Compiler based compiler toolchain, including Fujitsu MPI for MPI support.

homepage: (none)

version	toolchain
4.5.0	system

ffnet

Feed-forward neural network solution for python

homepage: http://ffnet.sourceforge.net/

version	versionsuffix	toolchain
0.8.3	-Python-2.7.11	intel/2016a

fftlib

A library that intercepts FFTW calls and adds features on top of it. In particular, it enables FFT plan reuse when there are multiple calls for the same geometry.

homepage: https://github.com/flwende/fftlib

version	toolchain
20170628	gompi/2020b

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

homepage: https://www.fftw.org

version	versionsuffix	toolchain
1.0.0	-fujitsu	FCC/4.5.0
2.1.5		intel/2016b, intel/2017a, intel/2018b
3.3.4		gmpich/2016a, gmvapich2/1.7.20, gmvapich2/2016a, gompi/2016.04, gompi/2016.06, gompi/2016.07, gompi/2016a, gompi/2016b, intel/2016a, intel/2016b
3.3.5		gompi/2016.07, gompi/2016.09, gompi/2016b, intel/2016b
3.3.6		gimpi/2017b, gimpic/2017b, gompi/2017a, gompi/2017b, gompic/2017b, intel/2016b, intel/2017a, intel/2017b, intelcuda/2017b
3.3.7		gimkl/2017a, gimpi/2018a, gmpich/2017.08, gompi/2018a, gompic/2018a, intel/2017b, intel/2018.00, intel/2018.01, intel/2018a, iomkl/2018a
3.3.7	-serial	GCC/6.4.0-2.28
3.3.8		gompi/2018.08, gompi/2018b, gompi/2019a, gompi/2019b, gompi/2020a, gompi/2020b, gompic/2018b, gompic/2019a, gompic/2019b, gompic/2020a, gompic/2020b, iimpi/2020b, intel/2018b, intel/2019a, intel/2019b, intel/2020a, intel/2020b, iomkl/2018b
3.3.8	-amd	gompi/2020a
3.3.8	-serial	GCC/9.3.0
3.3.9		gompi/2021a, intel/2021a

fgbio

A set of tools to analyze genomic data with a focus on Next Generation Sequencing.

homepage: https://fulcrumgenomics.github.io/fgbio

version	toolchain
1.3.0	system

FGSL

FGSL: A Fortran interface to the GNU Scientific Library

homepage: https://www.lrz.de/services/software/mathematik/gsl/fortran/

version	toolchain
1.1.0	intel/2016b

FHI-aims

FHI-aims is an efficient, accurate all-electron, full-potential electronic structure code package for computational molecular and materials science (non-periodic and periodic systems). The code supports DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is particularly efficient for molecular systems and nanostructures, while maintaining high numerical accuracy for all production tasks. Production calculations handle up to several thousand atoms and can efficiently use (ten) thousands of cores.

homepage: https://aimsclub.fhi-berlin.mpg.de/

version	toolchain
200112_2	intel/2019b

FIAT

The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.

homepage: https://bitbucket.org/fenics-project/fiat

version	versionsuffix	toolchain
1.6.0	-Python-2.7.11	foss/2016a, intel/2016a
2018.1.0	-Python-3.6.4	foss/2018a
2019.1.0	-Python-3.7.4	foss/2019b

FIGARO

FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.

homepage: https://github.com/Zymo-Research/figaro

version	toolchain
1.1.2	intel/2020b

FigureGen

FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps.

homepage: https://ccht.ccee.ncsu.edu/category/software/figuregen/

version	toolchain
51-20190516	foss/2019a

Fiji

Fiji is an image processing package—a ‘batteries-included’ distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1

homepage: https://fiji.sc/

version	toolchain
20170530	system
20191119-2057	system
20201104-1356	system

file

The file command is ‘a file type guesser’, that is, a command-line tool that tells you in words what kind of data a file contains.

homepage: https://www.darwinsys.com/file/

version	toolchain
5.17	GCC/4.8.2
5.25	intel/2016a
5.28	foss/2016b
5.30	intel/2017a
5.33	GCCcore/6.4.0
5.35	GCCcore/7.3.0
5.38	GCCcore/8.3.0, GCCcore/9.3.0
5.39	GCCcore/10.2.0

filevercmp

filevercmp function as in sort –version-sort.

homepage: https://github.com/ekg/filevercmp

version	toolchain
20141119	GCCcore/9.3.0

Filtlong

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter

homepage: https://github.com/rrwick/Filtlong

<

version	toolchain