Modules avx

Module	Type	Versions	Description
abaqus	phys	2021	Documentation: Abaqus Expand Description: Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. Homepage: http://www.simulia.com/products/abaqus_fea.html URL: http://www.simulia.com/products/abaqus_fea.html Keyword:phys
abyss	bio	2.2.5	Expand 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
actc	-	1.1	Expand Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc
admixture	bio	1.3.0	Expand Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture URL: http://software.genetics.ucla.edu/admixture Keyword:bio
advisor	tools	2020.3	Expand Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe URL: https://software.intel.com/intel-advisor-xe Keyword:tools
annovar	bio	20191024	Expand Description: ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Homepage: http://annovar.openbioinformatics.org/en/latest/ URL: http://annovar.openbioinformatics.org/en/latest/ Keyword:bio
anserini	-	0.9.4	Expand Description: An open-source information retreival toolkit built on Lucene that aims to bridge the gap between academic information retrieval and the practice of building real-world search applications. Usage: Binaries located in Anserini's target/appassembler/bin are on path. Anserini's folders bin, collections, docs, indexes, logs, runs, src, target, tools, as well as the files pom.xml and README.md are available at $EBROOTANSERINI. Eg. Indexing command for help: IndexCollection -h Homepage: https://github.com/castorini/anserini URL: https://github.com/castorini/anserini
ansys	phys	2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2	Documentation: Ansys Expand Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys
ansysedt	-	2021R2, 2023R2	Expand Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com
ant	tools	1.9.15, 1.10.8	Expand Description: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Homepage: https://ant.apache.org/ URL: https://ant.apache.org/ Keyword:tools
antlr	-	2.7.7	Expand Description: ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. Homepage: https://www.antlr2.org/ URL: https://www.antlr2.org/
apptainer	-	1.1.3, 1.1.5, 1.1.6, 1.1.8, 1.2.4	Expand Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org
aragorn	-	1.2.38	Expand 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/
arrow	tools	0.16.0, 10.0.1, 12.0.1, 13.0.0	Expand 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, python/3.9 Keyword:tools
ascp	tools	3.5.4	Expand Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ URL: http://downloads.asperasoft.com/ Keyword:tools
autodock_vina	chem	1.1.2	Expand Description: AutoDock Vina is an open-source program for doing molecular docking. Homepage: http://vina.scripps.edu/index.html URL: http://vina.scripps.edu/index.html Keyword:chem
bamtools	bio	2.5.1	Expand 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
bbmap	bio	38.86	Expand Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio
bcftools	bio	1.13	Expand 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
beagle	-	5.4	Expand Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html
bedtools	bio	2.30.0	Expand Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio
beef	chem	0.1.1	Expand Description: BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. Homepage: http://suncat.stanford.edu/facility/software/functional URL: http://suncat.stanford.edu/facility/software/functional Keyword:chem
bio-searchio-hmmer	-	1.7.3	Expand Description: Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org. Homepage: https://metacpan.org/pod/Bio::SearchIO::hmmer3 URL: https://metacpan.org/pod/Bio::SearchIO::hmmer3
bioawk	-	1.0	Expand 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
biobloomtools	-	2.3.3	Expand Description: BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes. This tool is intended to be a pipeline component to replace costly alignment steps. Homepage: https://github.com/bcgsc/biobloom URL: https://github.com/bcgsc/biobloom
bioperl	bio	1.7.7, 1.7.8	Expand 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: https://bioperl.org/ URL: https://bioperl.org/ Extensions: Bio::Procedural-1.7.4, BioPerl-1.7.8, XML::DOM::XPath-0.14, XML::Writer-0.900 Keyword:bio
blast	bio	2.2.26	Expand 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: http://blast.ncbi.nlm.nih.gov/ URL: http://blast.ncbi.nlm.nih.gov/ Keyword:bio
blast+	bio	2.12.0, 2.14.0	Documentation: BLAST Expand 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
blender	vis	3.6.0	Expand 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/ Keyword:vis
boost	tools	1.72.0, 1.80.0	Expand 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
boost-mpi	tools	1.72.0	Expand Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools
bowtie2	bio	2.4.1, 2.5.1	Expand 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
bustools	-	0.40.0	Expand Description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. Homepage: https://github.com/BUStools/bustools URL: https://github.com/BUStools/bustools
bwa	bio	0.7.17	Expand 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
cafe5	-	5.1.0	Expand Description: Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa. Homepage: https://github.com/hahnlab/CAFE5 URL: https://github.com/hahnlab/CAFE5
canu	bio	2.2	Expand Description: Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Homepage: https://github.com/marbl/canu URL: https://github.com/marbl/canu Keyword:bio
cap3	bio	20151002	Expand Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio
capnproto	-	0.7.0	Expand Description: Cap'n Proto is an insanely fast data interchange format and capability-based RPC system. Homepage: https://capnproto.org URL: https://capnproto.org
catch2	-	2.11.0	Expand Description: A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) Homepage: https://github.com/catchorg/Catch2 URL: https://github.com/catchorg/Catch2
ccsm	geo	4_0_a02	Expand 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
cd-hit	bio	4.8.1	Expand Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Homepage: http://weizhongli-lab.org/cd-hit/ URL: http://weizhongli-lab.org/cd-hit/ Keyword:bio
cdo	geo	1.9.8, 1.9.10	Expand 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
cellranger	bio	2.1.0	Expand 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
cereal	-	1.3.0	Expand 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/
cesm	geo	2.1.3	Expand 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/cesm2/ URL: http://www.cesm.ucar.edu/models/cesm2/ Keyword:geo
cfitsio	vis	3.48, 4.1.0	Expand 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/fitsio/ URL: https://heasarc.gsfc.nasa.gov/fitsio/ Keyword:vis
cgal	math	4.14.3, 5.5.2	Expand Description: The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. Homepage: https://www.cgal.org/ URL: https://www.cgal.org/ Keyword:math
cmake	tools	3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7	Expand Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. Homepage: https://www.cmake.org URL: https://www.cmake.org Keyword:tools
code-server	-	3.5.0, 3.12.0	Expand Description: Run VS Code on any machine anywhere and access it in the browser. Homepage: https://github.com/cdr/code-server URL: https://github.com/cdr/code-server
coinmp	-	1.8.4	Expand Description: CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects. Homepage: https://projects.coin-or.org/CoinMP URL: https://projects.coin-or.org/CoinMP
comsol	phys	5.6, 6.0.0.405, 6.1.0.357, 6.2	Expand Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys
corset	bio	1.09	Expand Description: Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. Homepage: https://github.com/Oshlack/Corset/wiki URL: https://github.com/Oshlack/Corset/wiki Keyword:bio
cppzmq	-	4.7.1	Expand Description: cppzmq is a C++ binding for libzmq Homepage: https://github.com/zeromq/cppzmq URL: https://github.com/zeromq/cppzmq
cromwell	tools	58	Expand Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/ URL: https://cromwell.readthedocs.io/ Keyword:tools
cst	phys	2020	Expand Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ URL: https://www.cst.com/ Keyword:phys
csvtk	-	0.23.0	Expand Description: Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts. Homepage: https://github.com/shenwei356/csvtk URL: https://github.com/shenwei356/csvtk
cuda	tools	10.2	Documentation: CUDA Expand Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit URL: https://developer.nvidia.com/cuda-toolkit Keyword:tools
