== Temporary log file in case of crash /tmp/eb-rvg3pj0d/easybuild-jo5_l5pb.log List of supported software ==========================

EasyBuild 4.3.3 supports 2248 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




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




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


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 - AMPL-MP - AmrPlusPlus - Anaconda2 - Anaconda3 - aNCI - angsd - Annif - annovar - ANSYS - ANSYS_CFD - ant - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - APBS - apex - APR - APR-util - ARAGORN - Arb - arcasHLA - ARCH - 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


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 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


Assembly Based ReAligner

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

version toolchain
2.22 iccifort/2019.5.281
2.23 GCC/9.3.0


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


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


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 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 converts independent triangles into triangle strips or fans.

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

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


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 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 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 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


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


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 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


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


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 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 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


” 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 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 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 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


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


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, the new short read genome assembler.

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

version toolchain
52488 foss/2016a


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 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


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


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


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 -Python-2.7.15 foss/2019a, intel/2019a


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 (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


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 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 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 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


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


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


An open-source library for mathematical programming.

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

version toolchain
3.1.0 GCCcore/6.4.0


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


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


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


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


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


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 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 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 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


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


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, 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 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


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


Convert various sequence formats to FASTA

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

version versionsuffix toolchain
0.4.2   GCCcore/8.3.0
0.4.2 -Perl-5.28.1 GCCcore/8.2.0


AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0

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

version toolchain
2.3.0 GCCcore/9.3.0


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


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


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/8.2.0, GCCcore/9.3.0


Apache Portable Runtime (APR) util libraries.

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

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


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 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 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


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


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


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 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: An Integrated Software for Population Genetics Data Analysis

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

version toolchain foss/2019b


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


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 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


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 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


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 intel/2019b
0.17.1   intel/2020b
0.17.1 -Python-3.8.2 foss/2020a, intel/2020a


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 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


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


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


ARWEN, tRNA detection in metazoan mitochondrial sequences

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

version toolchain
1.2.3 GCCcore/7.3.0


ASAP 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


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 -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, 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, intel/2020b


Automatic Segmentation of Hippocampal Subfields (ASHS)

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

version toolchain
rev103_20140612 system


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


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


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

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

version toolchain
2.2.1 gompi/2019a


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


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


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 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/9.3.0


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 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 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 intel/2018b intel/2018b


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 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


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


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


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 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/2020b


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: http://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


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


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 GCC/5.2.0


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


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 GCC/5.2.0


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


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

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

version versionsuffix toolchain
1.0 -20200324 foss/2019b


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


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


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


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 - 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 - 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 - bpytop - Bracken - BRAKER - BreakDancer - breseq - bsddb3 - BSMAPz - Bsoft - BSseeker2 - BUFRLIB - buildenv - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2


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

homepage: http://www.nubakery.org

version toolchain
1.1.1 intel/2016b


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 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 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


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 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, intel/2017b, intel/2018b


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 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 (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


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

homepage: http://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


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


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


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: Bayesian Inference of Recent Migration Using Multilocus Genotypes

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

version toolchain
3.0.4 foss/2016a


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 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 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 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 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 -amd64_linux26 system


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 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


bc is an arbitrary precision numeric processing language.

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

version toolchain
1.06.95 GCC/4.8.2


de Bruijn graph compaction in low memory

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

version toolchain
2.2.0 foss/2018a


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


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


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


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/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 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 -Python-3.8.2 foss/2020a


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 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/8.2.0-2.31.1, GCC/9.3.0


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/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


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 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: 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


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


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 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 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


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


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


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 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 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: 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


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 -Perl-5.28.1 GCC/8.2.0-2.31.1


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


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 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


Tools for processing BAM files

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

version toolchain
2.0.87 intel/2018a


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 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


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


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: http://bioservices.readthedocs.io/

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


Utilities to help analyze bisulfite-treated sequence data

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

version toolchain
0.1.4 foss/2016a


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 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/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


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


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


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 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


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


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/2020b


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 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


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


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


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, 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


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


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 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


