Modules sse3: Difference between revisions

| align="center" | 2021

| align="center" | 10.0.3

| align="center" | [https://abseil.io/ abseil]

| align="center" | [https://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]

| align="center" | 2.3.7

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /><br /></div>

| align="center" | 2020.3

| align="center" | 24.1.03

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: http://afni.nimh.nih.gov/ Keyword:bio<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/AmberTools.php URL: https://ambermd.org/AmberTools.php Keyword:chem<br /><br /><br /></div>

| align="center" | [https://github.com/ampl/mp ampl-mp]

| align="center" | 3.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source library for mathematical programming. Homepage: https://github.com/ampl/mp URL: https://github.com/ampl/mp<br /><br /><br /></div>

| align="center" | [https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus amrfinderplus]

| align="center" | -

| align="center" | 3.12.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus<br /><br /><br /></div>

| align="center" | 0.940

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd URL: http://www.popgen.dk/angsd Keyword:bio<br /><br /><br /></div>

| align="center" | 20191024

| align="center" | 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2

| align="center" | 1.9.15, 1.10.8, 1.10.14

| align="center" | [https://www.antlr2.org/ antlr]

| align="center" | [https://stnava.github.io/ANTs/ ants]

| align="center" | 2.5.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://stnava.github.io/ANTs/ Keyword:vis<br /><br /><br /></div>

| align="center" | [http://www.ansikte.se/ARAGORN/ aragorn]

| align="center" | [https://arma.sourceforge.net/ armadillo]

| align="center" | 12.6.4

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://arma.sourceforge.net/ Keyword:math<br /><br /><br /></div>

| align="center" | [https://github.com/opencollab/arpack-ng arpack-ng]

| align="center" | 3.9.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ URL: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div>

| align="center" | 2.5.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools URL: https://github.com/pezmaster31/bamtools Keyword:bio<br /><br /><br /></div>

| align="center" | 38.86, 39.06

| align="center" | [https://www.htslib.org/ bcftools]

| align="center" | 1.18, 1.19

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html URL: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html<br /><br /><br /></div>

| align="center" | 5.4, 5.4-240301

| align="center" | 4.0.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div>

| align="center" | 2.4.41

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: http://bedops.readthedocs.io/en/latest/index.html<br /><br /><br /></div>

| align="center" | 2.31.0

| align="center" | 4.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org URL: http://www.berkeleygw.org Keyword:phys<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: https://github.com/lh3/bioawk<br /><br /><br /></div>

| align="center" | 1.7.7, 1.7.8

| align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark]

| align="center" | 0.24.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/<br /><br /><br /></div>

| align="center" | [https://blast.ncbi.nlm.nih.gov/ blast+]

| align="center" | 2.14.1

| Documentation: [[BLAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>

| align="center" | 3.6.0, 4.0.2

| align="center" | 0.8.1, 0.9.0, 1.0

| align="center" | 1.72.0, 1.82.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>

| align="center" | 1.72.0, 1.82.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>

| align="center" | 2.5.2, 2.5.4

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio<br /><br /><br /></div>

| align="center" | [https://github.com/BUStools/bustools bustools]

| align="center" | 0.7.17, 0.7.18

| align="center" | [https://github.com/bwa-mem2/bwa-mem2 bwa-mem2]

| align="center" | -

| align="center" | 2.2.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. The original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license. Homepage: https://github.com/bwa-mem2/bwa-mem2 URL: https://github.com/bwa-mem2/bwa-mem2<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ URL: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo<br /><br /><br /></div>

| align="center" | 2.2.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo URL: https://code.zmaw.de/projects/cdo Keyword:geo<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome URL: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio<br /><br /><br /></div>

| align="center" | [https://uscilab.github.io/cereal/ cereal]

| align="center" | 1.3.0, 1.3.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://uscilab.github.io/cereal/<br /><br /><br /></div>

| align="center" | 2.1.3

| align="center" | [http://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]

| align="center" | 4.3.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/ URL: http://heasarc.gsfc.nasa.gov/fitsio/ Keyword:vis<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Serial version of CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem<br /><br /><br /></div>