cudnn	math	8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29	Expand Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn URL: https://developer.nvidia.com/cudnn Keyword:math
cufflinks	bio	2.2.1	Expand Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq Homepage: http://cole-trapnell-lab.github.io/cufflinks/ URL: http://cole-trapnell-lab.github.io/cufflinks/ Keyword:bio
cusparselt	-	0.4.0.7	Expand Description: NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix Homepage: https://docs.nvidia.com/cuda/cusparselt/index.html URL: https://docs.nvidia.com/cuda/cusparselt/index.html
custom-ctypes	-	1.1	Expand Description: This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names. Homepage: https://github.com/ComputeCanada/custom_ctypes/ URL: https://github.com/ComputeCanada/custom_ctypes/
cutensor	-	1.5.0.3, 1.7.0.1	Expand Description: cuTENSOR is a high-performance CUDA library for tensor primitives. Homepage: https://developer.nvidia.com/cutensor URL: https://developer.nvidia.com/cutensor
cvit	-	1.2.1	Expand Description: A genomic linkage feature visualization tools based on Perl. Homepage: https://sourceforge.net/projects/cvit/ URL: https://sourceforge.net/projects/cvit/ Extensions: Config::IniFiles-3.000002, Data::Dumper-2.173, ExtUtils::PkgConfig-1.16, GD-2.71, GD::Arrow-0.01, GD::SVG-0.33, GD::Text-0.86, SVG-2.84, Test::Fork-0.02
ddt-cpu	tools	20.2, 22.0.1	Documentation: ARM software Expand Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com URL: http://www.allinea.com
ddt-gpu	tools	20.2, 22.0.1	Documentation: ARM software Expand Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com URL: http://www.allinea.com
delly	-	0.8.5	Expand 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. Homepage: https://github.com/dellytools/delly URL: https://github.com/dellytools/delly
diamond	bio	2.1.6	Expand Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio
dl_monte	-	2.07	Expand Description: General-purpose Monte Carlo molecular simulation Homepage: https://gitlab.com/dl_monte URL: https://gitlab.com/dl_monte
dorado	-	0.2.1, 0.2.2, 0.3.0	Expand Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Homepage: https://github.com/nanoporetech/dorado URL: https://github.com/nanoporetech/dorado
dotnet-core	-	3.1.8, 5.0.12, 6.0.0	Expand 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. Contains the SDK and the Runtime. Homepage: https://www.microsoft.com/net/ URL: https://www.microsoft.com/net/
double-conversion	-	3.1.5	Expand Description: Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. Homepage: https://github.com/google/double-conversion URL: https://github.com/google/double-conversion
dssp	chem	3.1.4	Expand Description: The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. If you use DSSP, please quote these two articles: 1) A series of PDB related databases for everyday needs. Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Research 2015 January; 43(Database issue): D364-D368. 2) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824. Homepage: https://swift.cmbi.umcn.nl/gv/dssp/ URL: https://swift.cmbi.umcn.nl/gv/dssp/ Keyword:chem
eccodes	geo	2.15.0, 2.19.0, 2.21.0, 2.22.1	Expand 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 Keyword:geo
eigen	math	3.3.7	Expand 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
elpa	math	2020.05.001	Expand Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: https://elpa.rzg.mpg.de URL: https://elpa.rzg.mpg.de Keyword:math
emboss	bio	6.6.0	Expand Description: EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. Homepage: https://emboss.sourceforge.net/ URL: https://emboss.sourceforge.net/ Keyword:bio
energyplus	-	9.3.0, 23.2.0	Expand Description: EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings. Homepage: https://energyplus.net/downloads URL: https://energyplus.net/downloads
expat	tools	2.2.9, 2.2.10, 2.4.8	Expand 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: https://libexpat.github.io URL: https://libexpat.github.io Keyword:tools
falcon	bio	1.8.8	Expand Description: Falcon: a set of tools for fast aligning long reads for consensus and assembly Homepage: https://github.com/PacificBiosciences/FALCON URL: https://github.com/PacificBiosciences/FALCON Extensions: FALCON-1.8.8, networkx-1.10, pypeFLOW-20170504 Keyword:bio
fastahack	-	1.0.0	Expand Description: Utilities for indexing and sequence extraction from FASTA files. Homepage: https://github.com/ekg/fastahack URL: https://github.com/ekg/fastahack
fastani	-	1.32	Expand Description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Homepage: https://github.com/ParBLiSS/FastANI URL: https://github.com/ParBLiSS/FastANI
fastqc	bio	0.11.9, 0.12.0	Expand Description: FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio
fastsimcoal2	bio	2.6.0.3, 2.7.0.9	Expand Description: While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/ URL: http://cmpg.unibe.ch/software/fastsimcoal2/ Keyword:bio
fasttree	bio	2.1.11	Documentation: FastTree Expand Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Homepage: http://www.microbesonline.org/fasttree/ URL: http://www.microbesonline.org/fasttree/ Keyword:bio
fasttree-double	-	2.1.11	Documentation: FastTree Expand Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Homepage: http://www.microbesonline.org/fasttree/ URL: http://www.microbesonline.org/fasttree/
fermi-lite	-	20190320	Expand 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
fftw	math	3.3.8	Expand 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: http://www.fftw.org URL: http://www.fftw.org Keyword:math
fftw-mpi	math	3.3.8	Expand 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: http://www.fftw.org URL: http://www.fftw.org Keyword:math
filevercmp	-	20191210	Expand Description: filevercmp function as in sort --version-sort. Homepage: https://github.com/ekg/filevercmp URL: https://github.com/ekg/filevercmp
filtlong	bio	0.2.0	Expand 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
flexiblas	-	3.0.4	Expand 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
fmriprep	-	23.0.2, 23.1.3	Expand Description: fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI). Homepage: https://fmriprep.org/ URL: https://fmriprep.org/
fmt	-	5.3.0, 6.2.1, 7.0.3	Expand Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/
freebayes	bio	1.3.6	Expand 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
freesasa	-	2.1.0	Expand Description: FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA). Homepage: https://freesasa.github.io URL: https://freesasa.github.io
freesurfer	bio	5.3.0	Expand Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. Homepage: http://freesurfer.net/ URL: http://freesurfer.net/ Keyword:bio
freexl	tools	1.0.5	Expand Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. Homepage: https://www.gaia-gis.it/fossil/freexl/index URL: https://www.gaia-gis.it/fossil/freexl/index Keyword:tools
fsom	-	20141119	Expand 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
g2clib	geo	1.6.0	Expand 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
gamess-us	chem	20210930-R2P1, 2020.2	Documentation: GAMESS-US Expand 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. No LibXC or MSUCC modules. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem
gatk	bio	4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0	Expand Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio
gblocks	-	0.91b	Expand Description: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Homepage: http://molevol.cmima.csic.es/castresana/Gblocks.html URL: http://molevol.cmima.csic.es/castresana/Gblocks.html
gcc	tools	8.4.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0	Expand Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools
gcta	bio	1.93.2	Expand Description: GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following analyses. Homepage: http://cnsgenomics.com/software/gcta/ URL: http://cnsgenomics.com/software/gcta/ Keyword:bio
gdal	geo	3.0.4, 3.2.3, 3.5.1	Expand 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/3.8, python/3.9, python/3.10 Keyword:geo
gdrcopy	-	2.1	Expand Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy
geant4-data	-	10.7.3, 11.1.0	Expand Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/
genometools	bio	1.6.1	Expand Description: A comprehensive software library for efficient processing of structured genome annotations. Homepage: http://genometools.org URL: http://genometools.org Keyword:bio
gentoo	-	2020, 2023	Expand Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix
geos	geo	3.8.1, 3.9.1, 3.10.2	Expand 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