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


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


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


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

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

version toolchain
1.97 foss/2016a


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, iimpi/2020a
1.72.0 -no_mpi GCCcore/9.3.0
1.74.0   GCC/10.2.0, iccifort/2020.4.304


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, iimpi/2020a


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 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 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/9.3.0


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 intel/2017b
2.3.4 intel/2017b foss/2017b, intel/2017b, intel/2018a foss/2018b, intel/2018b foss/2017b 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/9.3.0


Bpipe - a tool for running and managing bioinformatics pipelines

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

version toolchain intel/2017a


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 (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 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 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 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


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


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 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


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


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 iccifort/2020.1.217


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 foss/2017b, foss/2018b, foss/2019b, intel/2016b, intel/2017a, intel/2019b


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: 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


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 foss/2018b


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/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, intel/2017b, intel/2018a, intel/2018b


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 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


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


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


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


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


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 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 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/8.3.0, GCCcore/9.3.0


C3D - cadaver - CaDiCaL - Caffe - cairo - cairomm - Calendrical - Calib - 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 - cdbfasta - cddlib - cDNA_Cupcake - CDO - cdsapi - 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 - 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 - 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 - CryptoMiniSat - 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


Convert3D Medical Image Processing Tool

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

version toolchain
1.0.0 system


cadaver is a command-line WebDAV client for Unix.

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

version toolchain
0.23.3 intel/2017a


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 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 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/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0


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 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 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


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 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


Copy number variant (CNV) calling from DNA sequencing data

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

version toolchain system


CAP3 assembly program

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

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


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


The Rust package manager

homepage: https://crates.io/

version toolchain
0.13.0 foss/2016b


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


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

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

version toolchain
20160617 foss/2016a
20180806 foss/2018a


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


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

homepage: http://catmap.readthedocs.io/

version versionsuffix toolchain
20170927 -Python-2.7.14 intel/2017b


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


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


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


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 (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


C interface to the BLAS

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

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


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


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


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 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


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 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/8.3.0, GCC/9.3.0, foss/2018b, iccifort/2019.5.281


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


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 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 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


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


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


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


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


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


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 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 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 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 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


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


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


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


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


Command-line Toolset for Bisulfite Sequencing Data Analysis

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

version toolchain
0.1.2 intel/2019b


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 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 (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 (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


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 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/9.3.0


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 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
1.1.2 -Python-3.7.4 foss/2019b, intel/2019b
1.1.3 -Python-3.8.2 intel/2020a


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

homepage: http://cheetahtemplate.org

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


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 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 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


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


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 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 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


CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

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

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


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


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


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 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


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


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


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


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


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 intel/2016a intel/2016a intel/2016a intel/2016a foss/2017b, intel/2017b intel/2017b foss/2017b, foss/2018b, intel/2017b, intel/2018b foss/2019b, foss/2020a


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


Efficient Inference of Recombination in Whole Bacterial Genomes

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

version toolchain
1.11 foss/2016b


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 (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 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 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: Finding dense clusters of motifs in DNA sequences

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

version toolchain
20160106 intel/2016a


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: http://cea-hpc.github.io/clustershell/

version toolchain
1.7.3 system


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


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


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

homepage: http://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


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 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


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


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 (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 (“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


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 system


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


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


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


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


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


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


Schrodinger-developed 2D Coordinate Generation

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

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


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


Tool to check available cores and OMP threads

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

version toolchain
1.1.1 system


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


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.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


Configurable talking characters in ASCII art

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

version toolchain
3.04 system


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


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


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 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 is a functional testing framework for command line applications.

homepage: https://bitheap.org/cram

version toolchain
0.7 GCCcore/8.2.0


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


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

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

version toolchain
19.06 system


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

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

version toolchain
19.06 system


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

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

version toolchain
19.06 system


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

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

version toolchain
19.06 system


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++ 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 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 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 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 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


CryptoMiniSat is an advanced SAT solver

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

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


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 is a developer’s tool for browsing source code.

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

version toolchain
15.9 system


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 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


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


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


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


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


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/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0


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 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


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


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   fosscuda/2017b, fosscuda/2018a, intelcuda/2017b   fosscuda/2018b   gcccuda/2019a -CUDA-10.0.130 system -CUDA-10.0.130 system -CUDA-10.1.243 system   gcccuda/2019a, gcccuda/2019b -CUDA-10.0.130 system -CUDA-11.0.2 system -CUDA-11.1.1 system -CUDA-11.1.1 system


Automated testing framework for C.

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

version toolchain
2.1-3 GCCcore/6.4.0


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


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


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 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-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


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 toolchain gcccuda/2019b


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 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


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


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


The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.

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

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


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 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


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


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 - dill - DIRAC - distributed - DL_POLY_Classic - dm-tree - DMTCP - DOLFIN - Doris - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - Drake - dropEst - DSA - DSRC - Dsuite - dtcmp - dtcwt - dxpy


∂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


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


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


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 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


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 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 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


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/7.3.0, GCCcore/8.3.0


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


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 GCCcore/10.2.0


Perl5 access to Berkeley DB version 1.x.

homepage: http://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


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 -Perl-5.28.1 foss/2019a


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


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


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 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 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 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 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 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


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


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


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: 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 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 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 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.

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

version versionsuffix toolchain
0.7.8 -linux_x86_64 system


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


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


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 (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


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


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+ 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


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 (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 is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

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


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 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: 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


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


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


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 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-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


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 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


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


.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


.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


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/9.3.0


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 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: http://www.doxygen.org

version toolchain 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


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


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


Digital Sorting Algorithm

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

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


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


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


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


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


DNAnexus Platform API bindings for Python

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

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


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 - ESMValTool - eSpeak-NG - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - ExifTool - Exonerate - expat - expect - eXpress - Extrae


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


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


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 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


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 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


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


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


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 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 is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments

homepage: http://eggnog-mapper.embl.de

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


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


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: a toolbox for rigid and nonrigid registration of images.

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

version toolchain
4.9.0 foss/2018a


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


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


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
2020.05.001 intel/2020a
2020.11.001 foss/2020b, intel/2020b


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 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


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/9.3.0


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 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 -X11-20170314 intel/2017a


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 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


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 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


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


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


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


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 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


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


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


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


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


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


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

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

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


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


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


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/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 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 GCCcore/10.2.0, GCCcore/9.3.0


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


Streaming quantification for high-throughput sequencing

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

version toolchain
1.5.1 intel/2017b


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: http://www.bsc.es/computer-sciences/performance-tools

version toolchain
3.4.1 foss/2017a
3.7.1 intel/2019a


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


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 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 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


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: 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


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


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


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


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 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


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 GCC/8.3.0, iccifort/2019.5.281, intel/2018a, intel/2018b


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: 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


Match up paired end fastq files quickly and efficiently.

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

version toolchain
1.0 GCCcore/8.2.0


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 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 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


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 is a QTL mapper

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

version toolchain
2.184 foss/2018b


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


Fast Robinson Foulds Supertrees

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

version toolchain
1.0-20190613 gompi/2019a


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 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/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0


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

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

version toolchain
20180422 foss/2019b


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 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


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


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


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
6.7.5   intel/2020a


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


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 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


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


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


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


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


Finite Field Linear Algebra Subroutines / Package

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

version toolchain
2.2.0 foss/2016a


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


Feed-forward neural network solution for python

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

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


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 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: http://www.fftw.org

version versionsuffix toolchain
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


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: 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 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


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


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 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 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 2.0.0-rc-69/1.52p.

homepage: https://fiji.sc/

version toolchain
20170530 system
20191119-2057 system


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


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
0.2.0 foss/2016b


circRNA detection from RNA-seq reads

homepage: https://github.com/marvin-jens/find_circ

version versionsuffix toolchain
1.2-20170228 -Python-2.7.14 intel/2017b


Find haplotypes and impute genotypes using multiple chip sets and sequence data

homepage: http://aipl.arsusda.gov/software/findhap/

version toolchain
4 system


findutils: The GNU find, locate, updatedb, and xargs utilities

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

version toolchain
4.4.2 GCC/4.8.2


A package for population structure inference from RAD-seq data

homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

version toolchain
20180709 intel/2018a


fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.

homepage: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

version toolchain
2.1.3 intel/2017b


Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.

homepage: https://github.com/Toblerity/Fiona

version versionsuffix toolchain
1.8.13 -Python-3.7.4 foss/2019b, fosscuda/2019b, intel/2019b
1.8.13.post1 -Python-3.7.2 foss/2019a
1.8.16 -Python-3.8.2 foss/2020a


Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.

homepage: https://www.mozilla.org/en-US/firefox/new/

version toolchain
44.0.2 system


FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy.

homepage: https://github.com/tud-zih-energy/FIRESTARTER/

version toolchain
2.0 gcccuda/2020a, gcccuda/2020b


FireWorks helps run calculation workflows, with a centralized workflow server controlling many worker nodes.

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

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


t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.

homepage: https://github.com/KlugerLab/FIt-SNE

version toolchain
1.1.0 gompi/2018b


FIX attempts to auto-classify ICA components into “good” vs “bad” components, so that the bad components can be removed from the 4D FMRI data.

homepage: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX

version versionsuffix toolchain
1.06.12 -Octave-Python-3.7.2 foss/2019a


X.org FixesProto protocol headers.

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

version toolchain
5.0 foss/2016a, gimkl/2.11.5, intel/2016a


FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

homepage: https://github.com/BrooksLabUCSC/flair

version versionsuffix toolchain
1.5 -Python-3.7.4 foss/2019b
1.5.1-20200630 -Python-3.7.4 foss/2019b


FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.

homepage: http://www.cs.ubc.ca/research/flann/

version versionsuffix toolchain
1.8.4 -Python-2.7.11 intel/2016a
1.8.4 -Python-2.7.14 intel/2017b


FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

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

version toolchain
1.2.11 GCC/8.3.0, foss/2016a, foss/2018a, foss/2018b
2.2.00 foss/2018b


Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors

homepage: https://www.palletsprojects.com/p/flask/

version versionsuffix toolchain
1.0.2 -Python-3.6.6 foss/2018b
1.1.2   GCCcore/10.2.0
1.1.2 -Python-3.7.4 GCCcore/8.3.0
1.1.2 -Python-3.8.2 GCCcore/9.3.0


FlatBuffers: Memory Efficient Serialization Library

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

version toolchain
1.12.0 GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0


Python Flatbuffers runtime library.

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

version versionsuffix toolchain
1.12   GCCcore/10.2.0
1.12 -Python-3.7.4 GCCcore/8.3.0


FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory.

homepage: http://www.flapw.de/

version toolchain
0.26e intel/2016a


Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

homepage: http://flex.sourceforge.net/

version toolchain
2.5.35 system
2.5.38 GCC/4.8.2
2.5.39 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/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, system
2.6.0 GCC/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.6.2 intel/2016b
2.6.3 GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/7.1.0, gimkl/2017a, system
2.6.4 GCCcore/10.1.0, GCCcore/10.2.0, GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/7.4.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, GCCcore/9.3.0, GCCcore/system, system


The program Flexbar preprocesses high-throughput sequencing data efficiently

homepage: https://github.com/seqan/flexbar

version toolchain
3.5.0 foss/2018b


Highly customizable, ambiguity-aware dotplots for visual sequence analyses

homepage: https://github.com/molbio-dresden/flexidot

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


FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.

homepage: http://www.flintlib.org

version toolchain
2.5.2 GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2018.3.222-GCC-7.3.0-2.30


FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

homepage: https://www.fltk.org

version toolchain
1.3.3 foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.4 foss/2017b, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018a, fosscuda/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intelcuda/2017b
1.3.5 GCC/8.2.0-2.31.1, GCC/8.3.0, GCCcore/9.3.0


ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

homepage: https://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent

version toolchain
14.5 system
15.0.7 system
16.0 system
17.1 system
18.0 system
18.1 system
18.2 system


Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

homepage: https://github.com/fenderglass/Flye

version versionsuffix toolchain
2.4 -Python-2.7.15 intel/2018b
2.6 -Python-3.7.2 foss/2019a
2.6 -Python-3.7.4 intel/2019b
2.8.1 -Python-3.8.2 intel/2020a


FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/

homepage: https://jmodelica.org/

version toolchain
2.0.3 intel/2018b


FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

homepage: https://fmriprep.readthedocs.io

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


fmt (formerly cppformat) is an open-source formatting library.

homepage: http://fmtlib.net/

version toolchain
3.0.1 foss/2016b, intel/2016b
3.0.2 GCCcore/6.4.0, intel/2017a
5.3.0 GCCcore/7.3.0, GCCcore/8.2.0
6.2.1 GCCcore/9.3.0
7.0.3 GCCcore/9.3.0


FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.

homepage: http://foldx.crg.es/

version toolchain
2.5.2 system
3.0-beta5.1 system
3.0-beta6 system
3.0-beta6.1 system


Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

homepage: https://www.freedesktop.org/wiki/Software/fontconfig/

version versionsuffix toolchain
2.11.94   foss/2016a, intel/2016a
2.11.95   foss/2016a, intel/2016a
2.12.1   GCCcore/5.4.0, GCCcore/6.3.0, foss/2016b, gimkl/2017a, intel/2016b
2.12.1 -libpng-1.6.29 GCCcore/6.3.0
2.12.4   GCCcore/6.4.0
2.12.6   GCCcore/6.4.0
2.13.0   GCCcore/6.4.0, GCCcore/7.3.0
2.13.1   GCCcore/8.2.0, GCCcore/8.3.0
2.13.92   GCCcore/10.2.0, GCCcore/9.3.0


X11 font extension wire protocol

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

version toolchain
2.1.3 foss/2016a, gimkl/2.11.5, intel/2016a


GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

version toolchain
2016.04 system
2016.06 system
2016.07 system
2016.09 system
2016a system
2016b system
2017a system
2017b system
2018.08 system
2018a system
2018b system
2019a system
2019b system
2020a system
2020b system


GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
2017b system
2018a system
2018b system
2019a system
2019b system
2020a system
2020b system


FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.

homepage: http://homepages.see.leeds.ac.uk/~earawa/FoX/

version toolchain
4.1.2 GCC/9.3.0, intel/2017b, intel/2018a


Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.

homepage: https://github.com/jordansissel/fpm

version versionsuffix toolchain
1.3.3 -Ruby-2.1.6 system


The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

homepage: https://github.com/Discngine/fpocket

version toolchain gompi/2020a


fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3’ regions in reads from high-throughput next-generation sequencing machines.

homepage: http://ccb.jhu.edu/software/fqtrim/

version toolchain
0.9.4 intel/2016b
0.9.5 intel/2017a


Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels.

homepage: http://sourceforge.net/projects/fqzcomp/

version toolchain
4.6 GCC/4.8.2


FragGeneScan is an application for finding (fragmented) genes in short reads.

homepage: http://omics.informatics.indiana.edu/FragGeneScan/

version toolchain
1.31 GCCcore/8.2.0, foss/2018b


A fast and flexible parentage inference program for natural populations.

homepage: https://www.bioinf.uni-leipzig.de/Software/FRANz

version toolchain
2.0.0 foss/2018a


FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.

homepage: http://www.freefem.org/

version versionsuffix toolchain
3.58 -downloaded-deps foss/2017b
3.60 -downloaded-deps intel/2018a
3.61-1 -downloaded-deps intel/2018a


freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

homepage: http://freeglut.sourceforge.net/

version versionsuffix toolchain
3.0.0   GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017b, foss/2018a, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a
3.0.0 -Mesa-11.2.1 foss/2016a, intel/2016a
3.2.1   GCCcore/8.3.0, GCCcore/9.3.0


FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today’s multimedia applications. FreeImage is easy to use, fast, multithreading safe.

homepage: http://freeimage.sourceforge.net

version toolchain
3.18.0 GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0


FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).

homepage: https://freesasa.github.io

version toolchain