| align="center" | 4.14.3, 5.5.2

| align="center" | [https://github.com/simnibs/charm-gems charm-gems]

| align="center" | -

| align="center" | 1.3.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations. Homepage: https://github.com/simnibs/charm-gems URL: https://github.com/simnibs/charm-gems Compatible modules: python/3.11, python/3.10 Extensions: charm-gems-1.3.3<br /><br /><br /></div>

| align="center" | [http://www.circos.ca/ circos]

| align="center" | 0.69-9

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: http://www.circos.ca/ Keyword:vis<br /><br /><br /></div>

| align="center" | [https://clang.llvm.org/ clang]

| align="center" | 17.0.6

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/ URL: https://clang.llvm.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>

| align="center" | [https://proj-clhep.web.cern.ch/proj-clhep/ clhep]

| align="center" | 2.4.6.2, 2.4.7.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br /><br /><br /></div>

| align="center" | 3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7

| align="center" | 3.5.0, 3.12.0

| align="center" | 5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2.0.415

| align="center" | 58

| align="center" | 2020

| align="center" | 8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29

| align="center" | 0.4.0.7, 0.5.0.1

| align="center" | 1.1, 1.2

| align="center" | 1.5.0.3, 1.7.0.1, 2.0.0.7

| align="center" | 6.13

| align="center" | [https://github.com/rordenlab/dcm2niix dcm2niix]

| align="center" | 1.0.20230411

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio<br /><br /><br /></div>

| align="center" | [https://www.linaroforge.com ddt-cpu]

| align="center" | 20.2, 22.0.1, 23.1.1

| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>

| align="center" | [https://www.linaroforge.com ddt-gpu]

| align="center" | 20.2, 22.0.1, 23.1.1

| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT, with support for CUDA. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>

| align="center" | [https://github.com/dellytools/delly/ delly]

| align="center" | -

| align="center" | 0.8.5, 1.1.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Homepage: https://github.com/dellytools/delly/ URL: https://github.com/dellytools/delly/<br /><br /><br /></div>

| align="center" | [https://github.com/dftd4/dftd4 dftd4]

| align="center" | chem

| align="center" | 3.6.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Generally Applicable Atomic-Charge Dependent London Dispersion Correction. Homepage: https://github.com/dftd4/dftd4 URL: https://github.com/dftd4/dftd4 Keyword:chem<br /><br /><br /></div>

| align="center" | 2.1.8

| align="center" | 5.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx URL: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem<br /><br /><br /></div>

| align="center" | 0.2.1, 0.2.2, 0.3.0, 0.4.1, 0.4.3, 0.5.3, 0.6.1, 0.7.0, 0.7.2

| align="center" | 3.1.8, 5.0.12, 6.0.0

| align="center" | [https://ecbuild.readthedocs.io/ ecbuild]

| align="center" | -

| align="center" | 3.8.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems Homepage: https://ecbuild.readthedocs.io/ URL: https://ecbuild.readthedocs.io/<br /><br /><br /></div>

| align="center" | [https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home eccodes]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.10, python/3.11 Extensions: cfgrib-0.9.10.4, eccodes-1.6.1 Keyword:geo<br /><br /><br /></div>

| align="center" | [https://www.ncbi.nlm.nih.gov/books/NBK25501/ edirect]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. Homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/ URL: https://www.ncbi.nlm.nih.gov/books/NBK25501/<br /><br /><br /></div>

| align="center" | [https://eigen.tuxfamily.org eigen]

| align="center" | 3.3.7, 3.4.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org URL: https://eigen.tuxfamily.org Keyword:math<br /><br /><br /></div>

| align="center" | [https://elpa.mpcdf.mpg.de/ elpa]

| align="center" | 2020.05.001, 2023.05.001

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications. Homepage: https://elpa.mpcdf.mpg.de/ URL: https://elpa.mpcdf.mpg.de/ Keyword:math<br /><br /><br /></div>

| align="center" | 3.11.0, 4.3.0

| align="center" | [https://www.earthsystemcog.org/projects/esmf/ esmf]