git-annex	tools	8.20200810, 10.20221003	Expand 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
git-lfs	-	2.11.0, 3.3.0	Expand 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
glew	-	2.1.0	Expand 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/
glm	vis	0.9.9.8	Expand Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm URL: https://github.com/g-truc/glm Keyword:vis
glost	tools	0.3.1	Expand Description: This is GLOST, the Greedy Launcher Of Small Tasks. Homepage: https://github.com/cea-hpc/glost URL: https://github.com/cea-hpc/glost Keyword:tools
gmt	geo	6.4.0	Expand 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
gnuplot	vis	5.2.8	Expand Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net/ URL: http://gnuplot.sourceforge.net/ Keyword:vis
go	tools	1.14.1, 1.18.3, 1.21.3	Expand Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: https://www.golang.org URL: https://www.golang.org Keyword:tools
googletest	tools	1.10.0	Expand 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
grace	vis	5.99.0	Expand 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
gromacs	chem	2020.4, 2021.4, 2022.3	Documentation: GROMACS Expand 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 CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem
gsl	math	2.6	Expand Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. Homepage: https://www.gnu.org/software/gsl/ URL: https://www.gnu.org/software/gsl/ Keyword:math
gsl-lite	-	0.40.0	Expand Description: A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later Homepage: https://github.com/gsl-lite/gsl-lite URL: https://github.com/gsl-lite/gsl-lite
gurobi	math	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	Expand Description: The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. Homepage: https://www.gurobi.com URL: https://www.gurobi.com Keyword:math
hapgen2	-	2.2.0	Expand Description: 'HAPGEN2' simulates case control datasets at SNP markers. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
haploview	-	4.2	Expand Description: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Homepage: https://www.broadinstitute.org/haploview/haploview URL: https://www.broadinstitute.org/haploview/haploview
hdf	io	4.2.15	Expand Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: https://www.hdfgroup.org/products/hdf4/ URL: https://www.hdfgroup.org/products/hdf4/ Keyword:io
hdf5	io	1.10.6, 1.10.7	Expand 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 Keyword:io
hdf5-mpi	io	1.10.6, 1.10.7	Expand 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 Keyword:io
hdfview	-	2.14	Expand Description: HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. Homepage: https://support.hdfgroup.org/products/java/hdfview/ URL: https://support.hdfgroup.org/products/java/hdfview/
hh-suite	bio	3.3.0	Expand Description: HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Homepage: https://github.com/soedinglab/hh-suite URL: https://github.com/soedinglab/hh-suite Keyword:bio
hisat2	bio	2.2.1	Expand 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://daehwankimlab.github.io/hisat2/ URL: https://daehwankimlab.github.io/hisat2/ Keyword:bio
hmmer	bio	3.3.2	Expand Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. Homepage: http://hmmer.org/ URL: http://hmmer.org/ Keyword:bio
hoomd-blue	-	3.6.0	Expand Description: HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface. Homepage: http://glotzerlab.engin.umich.edu/hoomd-blue/ URL: http://glotzerlab.engin.umich.edu/hoomd-blue/ Compatible modules: python/3.8, python/3.9, python/3.10
hoomd-blue-mpi	-	3.6.0	Expand Description: HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface. Homepage: http://glotzerlab.engin.umich.edu/hoomd-blue/ URL: http://glotzerlab.engin.umich.edu/hoomd-blue/ Compatible modules: python/3.8, python/3.9, python/3.10
htslib	bio	1.10.2, 1.13, 1.14	Expand Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio
hwloc	-	2.4.0, 2.7.1	Expand Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. Homepage: https://www.open-mpi.org/projects/hwloc/ URL: https://www.open-mpi.org/projects/hwloc/
igblast	bio	1.17.0, 1.18.0	Expand Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html URL: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio
igv	-	2.9.2	Expand Description: This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. Homepage: https://www.broadinstitute.org/software/igv/ URL: https://www.broadinstitute.org/software/igv/
imkl	math	2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0	Expand Description: Intel oneAPI Math Kernel Library Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html Keyword:math
impute2	bio	2.3.2	Expand 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
impute5	-	1.1.5	Expand Description: IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1 Homepage: https://jmarchini.org/software/#impute-5 URL: https://jmarchini.org/software/#impute-5
infernal	bio	1.1.3	Expand Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ URL: http://eddylab.org/infernal/ Keyword:bio
intel	tools	2020.1.217, 2021.2.0, 2022.1.0	Expand Description: Intel C, C++ and Fortran compilers (classic and oneAPI) Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html Keyword:tools
intel-opencl	-	2021.2.0	Expand Description: Intel's OpenCL CPU runtime Homepage: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html URL: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html
intelmpi	mpi	2019.7.217	Expand Description: Intel MPI Library, compatible with MPICH ABI Homepage: https://software.intel.com/en-us/intel-mpi-library/ URL: https://software.intel.com/en-us/intel-mpi-library/
intelxed	-	12.0.1	Expand Description: The X86 Encoder Decoder (XED), is a software library (and associated headers) for encoding and decoding X86 (IA32 and Intel64) instructions. Homepage: https://intelxed.github.io/ URL: https://intelxed.github.io/
interproscan	bio	5.55-88.0, 5.64-96.0, 5.52-86.0, 5.63-95.0, 5.50-84.0, 5.53-87.0, 5.56-89.0	Expand Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio
interproscan_data	-	5.64-96.0, 5.63-95.0	Expand Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/
intervaltree	-	0.1	Expand Description: An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. Homepage: https://github.com/ekg/intervaltree URL: https://github.com/ekg/intervaltree
ipp	tools	2020.1.217	Expand Description: Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. Homepage: https://software.intel.com/en-us/articles/intel-ipp/ URL: https://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools
ipykernel	-	2020a, 2020b, 2021a, 2022a, 2023a, 2023b	Expand Description: Bundle which contains ipykernel 2023b and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.4, debugpy-1.6.7.post1, decorator-5.1.1, executing-1.2.0, importlib_metadata-6.8.0, ipykernel-6.25.1, ipython-8.15.0, ipython_genutils-0.2.0, jedi-0.19.0, jupyter_client-8.3.1, jupyter_core-5.3.1, matplotlib_inline-0.1.6, nest_asyncio-1.5.7, packaging-23.1, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.6.2, prompt_toolkit-3.0.39, psutil-5.9.5, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.16.1, python-dateutil-2.8.2, pyzmq-25.1.1, six-1.16.0, stack_data-0.6.2, tornado-6.3.3, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.16.2
ipython-kernel	-	2.7, 3.9, 3.10, 3.11	Expand Description: IPython kernelspec for Python 3.11 Homepage: https://ipython.org/ URL: https://ipython.org/
iq-tree	bio	2.2.1	Expand Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio
ispc	-	1.10.0, 1.13.0, 1.18.0	Expand 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/
itac	tools	2021.5.0	Expand Description: The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. Homepage: https://software.intel.com/en-us/intel-trace-analyzer/ URL: https://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools
jasper	vis	2.0.16	Expand Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis
java	tools	11.0.16_8, 1.8.0_192, 11.0.2, 13.0.2, 14.0.2, 17.0.2	Documentation: Java Expand Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools
jellyfish	bio	2.3.0	Expand Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.genome.umd.edu/jellyfish.html URL: http://www.genome.umd.edu/jellyfish.html Keyword:bio
jsoncpp	-	1.9.4	Expand Description: JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Homepage: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html URL: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html
