Modules avx512: Difference between revisions

| align="center" | 2.0.2, 2.2.5

| align="center" | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 20180404

| <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>

| align="center" | [http://ambermd.org/amber.html amber]

| align="center" | 18.10-18.11, 18.14-18.17, 20.9-20.15, 20.12-20.15

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>

| align="center" | 20, 21, 22, 23

| <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 Amber20 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<br /><br /><br /></div>

| align="center" | 3.11.18, 3.11.26

| align="center" | 0.918, 0.929, 0.933, 0.935, 0.936, 0.939

| align="center" | 1.9.15, 1.10.8

| align="center" | 2.2.0, 2.3.2, 2.3.5, 2.4.4

| align="center" | [http://mbio-serv2.mbioekol.lu.se/ARAGORN/ aragorn]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: a program to detect tRNA genes and tmRNA genes in nucleotide sequences Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ URL: http://mbio-serv2.mbioekol.lu.se/ARAGORN/<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ URL: http://argtable.sourceforge.net/ Keyword:tools<br /><br /><br /></div>

| align="center" | 3.5.0, 3.7.0, 3.8.0, 3.9.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://arrayfire.com/ Compatible modules: python/3.7, python/3.8, python/3.9 Extensions: arrayfire-3.6.20181017<br /><br /><br /></div>

| align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1, 2.0.0, 4.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0

| <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/3.6.3, python/3.7.4, python/3.8.0 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>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html URL: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem<br /><br /><br /></div>

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

| align="center" | 2.4.1, 2.5.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio<br /><br /><br /></div>

| align="center" | 37.36, 37.78, 38.86

| align="center" | [https://samtools.github.io/bcftools/ bcftools]

| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.16

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF work in all situations. Unindexed VCF and BCF and streams work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed. Homepage: https://samtools.github.io/bcftools/ URL: https://samtools.github.io/bcftools/ Keyword:bio<br /><br /><br /></div>

| align="center" | 5.4

| align="center" | [http://beast2.org/ beast]

| Documentation: [[BEAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. - CC-Wiki: BEAST Homepage: http://beast2.org/ URL: http://beast2.org/ Keyword:bio<br /><br /><br /></div>

| align="center" | 2.27.1, 2.28.0, 2.29.2, 2.30.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/ URL: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div>

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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: http://www.bioperl.org/ Extensions: DBD::mysql-4.050, DBD::Pg-3.8.1, Devel::CheckLib-1.13, Devel::Cycle-1.12, IO::CaptureOutput-1.1104, PadWalker-2.3, Spiffy-0.46, Test::Base-0.89, Test::Memory::Cycle-1.06, Test::RequiresInternet-0.05, Test::Weaken-3.022000, Test::YAML-1.07, XML::DOM::XPath-0.14, XML::Filter::BufferText-1.01, XML::Parser-2.44, XML::RegExp-0.04, XML::XPathEngine-0.14, YAML-1.29 Keyword:bio<br /><br /><br /></div>

| align="center" | 0.22.1, 0.22.3

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. Homepage: https://github.com/PacificBiosciences/blasr Keyword:bio<br /><br /><br /></div>

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

| align="center" | 2.7.1, 2.8.1, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.12.0, 2.13.0

| align="center" | 2.79b, 2.92.0, 3.6.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: https://www.blender.org/ Compatible modules: python/3.7, python/3.8 Keyword:vis<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ URL: http://www.icams.de/content/departments/cmat/boltztrap/ Keyword:phys<br /><br /><br /></div>

| align="center" | 1.54.0, 1.60.0, 1.65.1, 1.66.0, 1.68.0, 1.72.0, 1.76.0, 1.80.0

| <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/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>

| align="center" | 1.68.0, 1.72.0, 1.80.0

| <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/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>

| align="center" | 2.3.4.3, 2.3.5, 2.3.5.1, 2.4.1, 2.4.2, 2.4.4, 2.5.1

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

| align="center" | 0.33.2, 0.35.2, 0.36.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (&lt;20 Mb). breseq is a command line tool implemented in C++ and R. Homepage: https://github.com/barricklab/breseq<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: http://bio-bwa.sourceforge.net/ Keyword:bio<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" | 1.7.2, 1.9.5, 1.9.8, 1.9.10, 2.0.4, 2.0.5

| <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" | [http://uscilab.github.io/cereal/ cereal]

| align="center" | 1.2.2, 1.3.0

| <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: http://uscilab.github.io/cereal/ URL: http://uscilab.github.io/cereal/<br /><br /><br /></div>

| align="center" | [http://www.cesm.ucar.edu/models/cesm1.2/ cesm]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm1.2/ URL: http://www.cesm.ucar.edu/models/cesm1.2/ Keyword:geo<br /><br /><br /></div>