| align="center" | 8.6.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://www.earthsystemcog.org/projects/esmf/ Compatible modules: python/3.10, python/3.11 Extensions: esmpy-8.6.0 Keyword:geo<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: http://www.etsf.eu/resources/software/libraries_and_tools Keyword:io<br /><br /><br /></div>

| align="center" | [https://libexpat.github.io expat]

| align="center" | tools

| align="center" | 2.2.9, 2.2.10

| align="center" | [https://github.com/facebookresearch/faiss faiss]

| align="center" | -

| align="center" | 1.7.4, 1.8.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>

| align="center" | [https://github.com/ekg/fastahack fastahack]

| align="center" | -

| align="center" | 1.0.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Utilities for indexing and sequence extraction from FASTA files. Homepage: https://github.com/ekg/fastahack URL: https://github.com/ekg/fastahack<br /><br /><br /></div>

| align="center" | 0.11.9, 0.12.0, 0.12.1

| align="center" | [https://github.com/lh3/fermi-lite fermi-lite]

| align="center" | -

| align="center" | 20190320

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Standalone C library for assembling Illumina short reads in small regions. Homepage: https://github.com/lh3/fermi-lite URL: https://github.com/lh3/fermi-lite<br /><br /><br /></div>

| align="center" | [http://ferret.pmel.noaa.gov/ ferret]

| align="center" | vis

| align="center" | 7.6.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. Ferret 7.6.0 is the final available version of Classic Ferret. The developers recommend using PyFerret instead. Homepage: http://ferret.pmel.noaa.gov/ URL: http://ferret.pmel.noaa.gov/ Keyword:vis<br /><br /><br /></div>

| align="center" | [https://www.fftw.org fftw]

| align="center" | math

| align="center" | 3.3.10

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math<br /><br /><br /></div>

| align="center" | [https://www.fftw.org fftw-mpi]

| align="center" | 3.3.10

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math<br /><br /><br /></div>

| align="center" | [https://github.com/ekg/filevercmp filevercmp]

| align="center" | -

| align="center" | 20191210

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: filevercmp function as in sort --version-sort. Homepage: https://github.com/ekg/filevercmp URL: https://github.com/ekg/filevercmp<br /><br /><br /></div>

| align="center" | 0.2.0, 0.2.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div>

| align="center" | 3.0.4, 3.3.1, 3.4.4

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release URL: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release<br /><br /><br /></div>

| align="center" | [http://www.flintlib.org/ flint]

| align="center" | math

| align="center" | 3.0.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: http://www.flintlib.org/ Keyword:math<br /><br /><br /></div>

| align="center" | [https://fmriprep.org/ fmriprep]

| align="center" | 5.3.0, 6.2.1, 7.0.3

| align="center" | [https://github.com/fplll/fplll fplll]

| align="center" | 5.4.5

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name. Homepage: https://github.com/fplll/fplll URL: https://github.com/fplll/fplll<br /><br /><br /></div>

| align="center" | [https://github.com/freebayes/freebayes freebayes]

| align="center" | 1.3.7

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Homepage: https://github.com/freebayes/freebayes URL: https://github.com/freebayes/freebayes Keyword:bio<br /><br /><br /></div>

| align="center" | [https://www.gaia-gis.it/fossil/freexl/index freexl]

| align="center" | [https://www.fmrib.ox.ac.uk/fsl/ fsl]

| align="center" | 6.0.7.7

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio<br /><br /><br /></div>

| align="center" | [https://github.com/ekg/fsom fsom]

| align="center" | 20151117

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tiny C library for managing SOM (Self-Organizing Maps) neural networks. Homepage: https://github.com/ekg/fsom URL: https://github.com/ekg/fsom<br /><br /><br /></div>

| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2c g2clib]

| align="center" | 1.6.0, 1.8.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This library contains C decoder/encoder routines for GRIB edition 2. This is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2c URL: https://github.com/NOAA-EMC/NCEPLIBS-g2c Keyword:geo<br /><br /><br /></div>

| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2/ g2lib]