judy	-	1.0.5	Expand Description: A C library that implements a dynamic array. Homepage: http://judy.sourceforge.net/ URL: http://judy.sourceforge.net/
julia	tools	1.8.1	Expand Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org URL: http://julialang.org Keyword:tools
kentutils	bio	453	Expand 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
kim-api	chem	2.1.3	Expand Description: Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. Homepage: https://openkim.org/ URL: https://openkim.org/ Keyword:chem
kma	-	1.3.0, 1.3.25, 1.4.14	Expand Description: KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. Homepage: https://bitbucket.org/genomicepidemiology/kma URL: https://bitbucket.org/genomicepidemiology/kma
kraken2	bio	2.1.2	Expand Description: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Homepage: https://github.com/DerrickWood/kraken2/wiki URL: https://github.com/DerrickWood/kraken2/wiki Keyword:bio
lammps-omp	chem	20210929	Documentation: LAMMPS Expand 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
ldc	-	0.17.6	Expand Description: The LLVM-based D Compiler Homepage: https://wiki.dlang.org/LDC URL: https://wiki.dlang.org/LDC
libcdms	-	3.1.2	Expand Description: Climate Data Management System Library. Homepage: https://github.com/CDAT/libcdms/ URL: https://github.com/CDAT/libcdms/
libcerf	math	1.13	Expand Description: libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. Homepage: https://jugit.fz-juelich.de/mlz/libcerf URL: https://jugit.fz-juelich.de/mlz/libcerf Keyword:math
libdap	-	3.20.6	Expand Description: A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. Homepage: https://www.opendap.org/software/libdap URL: https://www.opendap.org/software/libdap
libdrs	-	3.1.2	Expand Description: PCMDI's old DRS format implementation Homepage: https://github.com/CDAT/libdrs/ URL: https://github.com/CDAT/libdrs/
libevent	-	2.1.12	Expand Description: The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. Homepage: https://libevent.org/ URL: https://libevent.org/
libfabric	-	1.10.1, 1.12.1	Expand Description: Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. Homepage: https://ofiwg.github.io/libfabric/ URL: https://ofiwg.github.io/libfabric/
libffi	-	3.3	Expand Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. Homepage: https://sourceware.org/libffi/ URL: https://sourceware.org/libffi/
libgd	vis	2.3.0	Expand 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
libgeotiff	-	1.5.1, 1.6.0	Expand Description: Library for reading and writing coordinate system information from/to GeoTIFF files Homepage: https://directory.fsf.org/wiki/Libgeotiff URL: https://directory.fsf.org/wiki/Libgeotiff
libgeotiff-proj901	-	1.7.1	Expand Description: Library for reading and writing coordinate system information from/to GeoTIFF files Homepage: https://directory.fsf.org/wiki/Libgeotiff URL: https://directory.fsf.org/wiki/Libgeotiff
libharu	-	2.3.0	Expand 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/
librttopo	-	1.1.0	Expand 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
librttopo-proj9	-	1.1.0	Expand 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
libspatialindex	phys	1.8.5	Expand Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: https://libspatialindex.github.io URL: https://libspatialindex.github.io Keyword:phys
libspatialite	phys	4.3.0a, 5.0.1	Expand Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home URL: https://www.gaia-gis.it/fossil/libspatialite/home Keyword:phys
libspatialite-proj901	-	5.0.1	Expand Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home URL: https://www.gaia-gis.it/fossil/libspatialite/home
libstatgen	-	20190330	Expand Description: Useful set of classes for creating statistical genetic programs. Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen URL: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
libxc	chem	4.3.4	Expand 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: https://www.tddft.org/programs/libxc URL: https://www.tddft.org/programs/libxc Keyword:chem
libxslt	-	1.1.34	Expand Description: Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). Homepage: http://xmlsoft.org/ URL: http://xmlsoft.org/
lldb	-	11.0.0	Expand Description: The debugger component of the LLVM project Homepage: https://lldb.llvm.org/ URL: https://lldb.llvm.org/
llvm	tools	8.0.1, 9.0.1, 14.0.3	Expand Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools
lmdb	-	0.9.24	Expand Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. Homepage: https://symas.com/lmdb URL: https://symas.com/lmdb
ls-opt	phys	7.0.0	Expand Description: LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. Homepage: http://www.lstc.com/products/ls-opt URL: http://www.lstc.com/products/ls-opt Keyword:phys
ls-prepost	-	4.8.11, 4.9.9	Expand Description: LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. Homepage: http://lstc.com/products/ls-prepost URL: http://lstc.com/products/ls-prepost
lsd2	-	2.3	Expand Description: Least-squares methods to estimate rates and dates from phylogenies Homepage: https://github.com/tothuhien/lsd2 URL: https://github.com/tothuhien/lsd2
mafft	bio	7.471	Expand Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences), etc. Homepage: https://mafft.cbrc.jp/alignment/software/source.html URL: https://mafft.cbrc.jp/alignment/software/source.html Keyword:bio
mariadb	tools	10.6.12	Expand Description: MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. Homepage: https://mariadb.org/ URL: https://mariadb.org/ Compatible modules: python/3.10, python/3.9, python/3.8 Extensions: DBD::mysql-4.050, Devel::CheckLib-1.16, IO::CaptureOutput-1.1104, mysql-connector-python-8.0.32, PyMySQL-1.0.2 Keyword:tools
mariadb-connector-c	-	3.1.7	Expand Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/ URL: https://downloads.mariadb.org/connector-c/
mash	-	2.3	Expand Description: Fast genome and metagenome distance estimation using MinHash Homepage: http://mash.readthedocs.org URL: http://mash.readthedocs.org
matio	io	1.5.19	Expand Description: matio is an C library for reading and writing Matlab MAT files. Homepage: https://sourceforge.net/projects/matio/ URL: https://sourceforge.net/projects/matio/ Keyword:io
matlab	tools	2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3	Documentation: MATLAB Expand Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools
maven	tools	3.6.3	Expand Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools
mcr	tools	R2020b, R2022b, R2021b	Documentation: MATLAB Expand Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools
meta-farm	-	1.0.2	Expand Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.computecanada.ca/wiki/META_package_for_serial_farming URL: https://docs.computecanada.ca/wiki/META_package_for_serial_farming
metabat	bio	2.12.1	Expand Description: MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data Homepage: https://bitbucket.org/berkeleylab/metabat URL: https://bitbucket.org/berkeleylab/metabat Keyword:bio
metageneannotator	-	20080819	Expand Description: MetaGeneAnnotator is a gene-finding program for prokaryote and phage. Homepage: http://metagene.nig.ac.jp/ URL: http://metagene.nig.ac.jp/
metis	math	5.1.0	Expand Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math
mii	-	1.1.1, 1.1.2	Expand Description: A smart search engine for module environments. Homepage: https://github.com/codeandkey/mii URL: https://github.com/codeandkey/mii
minced	-	0.4.2	Expand Description: Mining CRISPRs in Environmental Datasets Homepage: https://github.com/ctSkennerton/minced URL: https://github.com/ctSkennerton/minced
minimac3	bio	2.0.1	Expand Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage: http://genome.sph.umich.edu/wiki/Minimac3 URL: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio
minimap2	bio	2.17	Expand Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio
mixcr	bio	4.1.2	Expand Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html URL: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio
mpi4py	tools	3.0.3, 3.1.3	Expand Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools
multichoose	-	1.0.3	Expand Description: generate multiset combinations (n multichoose k). Homepage: https://github.com/ekg/multichoose URL: https://github.com/ekg/multichoose
mummer	bio	4.0.0beta2	Expand Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ URL: http://mummer.sourceforge.net/ Keyword:bio
nanoflann	-	1.3.2	Expand Description: nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies Homepage: https://github.com/jlblancoc/nanoflann URL: https://github.com/jlblancoc/nanoflann