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

| align="center" | 3.41, 3.42, 3.48, 3.49, 4.1.0

| <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: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// URL: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// Keyword:vis<br /><br /><br /></div>

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

| <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. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience. Homepage: http://circos.ca/documentation/ URL: http://circos.ca/documentation/ Extensions: Config::General-2.63, Font::TTF::Font-1.06, GD-2.71, IO-1.39, SVG-2.84, Text::Balanced-2.03 Keyword:vis<br /><br /><br /></div>

| align="center" | 3.8.1, 3.9.0, 9.0.1, 11.0.0, 13.0.1

| <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/3.8, python/3.9, python/3.10 Keyword:tools<br /><br /><br /></div>

| align="center" | 2.4.1.0, 2.4.1.2, 2.4.1.3, 2.4.4.0, 2.4.6.2

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing Homepage: https://github.com/abyzovlab/CNVnator URL: https://github.com/abyzovlab/CNVnator Keyword:bio<br /><br /><br /></div>

| align="center" | 0.4.0.7

| align="center" | 1.1

| align="center" | 1.5.0.3, 1.7.0.1

| align="center" | 1.0.20180622, 1.0.20200331

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: dcm2niix is a 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" | [http://www.allinea.com ddt-cpu]

| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1

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

| align="center" | [http://www.allinea.com ddt-gpu]

| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1

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

| align="center" | 0.7.8, 0.8.5, 1.1.6

| align="center" | 0.8.38, 0.9.8, 0.9.14, 0.9.22, 0.9.32, 0.9.36, 2.0.2, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7

| align="center" | 0.2.1, 0.2.2, 0.3.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /><br /></div>

| align="center" | 2.8.2, 2.15.0, 2.18.0, 2.19.0, 2.22.1, 2.25.0

| <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/3.8, python/3.9, python/3.10 Extensions: cfgrib-0.9.10.1, eccodes-1.4.1 Keyword:geo<br /><br /><br /></div>

| align="center" | [https://eigen.tuxfamily.org/index.php?title=Main_Page eigen]

| <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/index.php?title=Main_Page URL: https://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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/ URL: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio<br /><br /><br /></div>

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

| align="center" | 2017.11.001, 2018.11.001, 2020.05.001

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

| align="center" | 2.17.7, 3.11.0, 3.13.5

| align="center" | 7.1.0r, 8.0.1, 8.2.0, 8.4.0

| <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/3.8, python/3.9, python/3.10 Keyword:geo<br /><br /><br /></div>

| align="center" | [https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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 URL: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Keyword:bio<br /><br /><br /></div>

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

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

| align="center" | 1.6.2, 1.6.5, 1.7.1, 1.7.3

| <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/3.6.3, python/3.7.4, python/3.8.0<br /><br /><br /></div>

| align="center" | 0.11.5, 0.11.8, 0.11.9, 0.12.0

| <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, 3.2.0

| <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 Extensions: LAPACK-3.9.0<br /><br /><br /></div>

| align="center" | 2.5.2, 2.7.1, 2.9.0

| align="center" | [https://sourceforge.net/projects/freepascal/ fpc]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A 32/64/16-bit Pascal compiler for Win32/64/CE, Linux, Mac OS X/iOS, FreeBSD, OS/2, Game Boy Advance, Nintendo NDS and DOS; semantically compatible with Delphi, Borland Pascal and Mac Pascal (partially) with extra features, e.g. operator overloading. Homepage: https://sourceforge.net/projects/freepascal/ Keyword:tools<br /><br /><br /></div>

| align="center" | 1.0.3, 1.0.5

| align="center" | 6.0.1, 6.0.3, 6.0.4

| align="center" | [https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2clib]

| align="center" | 1.6.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ URL: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>

| align="center" | [https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2lib]

| align="center" | 1.4.0, 3.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ URL: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>

| align="center" | 20210930-R2P1, 2020.2, 20170420-R1, 20180920-R3, 20190630-R1, 20220930-R2, 20230630-R1

| 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 is built with Intel compilers and IntelMPI. It includes experimental MU CoupledCluster theory code. 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" | 3.7, 3.8, 4.0.0.0, 4.0.8.1, 4.0.12.0, 4.1.0.0, 4.1.2.0, 4.1.7.0, 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0

| align="center" | 4.8.5, 4.9.4, 5.4.0, 6.4.0, 7.3.0, 8.3.0, 8.4.0, 9.1.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0

| align="center" | 2.71

| <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-2.71<br /><br /><br /></div>

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

| align="center" | 2.1.3, 2.2.1, 2.4.1, 3.0.1, 3.0.4, 3.2.3, 3.4.1, 3.5.1

| <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: http://www.gdal.org/ URL: http://www.gdal.org/ Compatible modules: python/2.7.14 (default), python/3.5.4, python/3.6.3, python/3.7.4 Extensions: pygdal-3.0.1.5 Keyword:geo<br /><br /><br /></div>

| align="center" | 2.1, 2.3

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

| align="center" | 9.6.p04, 10.02.p03, 10.04.p02, 10.06, 10.7.3, 11.1.0

| <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: http://geant4.cern.ch/ URL: http://geant4.cern.ch/ Keyword:phys<br /><br /><br /></div>

| align="center" | 10.7.3, 11.1.0

| align="center" | 0.97, 0.98.3

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software. Homepage: https://github.com/genometools/genometools Keyword:bio<br /><br /><br /></div>

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

| align="center" | 3.6.1, 3.7.2, 3.7.3, 3.8.1, 3.9.1, 3.10.2

| <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: http://trac.osgeo.org/geos URL: http://trac.osgeo.org/geos Compatible modules: python/2.7.14 (default), python/3.5.4, python/3.6.3, python/3.7.4 Keyword:geo<br /><br /><br /></div>

| align="center" | 6.20180807, 8.20200810, 10.20221003

| align="center" | 2.11.0, 3.3.0

| align="center" | 2.1.0

| align="center" | 3.0.6, 4.0.7, 4.7.0, 4.10.5, 4.11.1

| align="center" | [http://gmt.soest.hawaii.edu/ gmt]

| align="center" | 5.4.2, 6.2.0

| <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: http://gmt.soest.hawaii.edu/ URL: http://gmt.soest.hawaii.edu/ Keyword:geo<br /><br /><br /></div>

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

| align="center" | 5.2.5, 5.2.8, 5.4.2, 5.4.6

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

| align="center" | 1.7.1

| align="center" | 1.8.0, 1.10.0, 1.13.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Welcome to Google Test, Google-s C++ test framework! Please see the project page for more information as well as the mailing list for questions, discussions, and development. There is also an IRC channel on OFTC. Getting started information for Google Test is available in the Google Test Primer documentation. Google Mock is an extension to Google Test for writing and using C++ mock classes. See the separate Google Mock documentation. More detailed documentation for googletest (including build instructions) are in its interior googletest/README.md file. Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace URL: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. Homepage: https://graph-tool.skewed.de/ URL: https://graph-tool.skewed.de/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>

| align="center" | [https://grass.osgeo.org/download/software/sources/ grass]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GRASS: Geographic Resources Analysis Support System, commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. Homepage: https://grass.osgeo.org/download/software/sources/ URL: https://grass.osgeo.org/download/software/sources/ Keyword:geo<br /><br /><br /></div>

| align="center" | 2018.3, 2018.6, 2018.7, 2019.1, 2019.3, 2019.6, 2020.2, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2

| 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. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>

| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div>

| align="center" | 4.2.12, 4.2.15

| align="center" | 1.8.18, 1.8.20, 1.8.21, 1.8.22, 1.10.1, 1.10.3, 1.10.5, 1.10.6, 1.10.7, 1.12.1, 1.12.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: cached-property-1.5.2, h5py-3.6.0, numexpr-2.8.4, tables-3.7.0 Keyword:io<br /><br /><br /></div>

| align="center" | 1.8.18, 1.10.3, 1.10.6, 1.10.7, 1.12.1, 1.12.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: cached-property-1.5.2, h5py-3.6.0, numexpr-2.8.4, tables-3.7.0 Keyword:io<br /><br /><br /></div>

| align="center" | 3.81

| align="center" | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml URL: https://ccb.jhu.edu/software/hisat2/index.shtml Keyword:bio<br /><br /><br /></div>

| align="center" | 3.1b2, 3.2.1, 3.3.2

| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.14, 1.15.1, 1.16, 1.17

| align="center" | 2.4.0, 2.7.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HyPhy: Hypothesis testing using Phylogenies. HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. Homepage: https://veg.github.io/hyphy-site/ Keyword:bio<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ URL: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/<br /><br /><br /></div>

| align="center" | 0.7.1, 0.8.2, 0.9.10, 0.10.2

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: https://igraph.org URL: https://igraph.org Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Extensions: python-igraph-0.10.2 Keyword:math<br /><br /><br /></div>

| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl]

| align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ URL: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html URL: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div>

| align="center" | 1.1.2, 1.1.3, 1.1.4

| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel]

| align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ URL: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br /><br /><br /></div>

| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ intelmpi]

| align="center" | 2018.3.222, 2019.3.199, 2019.7.217, 2021.2.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI. Note: like Open MPI, this module's mpicc calls the toolchain compiler. mpiicc calls icc, and mpigcc calls gcc, and similar for C++ and Fortran. Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /><br /></div>

| align="center" | 3.12.13, 3.14.11

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains ipykernel 2023a and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.2, debugpy-1.6.6, decorator-5.1.1, executing-1.2.0, importlib_metadata-5.2.0, ipykernel-6.21.2, ipython-8.10.0, ipython_genutils-0.2.0, jedi-0.18.2, jupyter_client-8.0.3, jupyter_core-5.2.0, matplotlib_inline-0.1.6, nest_asyncio-1.5.6, packaging-23.0, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.5.2, prompt_toolkit-3.0.37, psutil-5.9.4, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.14.0, python-dateutil-2.8.2, pyzmq-25.0.0, six-1.16.0, stack_data-0.6.2, tornado-6.2, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.14.0<br /><br /><br /></div>

| align="center" | [http://ispc.github.io/ ispc]

| align="center" | 1.10.0, 1.13.0, 1.18.0

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. Homepage: http://ispc.github.io/ , https://github.com/ispc/ispc/ URL: http://ispc.github.io/ , https://github.com/ispc/ispc/<br /><br /><br /></div>

| align="center" | 4.13.1, 4.13.3, 5.0.1, 5.1.2, 5.2.1

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.10, python/3.9, python/3.8 Keyword:vis<br /><br /><br /></div>

| align="center" | 1.900.1, 2.0.16

| align="center" | [https://openjdk.java.net java]

| align="center" | 1.7.0_80, 1.8.0_121, 1.8.0_192, 11.0.16_8, 11.0.2, 13.0.1, 13.0.2, 14.0.2, 17.0.2

| Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: https://openjdk.java.net URL: https://openjdk.java.net Keyword:tools<br /><br /><br /></div>

| align="center" | 1.9.4

| align="center" | 1.0.2, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1

| align="center" | 1.6.2, 1.7.4

| align="center" | [http://msa.cgb.ki.se/ kalign]

| align="center" | 2.03

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A fast and accurate multiple sequence alignment algorithm. Homepage: http://msa.cgb.ki.se/ URL: http://msa.cgb.ki.se/<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ URL: http://genome.cse.ucsc.edu/ Keyword:bio<br /><br /><br /></div>

| align="center" | [https://lammps.sandia.gov/ lammps-omp]

| align="center" | 20190807, 20201029, 20210929, 20220623

| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Homepage: https://lammps.sandia.gov/ URL: https://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE URL: https://github.com/lanl/LATTE Keyword:chem<br /><br /><br /></div>

| align="center" | 1.5, 1.13, 1.17, 2.1

| align="center" | 3.20.6

| align="center" | 1.10.1, 1.11.0, 1.12.1, 1.15.1

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/ URL: https://libgd.github.io/ Keyword:vis<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ URL: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>

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

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: https://github.com/libharu/libharu/ URL: https://github.com/libharu/libharu/<br /><br /><br /></div>

| align="center" | [https://sourceforge.net/p/libint/ libint]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Homepage: https://sourceforge.net/p/libint/ URL: https://sourceforge.net/p/libint/ Keyword:chem<br /><br /><br /></div>

| align="center" | [https://launchpad.net/libpsml libpsml]

| align="center" | 1.1.8

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. Homepage: https://launchpad.net/libpsml URL: https://launchpad.net/libpsml<br /><br /><br /></div>

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>

| align="center" | [http://libspatialindex.github.io libspatialindex]

| align="center" | 1.8.5

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: http://libspatialindex.github.io URL: http://libspatialindex.github.io Keyword:phys<br /><br /><br /></div>

| align="center" | 4.3.0a, 5.0.1

| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc]

| align="center" | 2.2.2, 3.0.0, 3.0.1, 4.2.1, 4.2.3, 4.3.4, 5.0.0, 5.1.3, 5.2.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc URL: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem<br /><br /><br /></div>

| align="center" | 6.0.1, 7.0.0, 8.0.1, 9.0.1, 13.0.1, 14.0.3

| align="center" | 0.9.24

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ URL: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>

| align="center" | 1.9.7, 2.3

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv URL: https://github.com/arq5x/lumpy-sv Keyword:bio<br /><br /><br /></div>