| align="center" | 3.4.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2/ URL: https://github.com/NOAA-EMC/NCEPLIBS-g2/ Keyword:geo<br /><br /><br /></div>

| align="center" | 20230930-R2

| Documentation: [[GAMESS-US]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS-US is built with Intel compilers, mixed DDI, and OpenMPI 4.1. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem<br /><br /><br /></div>

| align="center" | 9.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography Homepage: http://www.opengatecollaboration.org/ URL: http://www.opengatecollaboration.org/ Keyword:bio<br /><br /><br /></div>

| align="center" | 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0

| align="center" | 8.4.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3, 13.3

| align="center" | [https://github.com/lstein/Perl-GD gd]

| align="center" | 2.77

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD.pm - Interface to Gd Graphics Library Homepage: https://github.com/lstein/Perl-GD URL: https://github.com/lstein/Perl-GD Extensions: ExtUtils::PkgConfig-1.16, GD-2.77<br /><br /><br /></div>

| align="center" | [https://www.gdal.org/ gdal]

| align="center" | 3.7.2, 3.9.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. Homepage: https://www.gdal.org/ URL: https://www.gdal.org/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12, python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12 Extensions: osgeo-3.9.1 Keyword:geo<br /><br /><br /></div>

| align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy]

| align="center" | [https://geant4.web.cern.ch/ geant4]

| align="center" | 11.1.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: https://geant4.web.cern.ch/ URL: https://geant4.web.cern.ch/ Keyword:phys<br /><br /><br /></div>

| align="center" | 10.7.3, 11.1.0, 11.1.2

| align="center" | [http://veda.cs.uiuc.edu/Seq2Expr/ gemma]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio<br /><br /><br /></div>

|-

| align="center" | [https://wiki.gentoo.org/wiki/Project:Prefix gentoo]

| align="center" | 2020, 2023

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix<br /><br /><br /></div>

| align="center" | [https://trac.osgeo.org/geos geos]

| align="center" | 3.12.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: https://trac.osgeo.org/geos URL: https://trac.osgeo.org/geos Keyword:geo<br /><br /><br /></div>

| align="center" | [http://git-annex.branchable.com/ git-annex]

| align="center" | tools

| align="center" | 8.20200810, 10.20221003, 10.20231129

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools<br /><br /><br /></div>

| align="center" | [https://git-lfs.github.com git-lfs]

| align="center" | 2.11.0, 3.3.0, 3.4.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com Homepage: https://git-lfs.github.com URL: https://git-lfs.github.com<br /><br /><br /></div>

| align="center" | [http://glew.sourceforge.net/ glew]

| align="center" | 2.2.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. Homepage: http://glew.sourceforge.net/ URL: http://glew.sourceforge.net/<br /><br /><br /></div>

| align="center" | 3.3.2, 3.3.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Extensions: glfw-2.6.2<br /><br /><br /></div>

| align="center" | 0.9.9.8

| align="center" | [https://gmsh.info/ gmsh]

| align="center" | phys

| align="center" | 4.12.2, 4.13.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys<br /><br /><br /></div>

| align="center" | [https://www.generic-mapping-tools.org/ gmt]

| align="center" | geo

| align="center" | 6.5.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: https://www.generic-mapping-tools.org/ URL: https://www.generic-mapping-tools.org/ Keyword:geo<br /><br /><br /></div>

| align="center" | [http://gnuplot.sourceforge.net gnuplot]

| align="center" | 5.2.8, 5.4.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net URL: http://gnuplot.sourceforge.net Keyword:vis<br /><br /><br /></div>

| align="center" | 1.14.1, 1.18.3, 1.21.3

| align="center" | [https://github.com/google/benchmark googlebenchmark]

| align="center" | [https://github.com/google/googletest googletest]

| align="center" | tools

| align="center" | 1.14.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools<br /><br /><br /></div>

| align="center" | 2023.3, 2024.1

| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>

| align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]

| align="center" | 2021.7-0.5.1

| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>

| align="center" | 2.6, 2.7

| align="center" | 0.40.0, 0.41.0

| align="center" | [https://www.gurobi.com gurobi]

| align="center" | 9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0, 11.0.1