nccl	tools	2.7.8, 2.8.4, 2.11.4	Expand Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools
nco	io	5.0.6	Expand Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: https://nco.sourceforge.net URL: https://nco.sourceforge.net Keyword:io
netcdf	io	4.7.4, 4.8.0	Expand Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-fortran	io	4.5.2, 4.5.3	Expand Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-fortran-mpi	io	4.5.2, 4.5.3	Expand Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
netcdf-mpi	io	4.7.4, 4.8.0	Expand Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io
nextflow	-	20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3	Expand Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io URL: https://www.nextflow.io
nextstrain.cli	-	3.1.0	Expand Description: This is the source code repository for a program called nextstrain, the Nextstrain command-line interface (CLI). It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch. Homepage: https://github.com/nextstrain/cli/tree/3.1.0 URL: https://github.com/nextstrain/cli/tree/3.1.0
ngmlr	-	0.2.7	Expand Description: Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a reference genome with a focus on reads that span structural variations. Homepage: https://github.com/philres/ngmlr URL: https://github.com/philres/ngmlr
ngs	-	2.10.5	Expand Description: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. Homepage: https://github.com/ncbi/ngs URL: https://github.com/ncbi/ngs
ninja-phylogenetics	-	0.97-cluster_only	Expand Description: Nearly Infinite Neighbor Joining Application Compute correct neighbor-joining phylogenies for inputs of more than 10,000 sequences. This is a C++/SSE port of the original Java code described in: Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin. (LNCS webpage,preprint) The Java version of NINJA was the fastest available tool computing neighbor-joining phylogenies ( 10x faster than the fastest implemenation of the canonical neighbor-joining algorithm - QuickTree ) at the time of it's release. In addition to generating phylogenies, Ninja can be used to output pairwise distances using several common sequence distance measures, and cluster sequences using a nearest-neighbor approach. Homepage: https://github.com/TravisWheelerLab/NINJA URL: https://github.com/TravisWheelerLab/NINJA
nodejs	tools	16.14.0	Expand Description: Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: http://nodejs.org URL: http://nodejs.org Keyword:tools
nspr	-	4.25, 4.29	Expand Description: Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR
nss	-	3.51, 3.57	Expand Description: Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS
ntl	math	11.4.3	Expand Description: NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. Homepage: http://www.shoup.net/ntl/ URL: http://www.shoup.net/ntl/ Keyword:math
nvhpc	tools	20.7, 22.1, 22.7, 23.7	Expand Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/
opa-psm2	-	11.2.185	Expand Description: Low-level user-space communications interface for the Intel(R) OPA family of products. Homepage: https://github.com/cornelisnetworks/opa-psm2/ URL: https://github.com/cornelisnetworks/opa-psm2/
openblas	math	0.3.9	Expand Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: https://xianyi.github.com/OpenBLAS/ URL: https://xianyi.github.com/OpenBLAS/ Keyword:math
openmm-alphafold	-	7.5.1	Expand Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.7, python/3.8
openmpi	mpi	4.0.3, 4.1.1	Expand Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi
openrefine	-	3.4.1	Expand Description: OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. Homepage: https://github.com/OpenRefine/OpenRefine URL: https://github.com/OpenRefine/OpenRefine
optix	-	6.5.0, 7.7.0	Expand Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU's massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix
orca	chem	4.2.1, 5.0.1, 5.0.2	Documentation: ORCA Expand Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ URL: http://cec.mpg.de/forum/ Keyword:chem
orthomcl	bio	2.0.9	Expand Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ URL: http://orthomcl.org/ Keyword:bio
ovito	-	3.3.3	Expand Description: OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes. The program is freely available for all major platforms under an open source license. It has served in a growing number of computational simulation studies as a powerful tool to analyze, understand and illustrate simulation results. Homepage: https://www.ovito.org URL: https://www.ovito.org
p4est	math	2.2	Expand Description: The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scales to hundreds of thousands of processor cores. It is free software released under GNU General Public Licence version 2, or (at your option) any later version. Homepage: http://www.p4est.org/ URL: http://www.p4est.org/ Keyword:math
packmol	chem	20.3.3	Expand Description: Packing Optimization for Molecular Dynamics Simulations Homepage: http://m3g.iqm.unicamp.br/packmol URL: http://m3g.iqm.unicamp.br/packmol Keyword:chem
paml	bio	4.9j	Expand Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio
panther	-	14.1	Expand Description: Panther is the database part of InterProScan software. It contains only data. Homepage: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/ URL: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/
parasail	-	2.5	Expand Description: parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. Homepage: https://github.com/jeffdaily/parasail URL: https://github.com/jeffdaily/parasail Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: parasail-1.2.4
pcre2	-	10.34, 10.35	Expand Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/
pear	bio	0.9.11	Expand Description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. Homepage: https://cme.h-its.org/exelixis/web/software/pear/ URL: https://cme.h-its.org/exelixis/web/software/pear/ Keyword:bio
perl	tools	5.30.2	Documentation: Perl Expand Description: Larry Wall's Practical Extraction and Report Language Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.111, Algorithm::Diff-1.1903, aliased-0.34, AnyEvent-7.17, App::Cmd-0.331, App::cpanminus-1.7044, AppConfig-1.71, Archive::Extract-0.86, Array::Utils-0.5, Authen::SASL-2.16, AutoLoader-5.74, B::Hooks::EndOfScope-0.24, B::Lint-1.20, boolean-0.46, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, Class::Accessor-0.51, Class::Data::Inheritable-0.08, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Singleton-1.5, Class::Trigger-0.14, Clone-0.43, Clone::Choose-0.010, Config::General-2.63, Config::INI-0.025, Config::MVP-2.200011, Config::Tiny-2.24, constant-1.33, CPANPLUS-0.9906, Crypt::DES-2.07, Crypt::Rijndael-1.14, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.23, Data::Dumper-2.173, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.110, Data::Section-0.200007, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.224, Date::Handler-1.2, Date::Language-2.32, DateTime-1.52, DateTime::Locale-1.25, DateTime::TimeZone-2.38, DateTime::Tiny-1.07, DBD::SQLite-1.64, DBI-1.643, DBIx::Admin::TableInfo-3.03, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.14, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.005, Devel::StackTrace-2.04, Digest::HMAC-1.03, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.014, Email::Date::Format-1.005, Encode-3.04, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.44, Expect-1.35, Exporter-5.74, Exporter::Declare-0.114, Exporter::Tiny-1.002001, ExtUtils::CBuilder-0.280234, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.21, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.44, ExtUtils::ParseXS-3.35, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.15, File::Grep-0.02, File::HomeDir-1.004, File::Listing-6.04, File::Next-1.18, File::Path-2.16, File::pushd-1.016, File::Remove-1.58, File::ShareDir-1.116, File::ShareDir::Install-0.13, File::Slurp-9999.30, File::Slurp::Tiny-0.004, File::Slurper-0.012, File::Spec-3.75, File::Temp-0.2309, File::Which-1.23, Font::TTF-1.06, Getopt::Long-2.51, Getopt::Long::Descriptive-0.105, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9704, Graph::ReadWrite-2.09, Hash::Merge-0.300, HTML::Entities::Interpolate-1.10, HTML::Form-6.07, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.07, HTTP::Cookies-6.08, HTTP::Daemon-6.06, HTTP::Date-6.05, HTTP::Negotiate-6.01, HTTP::Request-6.22, HTTP::Tiny-0.076, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, IO::File-1.42, IO::Handle-1.42, IO::HTML-1.001, IO::Seekable