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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/0/3d-dna.md
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# 3d-dna

3D de novo assembly (3D DNA) pipeline
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version | versionsuffix | toolchain
--------|---------------|----------
``180922`` | ``-Python-2.7.15`` | ``GCCcore/8.2.0``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/0/3to2.md
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# 3to2

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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``1.1.1`` | ``-Python-2.7.12`` | ``foss/2016b``
``1.1.1`` | ``-Python-2.7.12`` | ``intel/2016b``
``1.1.1`` | ``-Python-2.7.13`` | ``intel/2017a``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/0/4ti2.md
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# 4ti2

A software package for algebraic, geometric and combinatorial problems on linear spaces
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``1.6.9`` | ``GCC/11.3.0``
``1.6.9`` | ``GCC/8.2.0-2.31.1``
``1.6.9`` | ``intel/2018b``

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# List of supported software (0)

*0* - [../a/index.md](a) - [../b/index.md](b) - [../c/index.md](c) - [../d/index.md](d) - [../e/index.md](e) - [../f/index.md](f) - [../g/index.md](g) - [../h/index.md](h) - [../i/index.md](i) - [../j/index.md](j) - [../k/index.md](k) - [../l/index.md](l) - [../m/index.md](m) - [../n/index.md](n) - [../o/index.md](o) - [../p/index.md](p) - [../q/index.md](q) - [../r/index.md](r) - [../s/index.md](s) - [../t/index.md](t) - [../u/index.md](u) - [../v/index.md](v) - [../w/index.md](w) - [../x/index.md](x) - [../y/index.md](y) - [../z/index.md](z)

* [3d-dna](3d-dna.md)
* [3to2](3to2.md)
* [4ti2](4ti2.md)
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# ABAQUS

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
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``6.12.1`` | ``-linux-x86_64`` | ``system``
``6.13.5`` | ``-linux-x86_64`` | ``system``
``6.14.1`` | ``-linux-x86_64`` | ``system``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/a/ABINIT.md
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# ABINIT

Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
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``9.6.2`` | | ``intel/2021a``
``9.6.2`` | | ``intel/2021b``
``9.6.2`` | | ``intel/2022a``

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# ABRA2

Assembly Based ReAligner
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``2.22`` | ``iccifort/2019.5.281``
``2.23`` | ``GCC/10.2.0``
``2.23`` | ``GCC/9.3.0``

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# ABRicate

Mass screening of contigs for antimicrobial and virulence genes
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``0.9.9`` | ``-Perl-5.28.1`` | ``gompi/2019a``
``0.9.9`` | | ``gompi/2019b``
``1.0.0`` | | ``gompi/2021a``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/a/ABySS.md
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# ABySS

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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``2.1.5`` | ``foss/2019b``
``2.2.5`` | ``foss/2020b``
``2.3.7`` | ``foss/2023a``

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# ACTC

ACTC converts independent triangles into triangle strips or fans.
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``1.1`` | ``GCCcore/8.3.0``
``1.1`` | ``GCCcore/9.3.0``
``1.1`` | ``intel/2016b``

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# ADDA

ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes.
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version | toolchain
--------|----------
``1.3b4`` | ``foss/2019a``

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# ADF

ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT).
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``2014.11.r48287`` | | ``intel/2016a``
``2016.101`` | | ``system``
``2019.303`` | ``-intelmpi`` | ``system``

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# ADIOS

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
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``1.13.1`` | ``-Python-2.7.15`` | ``foss/2019a``
``1.13.1`` | ``-Python-3.8.2`` | ``foss/2020a``
``20210804`` | ``-Python-3.8.2`` | ``foss/2020a``

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# ADMIXTURE

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

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# ADOL-C

The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C.
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--------|----------
``2.7.0`` | ``gompi/2019a``
``2.7.2`` | ``gompi/2020a``

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# AEDT

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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version | toolchain
--------|----------
``2024R1`` | ``system``

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# AFNI

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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``19.0.01`` | ``-Python-2.7.14`` | ``intel/2017b``
``20160329`` | ``-Python-2.7.11`` | ``intel/2016a``
``24.0.02`` | | ``foss/2023a``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/a/AGAT.md
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# AGAT

AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
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--------|----------
``0.9.2`` | ``GCC/11.2.0``
``1.1.0`` | ``GCC/12.2.0``

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# AGFusion

AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
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version | versionsuffix | toolchain
--------|---------------|----------
``1.2`` | ``-Python-3.7.2`` | ``foss/2019a``

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7 changes: 7 additions & 0 deletions docs/version-specific/supported-software/a/AGeNT.md
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# AGeNT

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

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# AICSImageIO

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
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version | toolchain
--------|----------
``4.14.0`` | ``foss/2022a``

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