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‎docs/version-specific/supported-software.md

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‎docs/version-specific/supported-software/0/3d-dna.md

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# 3d-dna
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3D de novo assembly (3D DNA) pipeline
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*homepage*: <https://github.com/theaidenlab/3d-dna>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``180922`` | ``-Python-2.7.15`` | ``GCCcore/8.2.0``

‎docs/version-specific/supported-software/0/3to2.md

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# 3to2
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lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.
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*homepage*: <https://pypi.python.org/pypi/3to2>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``1.1.1`` | ``-Python-2.7.12`` | ``foss/2016b``
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``1.1.1`` | ``-Python-2.7.12`` | ``intel/2016b``
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``1.1.1`` | ``-Python-2.7.13`` | ``intel/2017a``

‎docs/version-specific/supported-software/0/4ti2.md

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# 4ti2
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A software package for algebraic, geometric and combinatorial problems on linear spaces
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*homepage*: <https://4ti2.github.io/>
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version | toolchain
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--------|----------
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``1.6.10`` | ``GCC/13.2.0``
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``1.6.9`` | ``GCC/11.3.0``
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``1.6.9`` | ``GCC/8.2.0-2.31.1``
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``1.6.9`` | ``intel/2018b``

‎docs/version-specific/supported-software/0/index.md

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# List of supported software (0)
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* [3d-dna](3d-dna.md)
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* [3to2](3to2.md)
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* [4ti2](4ti2.md)

‎docs/version-specific/supported-software/a/ABAQUS.md

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# ABAQUS
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Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
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*homepage*: <http://www.simulia.com/products/abaqus_fea.html>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``2017`` | ``-hotfix-1721`` | ``system``
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``2018`` | ``-hotfix-1806`` | ``system``
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``2020`` | | ``system``
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``2021`` | ``-hotfix-2132`` | ``system``
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``2022`` | ``-hotfix-2214`` | ``system``
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``2022`` | ``-hotfix-2223`` | ``system``
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``2022`` | | ``system``
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``6.12.1`` | ``-linux-x86_64`` | ``system``
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``6.13.5`` | ``-linux-x86_64`` | ``system``
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``6.14.1`` | ``-linux-x86_64`` | ``system``

‎docs/version-specific/supported-software/a/ABINIT.md

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# ABINIT
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Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
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*homepage*: <http://www.abinit.org/>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``7.0.3`` | ``-x86_64_linux_gnu4.5`` | ``system``
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``7.0.5`` | ``-x86_64_linux_gnu4.5`` | ``system``
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``7.10.5`` | ``-libxc`` | ``intel/2016.02-GCC-4.9``
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``7.10.5`` | | ``intel/2016.02-GCC-4.9``
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``7.2.1`` | ``-x86_64_linux_gnu4.5`` | ``system``
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``8.0.8`` | | ``intel/2016a``
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``8.0.8b`` | | ``foss/2016b``
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``8.0.8b`` | | ``intel/2016b``
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``8.10.2`` | | ``intel/2018b``
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``8.10.3`` | | ``intel/2018b``
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``8.2.2`` | | ``foss/2016b``
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``8.2.2`` | | ``intel/2016b``
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``8.4.4`` | | ``intel/2017b``
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``8.6.3`` | | ``intel/2018a``
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``9.10.3`` | | ``intel/2022a``
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``9.2.1`` | | ``foss/2019b``
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``9.2.1`` | | ``intel/2019b``
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``9.2.1`` | | ``intel/2020a``
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``9.4.1`` | | ``foss/2020b``
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``9.4.1`` | | ``intel/2020a``
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``9.4.1`` | | ``intel/2020b``
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``9.4.2`` | | ``foss/2021a``
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``9.4.2`` | | ``intel/2021a``
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``9.6.2`` | | ``foss/2022a``
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``9.6.2`` | | ``intel/2021a``
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``9.6.2`` | | ``intel/2021b``
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``9.6.2`` | | ``intel/2022a``

‎docs/version-specific/supported-software/a/ABRA2.md

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# ABRA2
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Assembly Based ReAligner
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*homepage*: <https://github.com/mozack/abra2>
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version | toolchain
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--------|----------
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``2.22`` | ``iccifort/2019.5.281``
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``2.23`` | ``GCC/10.2.0``
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``2.23`` | ``GCC/9.3.0``

‎docs/version-specific/supported-software/a/ABRicate.md

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# ABRicate
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Mass screening of contigs for antimicrobial and virulence genes
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*homepage*: <https://github.com/tseemann/abricate>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``0.9.9`` | ``-Perl-5.28.1`` | ``gompi/2019a``
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``0.9.9`` | | ``gompi/2019b``
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``1.0.0`` | | ``gompi/2021a``

‎docs/version-specific/supported-software/a/ABySS.md

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# ABySS
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Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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*homepage*: <http://www.bcgsc.ca/platform/bioinfo/software/abyss>
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version | toolchain
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--------|----------
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``1.9.0`` | ``foss/2016a``
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``2.0.2`` | ``foss/2016b``
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``2.0.2`` | ``foss/2018a``
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``2.0.2`` | ``gompi/2019a``
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``2.0.2`` | ``intel/2016b``
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``2.0.3`` | ``foss/2017b``
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``2.0.3`` | ``intel/2017b``
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``2.1.5`` | ``foss/2019b``
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``2.2.5`` | ``foss/2020b``
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``2.3.7`` | ``foss/2023a``

‎docs/version-specific/supported-software/a/ACTC.md

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# ACTC
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ACTC converts independent triangles into triangle strips or fans.
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*homepage*: <https://sourceforge.net/projects/actc>
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version | toolchain
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--------|----------
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``1.1`` | ``GCCcore/10.2.0``
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``1.1`` | ``GCCcore/11.3.0``
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``1.1`` | ``GCCcore/6.4.0``
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``1.1`` | ``GCCcore/7.3.0``
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``1.1`` | ``GCCcore/8.3.0``
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``1.1`` | ``GCCcore/9.3.0``
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``1.1`` | ``intel/2016b``

‎docs/version-specific/supported-software/a/ADDA.md

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# ADDA
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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.
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*homepage*: <https://github.com/adda-team/adda/wiki>
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version | toolchain
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--------|----------
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``1.3b4`` | ``foss/2019a``

‎docs/version-specific/supported-software/a/ADF.md

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# ADF
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ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT).
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*homepage*: <http://www.scm.com/>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``2009.01a.pc64_linux.intelmpi`` | | ``system``
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``2014.02`` | | ``system``
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``2014.11.r48287`` | | ``intel/2016a``
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``2016.101`` | | ``system``
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``2019.303`` | ``-intelmpi`` | ``system``

‎docs/version-specific/supported-software/a/ADIOS.md

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# ADIOS
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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.
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*homepage*: <https://www.olcf.ornl.gov/center-projects/adios/>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``1.13.1`` | ``-Python-2.7.15`` | ``foss/2019a``
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``1.13.1`` | ``-Python-3.8.2`` | ``foss/2020a``
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``20210804`` | ``-Python-3.8.2`` | ``foss/2020a``

‎docs/version-specific/supported-software/a/ADMIXTURE.md

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# ADMIXTURE
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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.
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*homepage*: <https://dalexander.github.io/admixture/>
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version | toolchain
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--------|----------
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``1.3.0`` | ``system``

‎docs/version-specific/supported-software/a/ADOL-C.md

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# ADOL-C
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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.
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*homepage*: <https://projects.coin-or.org/ADOL-C>
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version | toolchain
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--------|----------
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``2.7.0`` | ``gompi/2019a``
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``2.7.2`` | ``gompi/2020a``

‎docs/version-specific/supported-software/a/AEDT.md

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# AEDT
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The Ansys Electronics Desktop (AEDT) is a platform that enables true electronics system design. AEDT provides access to the Ansys gold-standard electromagnetics simulation solutions such as Ansys HFSS, Ansys Maxwell, Ansys Q3D Extractor, Ansys SIwave, and Ansys Icepak using electrical CAD (ECAD) and mechanical CAD (MCAD) workflows.
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*homepage*: <https://www.ansys.com/products/electronics>
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version | toolchain
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--------|----------
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``2024R1`` | ``system``

‎docs/version-specific/supported-software/a/AFNI.md

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# AFNI
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AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
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*homepage*: <http://afni.nimh.nih.gov/>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``18.1.09`` | ``-Python-3.6.4`` | ``intel/2018a``
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``18.3.00`` | ``-Python-3.6.6`` | ``foss/2018b``
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``19.0.01`` | ``-Python-2.7.14`` | ``foss/2017b``
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``19.0.01`` | ``-Python-2.7.14`` | ``intel/2017b``
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``20160329`` | ``-Python-2.7.11`` | ``intel/2016a``
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``24.0.02`` | | ``foss/2023a``

‎docs/version-specific/supported-software/a/AGAT.md

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# AGAT
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AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
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*homepage*: <https://agat.readthedocs.io/en/latest/>
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version | toolchain
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--------|----------
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``0.9.2`` | ``GCC/11.2.0``
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``1.1.0`` | ``GCC/12.2.0``

‎docs/version-specific/supported-software/a/AGFusion.md

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# AGFusion
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AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
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*homepage*: <https://github.com/murphycj/AGFusion>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``1.2`` | ``-Python-3.7.2`` | ``foss/2019a``

‎docs/version-specific/supported-software/a/AGeNT.md

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# AGeNT
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The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format. The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
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*homepage*: <https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879>
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version | toolchain
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--------|----------
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``3.0.6`` | ``system``

‎docs/version-specific/supported-software/a/AICSImageIO.md

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# AICSImageIO
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Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
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*homepage*: <https://github.com/AllenCellModeling/aicsimageio>
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version | toolchain
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--------|----------
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``4.14.0`` | ``foss/2022a``

‎docs/version-specific/supported-software/a/AIMAll.md

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# AIMAll
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AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.
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*homepage*: <http://aim.tkgristmill.com>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``19.10.12`` | ``-linux_64bit`` | ``intel/2020b``

‎docs/version-specific/supported-software/a/ALADIN.md

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# ALADIN
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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.
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*homepage*: <http://www.cnrm.meteo.fr/aladin/>
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version | toolchain
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--------|----------
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``36t1_op2bf1`` | ``intel/2016a``

‎docs/version-specific/supported-software/a/ALAMODE.md

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# ALAMODE
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ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.
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*homepage*: <http://alamode.readthedocs.io/en/latest/index.html>
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version | toolchain
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--------|----------
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``1.4.2`` | ``foss/2022b``

‎docs/version-specific/supported-software/a/ALFA.md

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# ALFA
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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.
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*homepage*: <https://github.com/biocompibens/ALFA>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``1.1.1`` | ``-Python-3.7.2`` | ``foss/2019a``

‎docs/version-specific/supported-software/a/ALL.md

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# ALL
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A Load Balancing Library (ALL) aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the Jülich Supercomputing Centre at Forschungszentrum Jülich.
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*homepage*: <https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing>
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version | toolchain
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--------|----------
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``0.9.2`` | ``foss/2022b``
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``0.9.2`` | ``foss/2023a``

‎docs/version-specific/supported-software/a/ALLPATHS-LG.md

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# ALLPATHS-LG
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ALLPATHS-LG, the new short read genome assembler.
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*homepage*: <http://www.broadinstitute.org/software/allpaths-lg/blog/>
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version | toolchain
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--------|----------
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``52488`` | ``foss/2016a``

‎docs/version-specific/supported-software/a/ALPS.md

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# ALPS
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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.
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*homepage*: <http://www.example.com>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``2.2.b4`` | ``-Python-2.7.11`` | ``intel/2016a``
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``2.3.0`` | ``-Python-2.7.12`` | ``foss/2016b``
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``2.3.0`` | ``-Python-3.5.2`` | ``foss/2016b``

‎docs/version-specific/supported-software/a/AMAPVox.md

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# AMAPVox
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LiDAR data voxelisation software
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*homepage*: <https://amap-dev.cirad.fr/projects/amapvox>
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version | versionsuffix | toolchain
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--------|---------------|----------
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``1.9.4`` | ``-Java-11`` | ``system``

‎docs/version-specific/supported-software/a/AMD-LibM.md

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# AMD-LibM
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AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.
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*homepage*: <https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/>
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version | toolchain
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--------|----------
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``3.2.2`` | ``GCC/7.3.0-2.30``
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``3.6.0-4`` | ``GCC/9.3.0``

‎docs/version-specific/supported-software/a/AMD-RNG.md

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# AMD-RNG
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AMD Random Number Generator Library is a pseudorandom number generator library.
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*homepage*: <https://developer.amd.com/amd-cpu-libraries/rng-library/>
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version | toolchain
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--------|----------
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``1.0`` | ``GCC/7.3.0-2.30``
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``2.2-4`` | ``GCC/9.3.0``

‎docs/version-specific/supported-software/a/AMD-SecureRNG.md

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# AMD-SecureRNG
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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.
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*homepage*: <https://developer.amd.com/amd-cpu-libraries/rng-library/>
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version | toolchain
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--------|----------
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``1.0`` | ``GCC/7.3.0-2.30``
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``2.2-4`` | ``GCC/9.3.0``

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