-1.42, IO::Select-1.42, IO::Socket-1.42, IO::Socket::SSL-2.067, IO::String-1.08, IO::Stringy-2.113, IO::Tty-1.14, IPC::Cmd-1.04, IPC::Run-20180523.0, IPC::Run3-0.048, JSON-4.02, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.16, List::MoreUtils-0.428, List::SomeUtils-0.58, List::Util-1.54, List::UtilsBy-0.11, Locale::Maketext::Simple-0.21, Log::Dispatch-2.69, Log::Dispatchouli-2.019, Log::Handler-0.88, Log::Log4perl-1.49, Log::Message-0.08, Log::Message::Simple-0.10, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.07, LWP::Simple-6.43, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::VecStat-0.08, MCE::Mutex-1.866, Meta::Builder-0.004, MIME::Base64-3.15, MIME::Lite-3.031, MIME::Types-2.17, Mixin::Linewise::Readers-0.108, Mock::Quick-1.111, Module::Build-0.4231, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.19, Module::CoreList-5.20200314, Module::Implementation-0.09, Module::Install-1.19, Module::Load-0.34, Module::Load::Conditional-0.70, Module::Metadata-1.000037, Module::Pluggable-5.2, Module::Runtime-0.016, Moo-2.003006, Moose-2.2012, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.005, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.200002, MooseX::Types-0.50, MooseX::Types::Perl-0.101343, Mouse-v2.5.9, Mozilla::CA-20180117, MRO::Compat-0.13, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.11, Net::HTTP-6.19, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.88, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.17, Package::Stash-0.38, Package::Stash::XS-0.29, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.07, Params::Validate-1.29, Params::ValidationCompiler-0.30, parent-0.238, Parse::RecDescent-1.967015, Path::Tiny-0.112, PDF::API2-2.037, Perl::OSType-1.010, PerlIO::utf8_strict-0.007, Pod::Elemental-0.103005, Pod::Escapes-1.07, Pod::Eventual-0.094001, Pod::LaTeX-0.61, Pod::Man-4.14, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.40, Pod::Weaver-4.015, Readonly-2.05, Regexp::Common-2017060201, Role::HasMessage-0.006, Role::Identifiable::HasIdent-0.007, Role::Tiny-2.001004, Scalar::List::Utils-1.54, Scalar::Util-1.54, Scalar::Util::Numeric-0.40, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, Socket-2.029, Software::License-0.103014, Specio-0.46, SQL::Abstract-1.86, SQL::Statement-1.412, Statistics::Basic-1.6611, Statistics::Descriptive-3.0702, Storable-3.15, strictures-2.000006, String::Flogger-1.101245, String::RewritePrefix-0.008, String::Truncate-1.100602, Sub::Exporter-0.987, Sub::Exporter::ForMethods-0.100052, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Install-0.928, Sub::Name-0.26, Sub::Quote-2.006006, Sub::Uplevel-0.2800, Sub::Uplevel-0.2800, SVG-2.84, Switch-2.17, Template-3.007, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.36, Term::UI-0.46, Test-1.26, Test::ClassAPI-1.07, Test::Deep-1.130, Test::Differences-0.67, Test::Exception-0.43, Test::Fatal-0.014, Test::Harness-3.42, Test::LeakTrace-0.16, Test::More-1.302172, Test::Most-0.35, Test::NoWarnings-1.04, Test::Output-1.031, Test::Pod-1.52, Test::Requires-0.10, Test::RequiresInternet-0.05, Test::Simple-1.302172, Test::Version-2.09, Test::Warn-0.36, Test::Warnings-0.029, Text::Aligner-0.13, Text::Balanced-2.03, Text::CSV-2.00, Text::Diff-1.45, Text::Format-0.61, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.30, Text::Soundex-3.05, Text::Table-1.133, Text::Template-1.58, Thread::Queue-3.13, Throwable-0.200013, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9760, Time::Local-1.30, Time::Piece-1.34, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.31, Try::Tiny-0.30, UNIVERSAL::moniker-0.08, URI-1.76, URI::Escape-3.31, version-0.9924, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::XPath-1.44, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.73 Keyword:tools
petsc	tools	3.14.1	Expand Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: petsc4py-3.14.0 Keyword:tools
picard	bio	2.23.3, 2.26.3	Expand Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio
pilon	bio	1.23, 1.24	Expand Description: Pilon is an automated genome assembly improvement and variant detection tool Homepage: https://github.com/broadinstitute/pilon URL: https://github.com/broadinstitute/pilon Keyword:bio
plink	bio	1.9b_6.21-x86_64, 2.00-10252019-avx2	Expand Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio
pmix	-	3.1.5, 3.2.3	Expand Description: Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. Homepage: https://pmix.org/ URL: https://pmix.org/
podman	-	4.1.1, 4.5.0	Expand Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io
postgresql	tools	12.4, 14.2	Expand Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: psycopg2-2.9.3 Keyword:tools
pplacer	bio	1.1.alpha19	Expand Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. Homepage: http://matsen.fhcrc.org/pplacer/ URL: http://matsen.fhcrc.org/pplacer/ Keyword:bio
prodigal	bio	2.6.3	Expand Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Homepage: https://github.com/hyattpd/Prodigal/ URL: https://github.com/hyattpd/Prodigal/ Keyword:bio
proj	geo	7.0.0, 7.2.1, 8.0.0, 9.0.1	Expand Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org URL: https://proj.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: pyproj-3.3.0 Keyword:geo
prokka	-	1.14.5	Expand Description: Prokka is a software tool for the rapid annotation of prokaryotic genomes. Homepage: https://www.vicbioinformatics.com/software.prokka.shtml URL: https://www.vicbioinformatics.com/software.prokka.shtml
protobuf	tools	3.12.3, 3.19.4, 3.21.3	Expand Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Keyword:tools
pypy	tools	5.8.0, 7.3.3	Expand Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html URL: https://pypy.org/index.html Keyword:tools
pytest	-	6.1.2, 6.2.5, 7.0.1, 7.4.0	Expand Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: iniconfig-2.0.0, packaging-23.1, pluggy-1.2.0, py-1.11.0, pytest-7.4.0, tomli-2.0.1
python	tools	2.7.18, 3.6.10, 3.7.7, 3.7.9, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.11.2, 3.11.5	Documentation: Python Expand Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: https://python.org/ URL: https://python.org/ Extensions: distlib-0.3.7, editables-0.5, filelock-3.12.2, flit_core-3.9.0, hatch_vcs-0.3.0, hatchling-1.18.0, packaging-23.1, pathspec-0.11.2, pip-23.2.1, platformdirs-3.10.0, pluggy-1.3.0, pyparsing-3.1.1, setuptools-68.1.2, setuptools_scm-7.1.0, six-1.16.0, tomli-2.0.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, virtualenv-20.24.3, wheel-0.41.2 Keyword:tools
python-build-bundle	-	2022a, 2023a, 2023b	Expand Description: Bundle which contains Python packages useful for building Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.11, python/3.10, python/3.9, python/3.8 Extensions: archspec-0.2.1, cachecontrol-0.13.1, cachy-0.3.0, certifi-2023.7.22, cffi-1.15.1, charset-normalizer-3.2.0, cleo-2.0.1, clikit-0.6.2, crashtest-0.4.1, cryptography-41.0.3, distlib-0.3.7, distro-1.8.0, editables-0.5, exceptiongroup-1.1.3, filelock-3.12.2, flit-core-3.9.0, flit-scm-1.7.0, hatch_fancy_pypi_readme-23.1.0, hatch_vcs-0.3.0, hatchling-1.18.0, html5lib-1.1, idna-3.4, importlib_metadata-6.8.0, importlib_resources-6.0.1, jeepney-0.8.0, keyring-24.2.0, keyrings.alt-5.0.0, meson-1.2.1, meson_python-0.14.0, msgpack-1.0.5, ninja-1.11.1, packaging-23.1, pastel-0.2.1, pathspec-0.11.2, pbr-5.11.1, pexpect-4.8.0, pkginfo-1.9.6, platformdirs-3.10.0, poetry-1.6.1, poetry_core-1.7.0, ptyprocess-0.7.0, pybind11-2.11.1, pycparser-2.21, pylev-1.4.0, pyparsing-3.1.1, pyproject-metadata-0.7.1, pytoml-0.1.21, requests-2.31.0, requests-toolbelt-1.0.0, scikit_build-0.17.6, scikit_build_core-0.5.0, SecretStorage-3.3.3, semantic_version-2.10.0, setuptools-68.1.2, setuptools-rust-1.7.0, setuptools_scm-7.1.0, shellingham-1.5.3, toml-0.10.2, tomli-2.0.1, tomlkit-0.12.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, urllib3-2.0.4, virtualenv-20.24.3, webencodings-0.5.1, wheel-0.41.2, zipp-3.16.2
qca	geo	2.3.0	Expand Description: Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. Homepage: http://delta.affinix.com/qca/ URL: http://delta.affinix.com/qca/ Keyword:geo
qgis	geo	3.16.10	Expand Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/ URL: http://www.qgis.org/ Compatible modules: python/3.7, python/3.8, python/3.9 Extensions: OWSLib-0.24.1, psycopg2-2.9.1, PyYAML-5.4.1 Keyword:geo
qiime2	-	2021.11, 2023.5	Expand Description: QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Homepage: http://qiime2.org/ URL: http://qiime2.org/
qjson	tools	0.9.0	Expand Description: QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa. Homepage: http://qjson.sourceforge.net/ URL: http://qjson.sourceforge.net/ Keyword:tools
qscintilla	tools	2.11.2	Expand Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla URL: https://www.riverbankcomputing.com/software/qscintilla Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8, python/3.9 Keyword:tools
qt	tools	5.12.8	Expand Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8, python/3.9 Extensions: enum34-1.1.10, PyQt5-5.12.3, PyQtWebEngine-5.12.1, sip-4.19.18 Keyword:tools
qt5webkit	-	5.212.0-alpha4	Expand Description: Qt Port of WebKit. WebKit is an open source web browser engine. Homepage: https://github.com/qt/qtwebkit URL: https://github.com/qt/qtwebkit
qtkeychain	-	0.9.1	Expand Description: Platform-independent Qt API for storing passwords securely. Homepage: https://github.com/frankosterfeld/qtkeychain URL: https://github.com/frankosterfeld/qtkeychain
quantumatk	-	2019.12	Expand Description: QuantumATK is a complete atomistic simulation toolkit. QuantumATK addresses key applications in the semiconductor industry and is a core component of the Synopsys Design-Technology Co-Optimization (DTCO) solution. Atomic-scale modeling tools in QuantumATK range from classical force fields for handling large and to some extent more realistic materials systems to ab initio tools that provide highly accurate results for smaller systems. Homepage: https://www.synopsys.com/silicon/quantumatk.html URL: https://www.synopsys.com/silicon/quantumatk.html
quantumespresso	chem	6.6	Documentation: Quantum ESPRESSO Expand Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: https://www.quantum-espresso.org URL: https://www.quantum-espresso.org Keyword:chem
qwt	tools	6.1.4	Expand Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: https://qwt.sourceforge.net/ URL: https://qwt.sourceforge.net/ Keyword:tools
qwtpolar	tools	1.1.1	Expand Description: The QwtPolar library contains classes for displaying values on a polar coordinate system. Homepage: http://qwtpolar.sourceforge.net/ URL: http://qwtpolar.sourceforge.net/ Keyword:tools
r	tools	4.0.2, 4.1.2, 4.2.1	Documentation: R Expand Description: R is a free software environment for statistical computing and graphics. Homepage: https://www.r-project.org/ URL: https://www.r-project.org/ Keyword:tools
racon	bio	1.4.13	Expand Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/lbcb-sci/racon URL: https://github.com/lbcb-sci/racon Keyword:bio
rapidjson	-	1.1.0	Expand Description: A fast JSON parser/generator for C++ with both SAX/DOM style API Homepage: https://rapidjson.org URL: https://rapidjson.org
re2c	-	1.3	Expand Description: re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. Homepage: https://re2c.org/ URL: https://re2c.org/
reframe	-	3.12.0	Expand Description: ReFrame is a framework for writing regression tests for HPC systems. Homepage: https://github.com/eth-cscs/reframe URL: https://github.com/eth-cscs/reframe Compatible modules: python/3.8.10, python/3.9.6, python/3.10.2 Extensions: attrs-21.4.0, certifi-2021.10.8, chardet-4.0.0, idna-3.3, importlib_resources-5.7.1, jsonschema-4.4.0, pyrsistent-0.18.1, reframe-3.12.0, requests-2.27.1, semver-2.13.0, urllib3-1.26.9, zipp-3.8.0
rmats	-	4.1.1, 4.1.2	Expand Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. Homepage: http://rnaseq-mats.sourceforge.net/ URL: http://rnaseq-mats.sourceforge.net/
ruby	tools	2.7.1	Expand Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Homepage: https://www.ruby-lang.org URL: https://www.ruby-lang.org Extensions: activesupport-5.2.4.2, addressable-2.7.0, arr-pm-0.0.10, backports-3.17.0, bundler-2.1.4, cabin-0.9.0, childprocess-3.0.0, clamp-1.3.1, concurrent-ruby-1.1.6, connection_pool-2.2.2, diff-lcs-1.3, ethon-0.12.0, faraday-0.17.3, faraday_middleware-0.14.0, ffi-1.12.2, gh-0.16.0, highline-2.0.3, i18n-1.8.2, json-2.2.0, launchy-2.5.0, minitest-5.14.0, multi_json-1.14.1, multipart-post-1.2.0, mustermann-1.1.1, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-4.0.3, pusher-client-0.6.2, rack-2.2.2, rack-protection-2.0.8.1, rack-test-1.1.0, rspec-3.9.0, rspec-core-3.9.1, rspec-expectations-3.9.1, rspec-mocks-3.9.1, rspec-support-3.9.2, ruby2_keywords-0.0.2, sinatra-2.0.8.1, thread_safe-0.3.6, tilt-2.0.10, typhoeus-1.3.1, tzinfo-1.2.7, websocket-1.2.8 Keyword:tools
rust	tools	1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0	Expand Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools
salmonbeta	bio	0.6.0	Expand Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Homepage: https://github.com/COMBINE-lab/salmon/ URL: https://github.com/COMBINE-lab/salmon/ Keyword:bio
sambamba	bio	0.8.0	Expand Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Homepage: https://lomereiter.github.io/sambamba/ URL: https://lomereiter.github.io/sambamba/ Keyword:bio
samtools	bio	0.1.20, 1.10, 1.11, 1.13, 1.17	Expand Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio
sbt	tools	1.3.13	Expand Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ URL: http://www.scala-sbt.org/ Keyword:tools
scalapack	math	2.1.0	Expand Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: https://www.netlib.org/scalapack/ URL: https://www.netlib.org/scalapack/ Keyword:math
scipy-stack	math	2020a, 2020b, 2021a, 2022a, 2023a, 2023b	Documentation: Python Expand Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: anyio-3.7.1, arff-0.9, argon2_cffi-23.1.0, argon2_cffi_bindings-21.2.0, async_generator-1.10, attrs-23.1.0, backports-abc-0.5, backports.shutil_get_terminal_size-1.0.0, bcrypt-4.0.1, beautifulsoup4-4.12.2, bitarray-2.8.1, bitstring-4.1.1, bleach-6.0.0, certifi-2023.7.22, cffi-1.15.1, chardet-5.2.0, charset_normalizer-3.2.0, contourpy-1.1.0, cryptography-39.0.1, cycler-0.11.0, Cython-0.29.36, deap-1.4.1, defusedxml-0.7.1, dnspython-2.4.2, ecdsa-0.18.0, entrypoints-0.4, fastjsonschema-2.18.0, fonttools-4.42.1, funcsigs-1.0.2, idna-3.4, importlib_resources-6.0.1, Jinja2-3.1.2, jsonschema-4.19.0, jsonschema_specifications-2023.7.1, kiwisolver-1.4.5, lockfile-0.12.2, MarkupSafe-2.1.3, matplotlib-3.7.2, mistune-3.0.1, mock-5.1.0, mpmath-1.3.0, netaddr-0.8.0, netifaces-0.11.0, nose-1.3.7, numpy-1.25.2, pandas-2.1.0, pandocfilters-1.5.0, paramiko-3.3.1, path-16.7.1, path.py-12.5.0, pathlib2-2.3.7.post1, paycheck-1.0.2, pbr-5.11.1, Pillow-10.0.0, pkgutil_resolve_name-1.3.10, prometheus_client-0.17.1, pycparser-2.21, PyNaCl-1.5.0, pyparsing-3.0.9, pyrsistent-0.19.3, python_json_logger-2.0.7, pytz-2023.3, PyYAML-6.0.1, referencing-0.30.2, requests-2.31.0, rfc3339_validator-0.1.4, rfc3986_validator-0.1.1, rpds_py-0.10.0, scipy-1.11.2, Send2Trash-1.8.2, simplegeneric-0.8.1, singledispatch-4.1.0, sniffio-1.3.0, soupsieve-2.4.1, sympy-1.12, terminado-0.17.1, testpath-0.6.0, tinycss2-1.2.1, typing_extensions-4.7.1, tzdata-2023.3, urllib3-2.0.4, webencodings-0.5.1, websocket_client-1.6.2 Keyword:math
sdsl	-	2.1.1-20191211	Expand Description: The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. Homepage: https://github.com/simongog/sdsl-lite URL: https://github.com/simongog/sdsl-lite
seqan-library	-	2.4.0	Expand Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ URL: https://www.seqan.de/
seqkit	-	0.13.2, 0.15.0, 2.3.1	Expand Description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. Homepage: https://bioinf.shenwei.me/seqkit/ URL: https://bioinf.shenwei.me/seqkit/
seqlib	-	1.2.0	Expand Description: C++ interface to HTSlib, BWA-MEM and Fermi. Homepage: https://github.com/walaj/SeqLib URL: https://github.com/walaj/SeqLib
seqtk	bio	1.3	Expand Description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Homepage: https://github.com/lh3/seqtk/ URL: https://github.com/lh3/seqtk/ Keyword:bio
shapeit	-	2.r904	Expand Description: SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
shrinkwrap	-	1.2.0	Expand Description: A std::streambuf wrapper for compression formats. Homepage: https://github.com/jonathonl/shrinkwrap URL: https://github.com/jonathonl/shrinkwrap
signalp	bio	4.1f	Expand Description: SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Keyword:bio
singular	-	4.2.1	Expand Description: Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. Homepage: https://www.singular.uni-kl.de/ URL: https://www.singular.uni-kl.de/
slepc	-	3.14.2	Expand Description: SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: slepc4py-3.14.0
slicer	-	4.11.20210226	Expand Description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Homepage: https://www.slicer.org/ URL: https://www.slicer.org/
smithwaterman	-	20160702	Expand Description: smith-waterman-gotoh alignment algorithm. Homepage: https://github.com/ekg/smithwaterman URL: https://github.com/ekg/smithwaterman
sniffles	-	1.0.12b	Expand Description: Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter), Minimap2 (sam file with Cigar and MD string) or NGMLR. Homepage: https://github.com/fritzsedlazeck/Sniffles URL: https://github.com/fritzsedlazeck/Sniffles
snpeff	bio	5.0	Expand Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: https://pcingola.github.io/SnpEff/ URL: https://pcingola.github.io/SnpEff/ Keyword:bio
soci	-	4.0.2	Expand Description: SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. Homepage: http://soci.sourceforge.net/ URL: http://soci.sourceforge.net/
spark	tools	3.0.0, 3.3.0	Documentation: Apache Spark Expand Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools
sparsehash	-	2.0.4	Expand Description: An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. Homepage: https://github.com/sparsehash/sparsehash URL: https://github.com/sparsehash/sparsehash
spectra	-	0.9.0	Expand Description: SpectrA stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. SpectrA is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence SpectrA can be easily embedded in C++ projects that require calculating eigenvalues of large matrices. Homepage: https://spectralib.org/index.html URL: https://spectralib.org/index.html
spoa	-	3.4.0	Expand Description: Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences Homepage: https://github.com/rvaser/spoa URL: https://github.com/rvaser/spoa
sqlite	-	3.38.5, 3.43.1	Expand Description: SQLite: SQL Database Engine in a C Library Homepage: https://www.sqlite.org/ URL: https://www.sqlite.org/
sra-toolkit	bio	2.10.8, 3.0.0	Expand Description: The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format Homepage: https://github.com/ncbi/sra-tools URL: https://github.com/ncbi/sra-tools Keyword:bio
ssw	-	1.1	Expand Description: SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library URL: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
starccm	phys	15.04.010-R8, 16.02.008-R8, 16.02.009-R8, 16.04.007-R8, 16.04.012-R8, 16.06.008-R8, 17.02.007-R8, 17.02.008-R8, 17.04.007-R8, 17.04.008-R8, 17.06.007-R8, 17.06.008-R8, 18.02.008-R8, 18.04.008-R8, 18.06.006-R8	Documentation: StarCCM Expand Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys
starccm-mixed	phys	15.04.010, 16.02.008, 16.02.009, 16.04.007, 16.04.012, 16.06.008, 17.02.007, 17.02.008, 17.04.007, 17.04.008, 17.06.007, 17.06.008, 18.02.008, 18.04.008, 18.06.006	Documentation: StarCCM Expand Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys
suitesparse	math	5.7.1	Expand Description: SuiteSparse is a collection of libraries manipulate sparse matrices. Homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html URL: https://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math
supernova	bio	2.1.1	Expand Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio
swi-prolog	-	9.0.3	Expand Description: SWI-Prolog offers a comprehensive free Prolog environment. Homepage: https://www.swi-prolog.org/ URL: https://www.swi-prolog.org/
swig	-	4.0.1	Expand Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/ URL: http://www.swig.org/
tabix	bio	0.2.6	Expand Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net URL: http://samtools.sourceforge.net Keyword:bio
tabixpp	-	1.1.0	Expand Description: C++ wrapper to tabix indexer Homepage: https://github.com/ekg/tabixpp URL: https://github.com/ekg/tabixpp
taxonkit	-	0.6.2	Expand Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/
tbb	tools	2020.2, 2021.8.0	Expand Description: Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. Homepage: https://github.com/oneapi-src/oneTBB URL: https://github.com/oneapi-src/oneTBB Keyword:tools
tbl2asn	-	25.8	Expand Description: Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank Homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ URL: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
tensorrt	-	8.6.1.6	Expand Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11
thrift	-	0.13.0, 0.16.0, 0.18.1	Expand Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11
tmhmm	bio	2.0c	Expand Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio
transdecoder	bio	5.5.0	Expand Description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Homepage: https://transdecoder.github.io/ URL: https://transdecoder.github.io/ Keyword:bio
transrate	bio	1.0.3	Expand Description: Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Homepage: http://hibberdlab.com/transrate/ URL: http://hibberdlab.com/transrate/ Keyword:bio
trilinos	tools	13.4.1	Expand Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: https://trilinos.org URL: https://trilinos.org Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:tools
trimmomatic	bio	0.39	Expand Description: Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. Homepage: http://www.usadellab.org/cms/?page=trimmomatic URL: http://www.usadellab.org/cms/?page=trimmomatic Keyword:bio
ucx	-	1.8.0, 1.9.0	Expand Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: http://www.openucx.org/ URL: http://www.openucx.org/
udunits	tools	2.2.26, 2.2.28	Expand Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: https://www.unidata.ucar.edu/software/udunits/ URL: https://www.unidata.ucar.edu/software/udunits/ Keyword:tools
unixodbc	-	2.3.9	Expand Description: unixODBC provides a uniform interface between application and database driver Homepage: https://www.unixodbc.org URL: https://www.unixodbc.org
varscan	-	2.4.2	Expand Description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data Homepage: https://github.com/dkoboldt/varscan URL: https://github.com/dkoboldt/varscan
vcflib	-	1.0.3	Expand Description: vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. Homepage: https://github.com/vcflib/vcflib URL: https://github.com/vcflib/vcflib
vcftools	bio	0.1.16	Expand Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. Homepage: https://vcftools.github.io URL: https://vcftools.github.io Keyword:bio
viennarna	bio	2.5.0	Expand Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/ URL: http://www.tbi.univie.ac.at/RNA/ Keyword:bio
visit	vis	2.13.3	Expand Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit URL: https://wci.llnl.gov/simulation/computer-codes/visit Keyword:vis
voro++	math	0.4.6	Expand Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ URL: http://math.lbl.gov/voro++/ Keyword:math
vtk	vis	8.2.0	Expand Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: https://www.vtk.org URL: https://www.vtk.org Compatible modules: python/3.8, python/3.7, python/3.6 Keyword:vis
vtune	tools	2020.1, 2022.2	Expand Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: https://software.intel.com/en-us/vtune URL: https://software.intel.com/en-us/vtune Keyword:tools
wasp	-	3.1.4, 4.0.3	Expand Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp
xml-libxml	-	2.0205	Expand Description: Perl binding for libxml2 Homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod URL: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod Extensions: Alien::Base-2.23, Alien::Libxml2-0.16, File::chdir-0.1010, XML::LibXML-2.0205
xmlf90	tools	1.5.4	Expand Description: xmlf90 is a suite of libraries to handle XML in Fortran. It has two major components: - A XML parsing library. The parser was designed to be a useful tool in the extraction and analysis of data in the context of scientific computing, and thus the priorities were efficiency and the ability to deal with very large XML files while maintaining a small memory footprint. The most complete programming interface is based on the very successful SAX (Simple API for XML) model, although a partial DOM interface and a very experimental XPATH interface are also present. - A library (xmlf90-wxml) that facilitates the writing of well-formed XML, including such features as automatic start-tag completion, attribute pretty-printing, and element indentation. There are also helper routines to handle the output of numerical arrays. Homepage: https://launchpad.net/xmlf90/ URL: https://launchpad.net/xmlf90/ Keyword:tools
xtensor	-	0.24.2	Expand Description: xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. Homepage: https://github.com/xtensor-stack/xtensor URL: https://github.com/xtensor-stack/xtensor
yaxt	tools	0.9.0, 0.9.1	Expand Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools