Modules avx

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Module Type Documentation Versions Description
abaqus phys 2020, 2021, 6.14.1

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

abinit chem 8.2.2

Description: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Homepage: http://www.abinit.org/ Keyword:chem

abyss bio 1.9.0, 1.5.2

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio

actc - 1.1

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

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 2019.3, 2018.3, 2020.3

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

afni bio 20180404

Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ Keyword:bio

almabte - 1.3.2

Description: almaBTE consists of a library and a collection of executables allowing the user to calculate thermal transport properties of heterogeneous structures, using only ab-initio data, and solving the phonon Boltzmann Transport Equation (BTE). Homepage: https://almabte.bitbucket.io/ URL: https://almabte.bitbucket.io/

almosthere - 1.0.10

Description: Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. Homepage: https://github.com/horta/almosthere URL: https://github.com/horta/almosthere

angsd bio 0.918

Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd Keyword:bio

annovar bio 2017Jul16, 20191024

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

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, 2019R2, 16.2.3, 2020R2, 2020R1, 18.1, 18.2, 2021R1, 2021R2, 17.2, 19.1, 19.2

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

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 - 1.10.8, 1.9.15

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/

appleseed vis 1.8.1-beta

Description: appleseed is an open source, physically-based global illumination rendering engine primarily designed for animation and visual effects. Homepage: https://github.com/appleseedhq/appleseed Keyword:vis

armadillo math 7.950.1

Description: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Homepage: http://arma.sourceforge.net/ Keyword:math

arpack-ng math 3.5.0, 3.4.0

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. - Homepage: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math

ascp tools 3.5.4

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

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 2.4.1

Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. - Homepage: https://github.com/pezmaster31/bamtools Keyword:bio

bamutil bio 1.0.13

Description: BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Homepage: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio

bazel tools 0.7.0, 0.11.1, 0.25.2, 0.19.2, 0.5.2, 0.27.0

Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: http://bazel.io/ Keyword:tools

bbmap bio 38.86, 37.36

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 1.4, 1.9, 1.13, 1.5

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

bcl2fastq2 bio 2.20.0

Description: bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html URL: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html Keyword:bio

beagle-lib bio 2.1.2

Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio

beast bio 1.8.2, 2.4.0

Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Homepage: http://beast.bio.ed.ac.uk/ Keyword:bio

bedtools bio 2.26.0

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 Keyword:bio

beef chem 0.1.1

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

bioawk - 1.0

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

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 1.7.5, 1.7.7, 1.7.1

Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: http://www.bioperl.org/ Extensions: DBD::mysql-4.050, DBD::Pg-3.8.1, Devel::CheckLib-1.13, Devel::Cycle-1.12, IO::CaptureOutput-1.1104, PadWalker-2.3, Spiffy-0.46, Test::Base-0.89, Test::Memory::Cycle-1.06, Test::RequiresInternet-0.05, Test::Weaken-3.022000, Test::YAML-1.07, XML::DOM::XPath-0.14, XML::Filter::BufferText-1.01, XML::Parser-2.44, XML::RegExp-0.04, XML::XPathEngine-0.14, YAML-1.29 Keyword:bio

bison - 3.7.1

Description: Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. Homepage: https://www.gnu.org/software/bison URL: https://www.gnu.org/software/bison

blast bio 2.2.26

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, 2.6.0, 2.10.0

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

blat bio 3.5

Description: BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. - Homepage: http://genome.ucsc.edu/FAQ/FAQblat.html Keyword:bio

bolt-lmm bio 2.3.4, 2.2

Description: The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. Like the GCTA software. Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ URL: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Keyword:bio

boost tools 1.65.1, 1.63.0, 1.68.0, 1.72.0, 1.60.0

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

boost-mpi tools 1.60.0, 1.65.1, 1.72.0

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

bowtie bio 1.1.2

Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. - Homepage: http://bowtie-bio.sourceforge.net/index.shtml Keyword:bio

bowtie2 bio 2.3.0, 2.4.1

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

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 0.7.15

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

caffe2 ai Caffe2 0.8.1

Description: Caffe2 is a lightweight, modular, and scalable deep learning framework. Building on the original Caffe, Caffe2 is designed with expression, speed, and modularity in mind. Homepage: https://github.com/caffe2/caffe2 Keyword:ai

canu bio 2.2, 1.6, 1.5, 1.9

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

canvas bio 1.25

Description: Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome. To run, do mono $EBROOTCANVAS/Canvas.dll ... Homepage: https://github.com/Illumina/canvas Keyword:bio

cap3 bio 20151002

Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio

catch2 - 2.11.0

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

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

Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ URL: http://weizhong-lab.ucsd.edu/cd-hit/ Keyword:bio

cdo geo 1.7.2, 1.9.8, 1.9.10

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

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

centrifuge bio 1.0.3-beta

Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge Keyword:bio

cereal - 1.3.0

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 2.1.1, 1_2_2

Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm1.2/ URL: http://www.cesm.ucar.edu/models/cesm1.2/ Keyword:geo

cesm/cesm/cesm - 2.1.3

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/

cfitsio vis 3.48

Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// URL: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// Keyword:vis

cgal math 4.9, 4.14.3

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

cgns phys 3.3.1

Description: The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. Homepage: https://cgns.github.io/ Keyword:phys

chapel-single tools 1.15.0

Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools

chapel-slurm-gasnetrun_ibv tools 1.15.0

Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools

circos vis 0.69-6

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

clang tools 3.9.0, 3.8.1

Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: http://clang.llvm.org/ Keyword:tools

clhep math 2.3.1.1

Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. - Homepage: http://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math

cmake tools 3.21.4, 3.16.3, 3.18.4, 3.12.3, 3.20.1

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

cnvnator bio 0.3.3

Description: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads Homepage: https://github.com/abyzovlab/CNVnator Keyword:bio

code-server - 3.12.0, 3.5.0, 3.4.1

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

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 5.3a, 5.5, 5.4, 5.6

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

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

cp2k chem 4.1, 6.1

Description: CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. Homepage: http://www.cp2k.org/ Keyword:chem

cpmd chem CPMD 3.17.1

Description: The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Homepage: http://cpmd.org Keyword:chem

cppzmq - 4.7.1

Description: cppzmq is a C++ binding for libzmq Homepage: https://github.com/zeromq/cppzmq URL: https://github.com/zeromq/cppzmq

cromwell tools 58, 34

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, 2018

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

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 9.0.176, 11.0, 8.0.44, 11.1.1, 10.0.130, 11.2.2, 7.5.18, 10.2, 10.1, 11.4

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 7.4, 5.1, 7.0, 8.2.0, 7.6.5, 8.0.3, 6.0, 7.5

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

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

cunit tools 2.1-3

Description: Automated testing framework for C. Homepage: https://sourceforge.net/projects/cunit/ Keyword:tools

cvit - 1.2.1

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

dalilite - 5

Description: DaliLite.v5 is a standalone program for protein structural alignment and structure database search. It is based on the Dali method (Dali stands for distance matrix alignment). It consists of two wrapper scripts: import.pl - convert PDB files to internal data format used by Dali, mirror PDB database dali.pl - perform pairwise structural alignments, all-against-all comparisons, or structural database searches The program was evaluated on the scope-140 benchmark. Homepage: http://ekhidna2.biocenter.helsinki.fi/dali URL: http://ekhidna2.biocenter.helsinki.fi/dali

dcm2niix bio 1.0.20200331

Description: dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio

ddt-cpu tools 20.2, 19.1.4, 18.3, 7.1

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, 19.1.4, 18.3, 7.1

Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com URL: http://www.allinea.com

dealii math 8.5.0

Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/ Keyword:math

delly - 0.8.5, 0.7.8

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 0.9.8

Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond Keyword:bio

dl_poly4 chem 4.08

Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem

dotnet-core - 5.0.12, 3.0.0, 6.0.0, 3.1.8

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/

dotnet-core-runtime tools 2.0.7, 1.1.8

Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Homepage: https://www.microsoft.com/net/ Keyword:tools

double-conversion - 3.1.5

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

eccodes geo 2.22.1, 2.19.0, 2.15.0, 2.18.0, 2.8.2, 2.21.0

Description: ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.7, python/3.8, python/3.9 Extensions: cfgrib-0.9.9.0, eccodes-1.3.2 Keyword:geo

eclipse tools 4.6.0

Description: Eclipse is an integrated development environment (IDE) used in computer programming, and is the most widely used Java IDE.[6] It contains a base workspace and an extensible plug-in system for customizing the environment. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including: Ada, ABAP, C, C++, COBOL, D, Fortran, Haskell, JavaScript, Julia,[7] Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby (including Ruby on Rails framework), Rust, Scala, Clojure, Groovy, Scheme, and Erlang. It can also be used to develop documents with LaTeX (via a TeXlipse plug-in) and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others. - Homepage: https://www.perl.org/ Keyword:tools

eigen math 3.2.2, 3.3.5, 3.3.2, 3.2.10, 3.3.7

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, 2017.11.001

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

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

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

enso - 1.271

Description: Energetic sorting of conformer rotamer ensembles Homepage: https://github.com/grimme-lab/enso URL: https://github.com/grimme-lab/enso

erlangotp tools 20.0

Description: Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system. Homepage: http://www.erlang.org/ Keyword:tools

esmf geo 7.0.1

Description: The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. Homepage: http://sourceforge.net/projects/esmf Keyword:geo

expat tools 2.2.6, 2.2.9, 2.2.10

Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) Homepage: http://expat.sourceforge.net/ URL: http://expat.sourceforge.net/ Keyword:tools

fast-gbs bio 2017-01-25

Description: A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries. Homepage: https://bitbucket.org/jerlar73/fast-gbs Keyword:bio

fasta bio 36.3.8h

Description: The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Homepage: http://fasta.bioch.virginia.edu URL: http://fasta.bioch.virginia.edu Keyword:bio

fastqc bio 0.11.9, 0.11.5, 0.11.8

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

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 2.1.10

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/ Keyword:bio

fastx-toolkit bio 0.0.14

Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio

feko phys 2018

Description: FEKO is a comprehensive computational electromagnetics (CEM) code used widely in the telecommunications, automobile, space and defense industries. Homepage: https://altairhyperworks.com/product/FEKO Keyword:phys

fftw math 3.3.6, 3.3.8

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 3.3.6, 2.1.5, 3.3.8

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

filtlong bio 0.2.0

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

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

fluent phys ANSYS 16.1

Description: ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications, ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Fluent covers a broad reach, including special models with capabilities to model in-cylinder combustion, aero-acoustics, turbomachinery and multiphase systems. Homepage: https://www.ansys.com/products/fluids/ansys-fluent Keyword:phys

fmt - 6.1.1, 5.3.0, 6.2.1, 7.0.3

Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/

fpc tools 3.0.0

Description: A 32/64/16-bit Pascal compiler for Win32/64/CE, Linux, Mac OS X/iOS, FreeBSD, OS/2, Game Boy Advance, Nintendo NDS and DOS; semantically compatible with Delphi, Borland Pascal and Mac Pascal (partially) with extra features, e.g. operator overloading. Homepage: https://sourceforge.net/projects/freepascal/ Keyword:tools

freebayes bio 1.1.0

Description: Bayesian haplotype-based polymorphism discovery and genotyping. Homepage: https://github.com/ekg/freebayes Keyword:bio

freesurfer bio 5.3.0

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

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

fxtract - 2.3

Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract

g2clib geo 1.6.0

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

g2lib geo 1.4.0

Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo

gamess-us chem GAMESS-US 20170420-R1

Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. Homepage: http://www.msg.chem.iastate.edu/gamess/index.html Keyword:chem

gatk bio 4.2.4.0, 4.0.8.1, 4.2.2.0, 3.8, 3.7, 4.1.8.1, 4.1.8.0, 4.0.12.0, 4.1.7.0, 4.0.0.0, 4.1.0.0, 4.1.2.0

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

gatk-queue bio 3.8-0

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/ Keyword:bio

gblocks - 0.91b

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 7.3.0, 8.3.0, 9.1.0, 10.3.0, 9.3.0, 10.2.0, 6.4.0, 4.9.4, 8.4.0, 5.4.0, 4.8.5

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

gcc-offload - 9.1.0

Description: The GNU Compiler with OpenMP/OpenACC offload support for Nvidia PTX Homepage: http://gcc.gnu.org/ URL: http://gcc.gnu.org/

gdal geo 2.1.3, 3.0.4, 3.2.3, 3.0.1, 2.2.1

Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. Homepage: http://www.gdal.org/ URL: http://www.gdal.org/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Extensions: pygdal-3.0.1.5 Keyword:geo

gdrcopy - 2.1

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 phys 10.02.p03

Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: http://geant4.cern.ch/ Keyword:phys

genometools bio 1.6.1

Description: A comprehensive software library for efficient processing of structured genome annotations. Homepage: http://genometools.org URL: http://genometools.org Keyword:bio

geos geo 3.6.1, 3.8.1, 3.9.1, 3.7.2

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: http://trac.osgeo.org/geos URL: http://trac.osgeo.org/geos Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Keyword:geo

gffcompare - 0.11.6

Description: GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. Homepage: https://github.com/gpertea/gffcompare URL: https://github.com/gpertea/gffcompare

gffread - 0.11.7

Description: GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. Homepage: https://github.com/gpertea/gffread URL: https://github.com/gpertea/gffread

ghostscript - 9.26

Description: Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. Homepage: http://ghostscript.com

git-annex tools 6.20180807, 8.20200810

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

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

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 0.9.7.2

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 Keyword:vis

glpk math 4.61

Description: The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. - Homepage: https://www.gnu.org/software/glpk/ Keyword:math

gmap-gsnap bio 2017-04-13

Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program - Homepage: http://research-pub.gene.com/gmap/ Keyword:bio

gmp - 6.1.2

Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. Homepage: http://gmplib.org/ URL: http://gmplib.org/

gmpich - 2019.05

Description: gcc and GFortran based compiler toolchain, including MPICH for MPI support. Homepage: (none)

gnuplot vis 5.2.8

Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net/ URL: http://gnuplot.sourceforge.net/ Keyword:vis

go tools 1.10.3, 1.14.4, 1.14.1

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

grackle phys 2.1

Description: Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Homepage: http://grackle.readthedocs.io Keyword:phys

gromacs chem GROMACS 5.0.7, 5.1.4, 2021.4, 2016.3, 2018.1, 4.6.7, 2019.3, 2020.4

Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem

gromacs-plumed chem GROMACS 2016.3

Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem

gsl math 2.2.1, 2.5, 1.16, 2.3, 2.6

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

gtest - 1.10.0

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

gtk+3 tools 3.20.9

Description: GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces. Offering a complete set of widgets, GTK+ is suitable for projects ranging from small one-off tools to complete application suites. Homepage: https://www.gtk.org/ Keyword:tools

gtool - 0.7.5

Description: GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. Homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html URL: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

guile tools 1.8.8

Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile Keyword:tools

gurobi math 9.1.0, 8.1.1, 9.0.3, 9.5.0, 9.0.1, 9.0.2, 9.1.2

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

h4toh5 io 2.2.2

Description: The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects. Homepage: http://www.hdfgroup.org/h4toh5/ Keyword:io

hapgen2 - 2.2.0
haploview - 4.2

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 4.2.12, 4.2.15

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 1.8.18, 1.10.3, 1.10.6, 1.10.7

Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io

hdf5-mpi io 1.10.6, 1.8.18, 1.10.3, 1.10.7

Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io

hdfview - 2.14

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/

heasoft phys 6.26.1

Description: A Unified Release of the FTOOLS and XANADU Software Packages XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases Homepage: https://heasarc.nasa.gov/lheasoft/ URL: https://heasarc.nasa.gov/lheasoft/ Keyword:phys

hh-suite bio 3.3.0

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 2.1.0, 2.2.1

Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml URL: https://ccb.jhu.edu/software/hisat2/index.shtml Keyword:bio

hmmer bio 2.3.2, 3.1b2

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/ Keyword:bio

hpl tools 2.2

Description: HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. - Homepage: http://www.netlib.org/benchmark/hpl/ Keyword:tools

htslib bio 1.5, 1.4, 1.13, 1.9

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

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/

ichthyop - 3.3.3

Description: Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics. It incorporates the most important processes involved in fish early life: spawning, movement, growth, mortality and recruitment. The tool uses as input time series of velocity, temperature and salinity fields archived from ROMS, MARS, NEMO or SYMPHONIE oceanic models (either files or OpenDAP). Homepage: http://www.ichthyop.org/

igblast bio 1.17.0, 1.7.0, 1.16.0

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

igraph math 0.7.1

Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: http://igraph.org Keyword:math

igv - 2.9.2

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/

imagemagick - 7.0.8-53

Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images Homepage: http://www.imagemagick.org/

imkl math 2017.1.132, 2019.3.199, 2021.2.0, 2018.1.163, 2019.2.187, 11.3.4.258, 2020.1.217, 2021.4.0, 2018.3.222, 2017.4.239, 11.1.4.214

Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ URL: http://software.intel.com/en-us/intel-mkl/ Keyword:math

impi mpi 2017.4.239

Description: Intel MPI Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/

impute2 bio 2.3.2

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

infernal bio 1.1.2

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

inspector tools 2018.3

Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools

intel tools 2017.5, 2017.1, 2018.3, 2021.2.0, 2020.1.217, 2019.3, 2014.6, 2016.4

Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ URL: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools

intel-opencl - 2021.2.0
intelxed - 12.0.1

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 5.40-77.0, 5.52-86.0, 5.53-87.0, 5.23-62.0, 5.50-84.0

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

ipp tools 2020.1.217, 9.0.4, 2017.1.132

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

Description: Bundle which contains ipykernel 2020a and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Extensions: backcall-0.1.0, backports-abc-0.5, backports.shutil-get-terminal-size-1.0.0, decorator-4.4.2, enum34-1.1.10, futures-3.3.0, ipykernel-4.10.1, ipykernel-5.2.1, ipython-5.10.0, ipython-7.14.0, ipython-genutils-0.2.0, jedi-0.17.0, jupyter-client-5.3.4, jupyter-client-6.1.3, jupyter-core-4.6.3, parso-0.7.0, pexpect-4.8.0, pickleshare-0.7.5, prompt-toolkit-1.0.18, prompt-toolkit-3.0.5, ptyprocess-0.6.0, Pygments-2.5.2, Pygments-2.6.1, python-dateutil-2.8.1, pyzmq-17.1.2, pyzmq-19.0.0, simplegeneric-0.8.1, tornado-5.1.1, tornado-6.0.4, traitlets-4.3.3, wcwidth-0.1.9

ipython-kernel - 2.7, 3.7, 3.5, 3.8, 3.6, 3.9

Description: IPython kernelspec for Python 2.7 Homepage: https://ipython.org/ URL: https://ipython.org/

iq-tree bio 1.5.5

Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ Keyword:bio

ispc - 1.13.0, 1.10.0

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 2018.3.022

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: http://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools

itk vis 4.12.2

Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org Keyword:vis

jags math 4.2.0, 4.3.0

Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation Homepage: http://mcmc-jags.sourceforge.net/ URL: http://mcmc-jags.sourceforge.net/ Keyword:math

jasper vis 1.900.1, 2.0.16

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 13.0.2, 13.0.1, 1.7.0_80, 1.8.0_192, 14.0.2, 1.8.0_121, 11.0.2

Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: https://openjdk.java.net URL: https://openjdk.java.net Keyword:tools

jellyfish bio 2.2.6, 1.1.11

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Keyword:bio

julia tools 1.3.0, 0.6.0, 1.0.0, 0.5.1, 1.0.2

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org URL: http://julialang.org Keyword:tools

kallisto bio 0.44.0

Description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Homepage: http://pachterlab.github.io/kallisto/ Keyword:bio

kim chem 1.8.2

Description: OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines. Homepage: https://openkim.org/ Keyword:chem

kim-api - 2.1.3

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/

kma - 1.3.0

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

knime - 4.1.0

Description: KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. Homepage: https://www.knime.com/ URL: https://www.knime.com/

kraken bio 0.10.5-beta

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: http://ccb.jhu.edu/software/kraken/ Keyword:bio

lammps chem 20170331

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-OMP, -OPT, -USER-MISC, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem

lammps-omp chem 20170811, 20170331

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem

lammps-user-intel chem 20170331, 20170811

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-VTK, -QEQ, -USER-ATC, -MANYBODY Homepage: http://lammps.sandia.gov/ Keyword:chem

libcdms - 3.1.2

Description: Climate Data Management System Library. Homepage: https://github.com/CDAT/libcdms/ URL: https://github.com/CDAT/libcdms/

libcerf math 1.13

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

libconfig tools 1.7.2

Description: Libconfig is a simple library for processing structured configuration files Homepage: http://www.hyperrealm.com/libconfig/ Keyword:tools

libdrs - 3.1.2

Description: PCMDI's old DRS format implementation Homepage: https://github.com/CDAT/libdrs/ URL: https://github.com/CDAT/libdrs/

libevent - 2.1.12, 2.1.11

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

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

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

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

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

libgpuarray math 0.6.9

Description: Homepage: http://deeplearning.net/software/libgpuarray Keyword:math

libgtextutils bio 0.7

Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio

libharu - 2.3.0

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/

libint chem 1.1.6, 2.2.0

Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. - Homepage: https://github.com/evaleev/libint Keyword:chem

libmesh math 1.2.1

Description: The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. Homepage: https://github.com/libMesh/libmesh Keyword:math

libqglviewer - 2.7.1

Description: libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. Homepage: http://libqglviewer.com/ URL: http://libqglviewer.com/

librttopo - 1.1.0

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

libsodium - 1.0.18

Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Homepage: https://doc.libsodium.org/ URL: https://doc.libsodium.org/

libspatialindex phys 1.8.5

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

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

libstatgen - 20190330

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

libsvm - 3.24

Description: LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). Homepage: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ URL: https://www.csie.ntu.edu.tw/~cjlin/libsvm/

libxc chem 4.3.4, 4.2.1, 3.0.0, 4.2.3

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc URL: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem

libxslt - 1.1.34

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/

libxsmm math 1.8

Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). - Homepage: https://github.com/hfp/libxsmm Keyword:math

liknorm - 1.5.1

Description: C library for computing moments of the product of an exponential-family likelihood with a Normal distribution. Homepage: https://github.com/limix/liknorm URL: https://github.com/limix/liknorm

limix-bgen - 3.0.3

Description: A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. Homepage: https://github.com/limix/bgen URL: https://github.com/limix/bgen

littlecms - 2.9

Description: Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Homepage: http://www.littlecms.com/

lldb - 11.0.0

Description: The debugger component of the LLVM project Homepage: https://lldb.llvm.org/ URL: https://lldb.llvm.org/

llvm tools 6.0.1, 7.0.0, 9.0.1, 8.0.1

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

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 5.2.1, 7.0.0

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 - 4.7.13, 4.7.8, 4.8.11

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

lumpy bio 0.2.13

Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv Keyword:bio

mach bio 1.0.18

Description: MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. - Homepage: http://csg.sph.umich.edu/abecasis/MACH/ Keyword:bio

mafft bio 7.310

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 < ~10,000 sequences), etc. Homepage: http://mafft.cbrc.jp/alignment/software/ Keyword:bio

magma math 2.5.0, 2.2.0, 2.4.0

Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: http://icl.cs.utk.edu/magma/ URL: http://icl.cs.utk.edu/magma/ Keyword:math

make tools 3.82

Description: make-3.82: GNU version of make utility Homepage: http://www.gnu.org/software/make/make.html Keyword:tools

manta bio 1.2.2

Description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, and most WGS tumor/normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor samples as well. Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format. See the user guide for a full description of capabilities and limitations. Homepage: https://github.com/Illumina/manta Keyword:bio

mariadb tools 10.4.11, 10.1.21

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/ Extensions: DBD::mysql-4.050, Devel::CheckLib-1.13, IO::CaptureOutput-1.1104 Keyword:tools

mariadb-connector-c - 3.1.7

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/

matio io 1.5.2

Description: matio is an C library for reading and writing Matlab MAT files. Homepage: http://sourceforge.net/projects/matio/ Keyword:io

matlab tools 2018a, 2019b, 2021a.1, 2020b.6, 2020a, 2016b, 2014a, 2017a, 2021a.5, 2020b.4, 2019a, 2018b

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 3.5.0, 3.6.3

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

maxbin bio 2.2.4

Description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished. Homepage: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Keyword:bio

mcr tools R2020b, R2014a, R2013a, R2020a, R2013b, R2017a, R2019b, R2017b, R2016a, R2015a, R2019a, R2015b, R2018b, R2014b, R2016b, R2018a

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: http://www.mathworks.com/products/compiler/mcr/ URL: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools

megahit bio 1.1.1

Description: MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. Homepage: https://github.com/voutcn/megahit Keyword:bio

meraculous bio 2.2.4

Description: Distributed and scalable assembler for eukaryotic genomes. Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. Homepage: http://jgi.doe.gov/data-and-tools/meraculous/ Keyword:bio

mesa vis 18.3.6

Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Homepage: https://www.mesa3d.org/ URL: https://www.mesa3d.org/ Keyword:vis

meta-farm - 1.0.2

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

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

Description: MetaGeneAnnotator is a gene-finding program for prokaryote and phage. Homepage: http://metagene.nig.ac.jp/ URL: http://metagene.nig.ac.jp/

metal bio 2011-03-25

Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio

metaphlan bio 2.2.0

Description: MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. Homepage: https://bitbucket.org/biobakery/metaphlan2 Keyword:bio

metis math 5.1.0, 4.0.3

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, 1.1.0

Description: A smart search engine for module environments. Homepage: https://github.com/codeandkey/mii URL: https://github.com/codeandkey/mii

minia bio 2.0.7

Description: Minia is a short-read assembler based on a de Bruijn graph Homepage: http://minia.genouest.org/ Keyword:bio

minimac2 bio 2014.9.15

Description: minimac2 is an improved version of Minimac. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. - Homepage: http://genome.sph.umich.edu/wiki/Minimac2 Keyword:bio

minimac3 bio 2.0.1

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 2.13, 2.17

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 2.1.5, 2.1.10, 3.0.13

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

mkl-dnn ai 0.16

Description: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) Homepage: https://01.org/mkl-dnn Keyword:ai

molden chem 5.7

Description: Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac Homepage: http://www.cmbi.ru.nl/molden/ Keyword:chem

mono tools 4.6.2.7, 5.4.0.56, 5.16.0.179

Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: http://www.mono-project.com/ URL: http://www.mono-project.com/ Keyword:tools

mothur bio 1.39.4, 1.40.4

Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ Keyword:bio

mpi.net mpi 13-08-2017

Description: MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment. Homepage: https://github.com/jmp75/MPI.NET Keyword:mpi

mpi4py tools 3.0.0, 3.0.3, 2.0.0

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/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools

mrbayes bio 3.2.6

Description: MrBayes is a program for the Bayesian estimation of phylogeny. - Homepage: http://mrbayes.csit.fsu.edu Keyword:bio

multiwfn chem 3.5

Description: A multifunctional wavefunction analyzer. Homepage: http://sobereva.com/multiwfn/ Keyword:chem

mummer bio 4.0.0beta2, 3.23

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/ Keyword:bio

mummer-64bit bio 3.23

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/ Keyword:bio

muscle bio 3.8.31

Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. Homepage: https://drive5.com/muscle/ URL: https://drive5.com/muscle/ Keyword:bio

mysql tools 5.7

Description: MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ Keyword:tools

namd-mpi chem NAMD 2.12

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem

namd-multicore chem 2.12, 2.13

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ URL: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem

namd-verbs chem NAMD 2.12

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem

namd-verbs-smp chem NAMD 2.12

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem

nanoflann - 1.3.2

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, 2.3.5, 2.8.4, 2.4.2, 2.11.4

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

ncl vis 6.4.0

Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: http://www.ncl.ucar.edu Keyword:vis

nco io 4.6.6

Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: http://nco.sourceforge.net Keyword:io

ncview vis 2.1.7

Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis

netcdf io 4.4.1.1, 4.7.4, 4.8.0, 4.6.1

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: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io

netcdf-c++ io 4.2

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: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io

netcdf-c++-mpi io 4.2

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: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io

netcdf-c++4-mpi io 4.3.0

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: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io

netcdf-fortran io 4.5.3, 4.4.4, 4.5.2

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 4.4.4, 4.5.3, 4.5.2

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 4.4.1.1, 4.1.3, 4.8.0, 4.7.4

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

nettle - 3.3

Description: Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. Homepage: http://www.lysator.liu.se/~nisse/nettle/

networkx tools 1.1, 2.1

Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools

nextflow - 20.04.1, 19.10.0, 19.04.0, 21.04.3, 20.10.0

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/

nextgenmap bio 0.5.4, 0.5.0

Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio

ngs - 2.10.5

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

ngstools bio 1.0.1

Description: ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data. An application note illustrating its application has published (Fumagalli et al., 2014). Homepage: https://github.com/mfumagalli/ngsTools Keyword:bio

ninja - 1.9.0

Description: Ninja is a small build system with a focus on speed. Homepage: https://ninja-build.org/ URL: https://ninja-build.org/

ninja-phylogenetics - 0.97-cluster_only

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

nlopt math 2.4.2

Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt Keyword:math

nspr - 4.21, 4.25, 4.29

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 - 3.57, 3.45, 3.51

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, 11.3.0

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

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/

nwchem chem 6.6.revision27746

Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: http://www.nwchem-sw.org Keyword:chem

oasys-ls-dyna phys 14.1

Description: The Oasys Suite of software, exclusively written for LS-DYNA, is at the leading edge of the pre- and post-processing markets and is used worldwide by many of the largest LS-DYNA customers. Homepage: http://www.oasys-software.com/dyna/en/ Keyword:phys

octave tools 4.2.1

Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: http://www.gnu.org/software/octave/ Keyword:tools

opa-psm2 - 11.2.185

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/

openbabel chem 2.4.1

Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: http://openbabel.org Keyword:chem

openblas math 0.2.20, 0.3.4, 0.3.9

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

opencolorio vis 1.0.9

Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ Keyword:vis

opencv vis 3.3.0, 4.2.0, 2.4.13.3

Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.6.3, python/3.7.4 Keyword:vis

openexr vis 2.2.1

Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: http://www.openexr.com/ Keyword:vis

openfoam phys 5.0, 4.1, 2.3.1, 3.0.1, 7

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/ URL: http://www.openfoam.org/ Keyword:phys

openimageio vis 1.8.7

Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: http://openimageio.org/ Keyword:vis

openmm chem OpenMM 7.1.1

Description: OpenMM is a toolkit for molecular simulation. - CC-Wiki: OpenMM Homepage: https://simtk.org/home/openmm URL: https://simtk.org/home/openmm Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Keyword:chem

openmpi mpi 2.1.1, 4.0.3, 2.0.2, 1.6.5, 3.1.2, 1.8.8, 4.0.1, 4.1.1

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

openpgm tools 5.2.122

Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: http://code.google.com/p/openpgm/ Keyword:tools

openrefine - 3.3, 3.4.1

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

opensees - 3.0.2, 3.0.0

Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/

optix - 6.5.0

Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPUs 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 4.0.0.2, 4.2.1, 5.0.1, 4.0.1.2

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

orfm - 0.7.1

Description: A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences. Homepage: https://github.com/wwood/OrfM

orthomcl bio 2.0.9

Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ URL: http://orthomcl.org/ Keyword:bio

osl vis 1.9.6

Description: Advanced shading language for production GI renderers Homepage: https://github.com/imageworks/OpenShadingLanguage Keyword:vis

osu-micro-benchmarks tools 5.3.2

Description: OSU Micro-Benchmarks Homepage: http://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools

ovito - 3.3.3

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, 1.1

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

panther - 14.1

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/

papi tools 5.6.0

Description: PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. Homepage: http://icl.cs.utk.edu/projects/papi/ Keyword:tools

parabricks - 2.5.0

Description: Analyzing genomic data is computationally intensive. Time and cost are significant barriers to using genomics data for precision medicine. The NVIDIA Parabricks Genomics Analysis Toolkit breaks down those barriers, providing GPU-accelerated genomic analysis. Data that once took days to analyze can now be done in under an hour. Homepage: https://developer.nvidia.com/nvidia-parabricks URL: https://developer.nvidia.com/nvidia-parabricks

parallel tools 20160722

Description: parallel: Build and execute shell commands in parallel Homepage: http://savannah.gnu.org/projects/parallel/ Keyword:tools

paraview vis 5.3.0

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis

paraview-offscreen vis 5.3.0

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis

paraview-offscreen-gpu vis Visualization 5.4.0

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis

parmetis math 4.0.3

Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math

pcl math 1.8.1

Description: The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. Homepage: http://pointclouds.org/ Keyword:math

pcre - 8.44, 8.39

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/

pcre2 - 10.35, 10.34, 10.31

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/

pdt - 3.25

Description: Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. Homepage: https://www.cs.uoregon.edu/research/pdt/ URL: https://www.cs.uoregon.edu/research/pdt/

pear bio 0.9.11, 0.9.10

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

penncnv bio 1.0.5, 1.0.4

Description: PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. Homepage: http://penncnv.openbioinformatics.org/en/latest/ Keyword:bio

perl tools 5.16.3, 5.30.2, 5.22.2, 5.22.4

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

perl4-corelibs tools 0.003

Description: Libraries historically supplied with Perl 4 Homepage: https://metacpan.org/pod/Perl4::CoreLibs Keyword:tools

petsc tools 3.14.1, 3.7.5, 3.8.2, 3.11.3

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

petsc-64bits tools 3.7.5

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 Keyword:tools

petsc-debug tools 3.8.2

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 Keyword:tools

pgi tools 13.10, 16.9, 17.3, 19.4

Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/ URL: http://www.pgroup.com/

phylip bio 3.697

Description: PHYLIP is a free package of programs for inferring phylogenies. Homepage: http://evolution.genetics.washington.edu/phylip URL: http://evolution.genetics.washington.edu/phylip Keyword:bio

picard bio 2.26.3, 2.23.2, 2.10.7, 2.20.6, 2.18.9, 2.23.3, 2.17.3, 2.1.1

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 1.22, 1.23, 1.24

Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.23.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.23.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio

plink bio 1.07, 1.9b_4.1-x86_64, 1.9b_5.2-x86_64, 2.00-10252019-avx2, 1.9b_6.21-x86_64, 2.00a2.3_x86_64

Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio

plumed chem 2.3.0, 2.3.2

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem

pmix - 1.2.5, 3.1.5, 3.2.3

Description: Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to resolve these questions by providing 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/

pnetcdf io 1.8.1

Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io

postgresql tools 12.1, 11.6, 10.2, 9.6.6, 12.4

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/3.7, python/3.6, python/2.7 Extensions: psycopg2-2.8.6 Keyword:tools

pplacer bio 1.1.alpha19

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

prinseq bio 0.20.4

Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net Extensions: Cairo-1.106, Contextual::Return-0.004008, Digest::MD5-2.54, ExtUtils::Depends-0.405, ExtUtils::PkgConfig-1.15, File::Spec-3.62, File::Temp-0.2304, Getopt::Long-2.48, JSON-2.90, Math::Cephes::Matrix-0.5304, Math::MatrixReal-2.12, MIME::Base64-3.15, Pod::Usage-1.68, Statistics::PCA-0.0.1, Text::SimpleTable-2.03, Want-0.26 Keyword:bio

probmask - 2011.12

Description: Probmask (ZORRO) is a probabilistic alignment masking program Homepage: https://sourceforge.net/projects/probmask/

prodigal bio 2.6.3

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: http://prodigal.ornl.gov/ Keyword:bio

proj geo 7.0.0, 7.2.1, 4.9.3, 6.0.0, 6.3.0, 8.0.0

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/3.6, python/3.7, python/3.8 Extensions: pyproj-3.0.1 Keyword:geo

protobuf tools 3.7.1, 3.3.0, 3.9.1, 3.11.1, 3.12.3, 3.6.1

Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0 Keyword:tools

pypy tools 5.8.0, 7.3.3

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

Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: attrs-20.3.0, importlib-metadata-3.1.1, iniconfig-1.1.1, packaging-20.7, pluggy-0.13.1, py-1.9.0, pyparsing-2.4.7, pytest-6.1.2, pytest-mpi-0.4, toml-0.10.2, zipp-3.4.0

python tools 3.5.4, 3.8.10, 2.7.13, 3.6.10, 3.7.9, 3.7.4, 2.7.14, 3.5.2, 2.7.18, 3.6.3, 3.8.2, 3.7.0, 3.8.0, 3.9.6

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: appdirs-1.4.3, configparser-4.0.2, contextlib2-0.6.0.post1, distlib-0.3.0, filelock-3.0.12, importlib_metadata-1.6.0, importlib_resources-1.4.0, pathlib2-2.3.5, pip-20.0.2, scandir-1.10.0, setuptools-44.0.0, singledispatch-3.4.0.3, six-1.14.0, typing-3.7.4.1, virtualenv-20.0.18, wheel-0.34.2, zipp-1.2.0 Keyword:tools

python27-mpi4py tools 2.0.0

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 Keyword:tools

python27-scipy-stack math 2017a

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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, backports_abc-0.4, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, functools32-3.2.3-2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pysqlite-2.8.3, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math

python35-mpi4py tools 2.0.0

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 Keyword:tools

python35-scipy-stack math 2017a

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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math

qca geo 2.3.0

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

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

qhull math 2015.2

Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Homepage: http://www.qhull.org Keyword:math

qjson tools 0.9.0

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

qrupdate math 1.1.2

Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ Keyword:math

qscintilla tools 2.10.7, 2.11.2

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 5.9.6, 4.8.7, 5.12.3, 5.6.1, 5.12.8, 5.11.3, 5.10.1, 3.3.8, 5.13.1

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

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

Description: Platform-independent Qt API for storing passwords securely. Homepage: https://github.com/frankosterfeld/qtkeychain URL: https://github.com/frankosterfeld/qtkeychain

quantumatk - 2019.12

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 6.3, 6.4.1, 6.1, 6.6, 6.0, 6.2.2

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). This module includes thermo_pw add-on package. Homepage: http://www.pwscf.org/ URL: http://www.pwscf.org/ Keyword:chem

qwt tools 6.1.4

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

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 3.3.3, 3.4.3, 3.5.2, 4.0.2, 4.0.0, 3.4.0, 3.6.1, 4.1.2, 3.5.0

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ URL: http://www.r-project.org/ Keyword:tools

r-bundle-bioconductor bio 3.4

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Extensions: abind-1.4-5, acepack-1.4.1, ade4-1.7-6, affy-1.52.0, affycoretools-1.46.5, affyio-1.44.0, AgiMicroRna-2.24.0, ALDEx2-1.6.0, annaffy-1.46.0, annotate-1.52.1, AnnotationDbi-1.36.2, AnnotationForge-1.16.1, AnnotationHub-2.6.5, ape-4.1, assertthat-0.2.0, assertthat-0.2.0, backports-1.1.0, base64-2.0, base64enc-0.1-3, baySeq-2.8.0, beanplot-1.2, BH-1.62.0-1, BiasedUrn-1.07, bindr-0.1, bindrcpp-0.2, Biobase-2.34.0, BiocGenerics-0.20.0, BiocInstaller-1.24.0, BiocParallel-1.8.2, biomaRt-2.30.0, biomformat-1.2.0, Biostrings-2.42.1, biovizBase-1.22.0, bit-1.1-12, bit64-0.9-7, bitops-1.0-6, blob-1.1.0, BSgenome-1.42.0, BSgenome.Hsapiens.UCSC.hg19-1.4.0, bumphunter-1.14.0, Category-2.40.0, caTools-1.17.1, CGHbase-1.34.0, checkmate-1.8.2, clusterRepro-0.5-1.1, coin-1.2-0, colorspace-1.3-2, corpcor-1.6.9, cummeRbund-2.16.0, curl-2.7, dada2-1.2.2, data.table-1.10.4, DBI-0.7, DEGseq-1.28.0, DEoptimR-1.0-8, derfinder-1.8.5, derfinderHelper-1.8.1, DESeq2-1.14.1, dichromat-2.0-0, digest-0.6.12, digest-0.6.12, diptest-0.75-7, doParallel-1.0.10, doRNG-1.6.6, dplyr-0.7.1, DynDoc-1.52.0, edgeR-3.16.5, ellipse-0.3-8, ensembldb-1.6.2, evaluate-0.10.1, fastcluster-1.1.22, FDb.InfiniumMethylation.hg19-2.2.0, ff-2.2-13, flexmix-2.3-14, foreach-1.4.3, Formula-1.2-1, fpc-2.1-10, futile.logger-1.4.3, futile.logger-1.4.3, futile.logger-1.4.3, futile.options-1.0.0, futile.options-1.0.0, futile.options-1.0.0, gcrma-2.46.0, gdata-2.18.0, gdsfmt-1.10.1, genefilter-1.56.0, geneLenDataBase-1.10.0, geneplotter-1.52.0, GenomeGraphs-1.34.0, GenomeInfoDb-1.10.3, GenomicAlignments-1.10.1, GenomicFeatures-1.26.4, GenomicFiles-1.10.3, GenomicRanges-1.26.4, genoset-1.30.0, GEOquery-2.40.0, GGally-1.3.1, ggbio-1.22.4, ggplot2-2.2.1, glmnet-2.0-10, glue-1.1.1, GO.db-3.4.0, goseq-1.26.0, GOstats-2.40.0, gplots-3.0.1, graph-1.52.0, gridBase-0.4-7, gridExtra-2.2.1, GSEABase-1.36.0, gtable-0.2.0, gtools-3.5.0, Gviz-1.18.2, HCsnip-1.14.0, hgu133plus2.db-3.2.3, highr-0.6, Hmisc-4.0-3, Homo.sapiens-1.3.1, htmlTable-1.9, htmltools-0.3.6, htmlwidgets-0.8, httpuv-1.3.3, httr-1.2.1, hwriter-1.3.2, igraph-1.0.1, illuminaio-0.16.0, impute-1.48.0, interactiveDisplayBase-1.12.0, IRanges-2.8.2, irlba-2.2.1, iterators-1.0.8, jsonlite-1.5, KEGG.db-3.2.3, KEGGgraph-1.32.0, KEGGprofile-1.16.0, KEGGREST-1.14.1, kernlab-0.9-25, knitr-1.16, labeling-0.3, lambda.r-1.1.9, lambda.r-1.1.9, lambda.r-1.1.9, latticeExtra-0.6-28, lazyeval-0.2.0, limma-3.30.13, locfit-1.5-9.1, logspline-2.1.9, lumi-2.26.4, magrittr-1.5, markdown-0.8, marray-1.52.0, maSigPro-1.46.0, matrixStats-0.52.2, mclust-5.3, memoise-1.1.0, metagenomeSeq-1.16.0, methylumi-2.20.0, mime-0.5, minfi-1.20.2, mixOmics-6.1.1, mixOmics-6.1.3, modeltools-0.2-21, multcomp-1.4-6, multtest-2.30.0, munsell-0.4.3, mvtnorm-1.0-6, nleqslv-3.3, NMF-0.20.6, NOISeq-2.18.0, nor1mix-1.2-2, oligoClasses-1.36.0, openssl-0.9.6, org.Hs.eg.db-3.4.0, OrganismDbi-1.16.0, pcaMethods-1.66.0, penalized-0.9-50, perm-1.0-0.0, perm-1.0-0.0, permute-0.9-4, PFAM.db-3.4.0, phyloseq-1.19.1, pkgconfig-2.0.1, pkgmaker-0.22, plogr-0.1-1, plyr-1.8.4, png-0.1-7, polyester-1.10.1, prabclus-2.2-6, preprocessCore-1.36.0, prettyunits-1.0.2, progress-1.1.2, quadprog-1.5-5, qvalue-2.6.0, R.methodsS3-1.7.1, R.oo-1.21.0, R.utils-2.5.0, R6-2.2.2, randomForestSRC-2.4.2, RBGL-1.50.0, RColorBrewer-1.1-2, Rcpp-0.12.11, RcppArmadillo-0.7.900.2.0, RcppParallel-4.3.20, RCurl-1.95-4.5, registry-0.3, ReportingTools-2.14.0, reshape-0.8.6, reshape2-1.4.2, rgl-0.98.1, Rgraphviz-2.18.0, rhdf5-2.18.0, rlang-0.1.1, RNASeqPower-1.14.0, rngtools-1.2.4, robustbase-0.92-7, Rsamtools-1.26.2, RSQLite-2.0, Rsubread-1.24.2, rtracklayer-1.34.2, S4Vectors-0.12.2, samr-2.0, sandwich-2.3-4, scales-0.4.1, shiny-1.0.3, ShortRead-1.32.1, sigaR-1.22.0, siggenes-1.48.0, sm-2.2-5.4, snow-0.4-2, snowfall-1.84-6.1, SNPRelate-1.8.0, sourcetools-0.1.6, SPIA-2.26.0, stringi-1.1.5, stringr-1.2.0, SummarizedExperiment-1.4.0, TeachingDemos-2.10, TH.data-1.0-8, tibble-1.3.3, tidyr-0.6.3, trimcluster-0.1-2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, VariantAnnotation-1.20.3, vegan-2.4-3, venn-1.2, viridis-0.4.0, viridisLite-0.2.0, XML-3.98-1.9, xtable-1.8-2, xtable-1.8-2, XVector-0.14.1, yaml-2.1.14, zlibbioc-1.20.0, zoo-1.8-0 Keyword:bio

racon bio 20170719, 1.4.13

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

randomlib - 1.10

Description: RandomLib is a C++ interface to the Mersenne Twister random number generator, MT19937 and to the SIMD-oriented Fast Mersenne Twister random number generator, SFMT19937. It provides convenient access to random integers and reals at a variety of precisions. RandomLib also contains new algorithms which permit exact sampling from the normal and discrete normal distributions (provided that the underlying generator is perfect). The emphasis in this implementation is on providing a reliable source of random numbers for scientific applications where there's a premium on accuracy, repeatability, portability, and ease of use. By default, this library uses SFMT's improved method for seeding the generator and it allows access to both the 32-bit and 64-bit versions of MT19937 and SFMT19937 and includes implementations of the SFMT19937 using SSE2 and AltiVec instructions. Homepage: http://randomlib.sourceforge.net/html/ URL: http://randomlib.sourceforge.net/html/

rapidjson - 1.1.0

Description: A fast JSON parser/generator for C++ with both SAX/DOM style API Homepage: https://rapidjson.org URL: https://rapidjson.org

raxml bio 8.2.11

Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. Homepage: https://github.com/stamatak/standard-RAxML URL: https://github.com/stamatak/standard-RAxML Keyword:bio

ray bio 3.0.0

Description: Ray -- Parallel genome assemblies for parallel DNA sequencing. Homepage: https://github.com/zorino/ray Keyword:bio

rdkit chem 2019.03.4

Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/ URL: http://www.rdkit.org/ Compatible modules: python/3.5.4, python/3.6.3, python/3.7.4 Keyword:chem

re2c - 1.3, 1.2.1

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/

recon bio 1.08

Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/ Keyword:bio

reduce - 20180820

Description: Reduce - tool for adding and correcting hydrogens in PDB files Homepage: https://github.com/rlabduke/reduce

reframe - 2.21

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/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0

relion chem 2.1.0

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Keyword:chem

remora tools 1.8.2

Description: REsource MOnitoring for Remote Applications Homepage: https://github.com/TACC/remora Keyword:tools

repasthpc bio 2.2.0

Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. - Homepage: https://repast.github.io/ Keyword:bio

repeatscout bio 1.0.5

Description: RepeatScout is a tool to discover repetitive substrings in DNA. Homepage: https://bix.ucsd.edu/repeatscout/ Keyword:bio

rlooper - 1.0

Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/chedinlab/rlooper.git

rnammer bio 1.2

Description: RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The method is described in detail in the following article: RNammer: consistent annotation of rRNA genes in genomic sequences. Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T Ussery DW. Nucleic Acids Res. Apr 22, 2007. Homepage: http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer Keyword:bio

root tools 5.34.36, 6.08.02

Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: http://root.cern.ch/drupal/ Keyword:tools

rosetta chem 3.8

Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. Homepage: https://www.rosettacommons.org Keyword:chem

rsem bio 1.3.0

Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ Keyword:bio

rstudio-server tools 1.1.447, 1.1.206, 1.2.1335

Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools

rtk bio 1.4.0

Description: Insighteconstruction Toolkit (RTK) is an open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK). RTK is developped by the RTK consortium. RTK provides or will provide Basic operators for reconstruction, e.g., filtering, forward, projection and backprojection Multithreaded CPU and GPU versions Tools for respiratory motion correction I/O for several scanners Preprocessing of raw data for scatter correction Homepage: https://itk.org Keyword:bio

ruby tools 2.7.1, 2.6.1, 2.3.1

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

rubygems tools 2.3.1

Description: Bundle which contains a collection of popular RubyGems, including ffi, childprocess, json, cabin, backports, arr-pm, clamp, multipart-post, faraday, faraday_middleware, highline, net-http-pipeline, net-http-persistent, multi_json, public_suffix, addressable, gh, launchy, ethon, typhoeus, websocket, pusher-client, diff-lcs, rspec-support, rspec-mocks, rspec-expections, rspec-core, rspec, rack, rack-protection, tilt, sinatra, rack-test, bundler. Homepage: https://rubygems.org Extensions: addressable-2.4.0, arr-pm-0.0.10, backports-3.6.8, bundler-1.15.4, cabin-0.9.0, childprocess-0.5.9, clamp-1.1.1, diff-lcs-1.2.5, ethon-0.10.1, faraday-0.10.0, faraday_middleware-0.10.1, ffi-1.9.14, gh-0.15.0, highline-1.7.8, json-2.0.2, launchy-2.4.3, multi_json-1.12.1, multipart-post-2.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-2.0.4, pusher-client-0.6.2, rack-1.6.5, rack-protection-1.5.3, rack-test-0.6.3, rspec-3.5.0, rspec-core-3.5.4, rspec-expectations-3.5.0, rspec-mocks-3.5.0, rspec-support-3.5.0, sinatra-1.4.7, tilt-2.0.5, typhoeus-0.6.9, websocket-1.2.3 Keyword:tools

rust tools 1.41.0, 1.28.0, 1.47.0, 1.53.0

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

salmon bio 0.11.3

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon Keyword:bio

salmonbeta bio 0.6.0

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 0.7.1, 0.8.0, 0.6.7

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

samblaster bio 0.1.24

Description: samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Homepage: https://github.com/GregoryFaust/samblaster Keyword:bio

samtools bio 1.3.1, 1.13, 1.10, 1.5, 0.1.20

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 1.1.1, 1.3.13

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, 2.0.2

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 2019b, 2017b, 2019a, 2021a, 2018b, 2020a, 2020b

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/2.7, python/3.6, python/3.7, python/3.8 Extensions: arff-0.9, asn1crypto-0.24.0, attrs-19.3.0, backports-abc-0.5, backports.functools-lru-cache-1.6.1, backports.os-0.1.1, backports.shutil-get-terminal-size-1.0.0, bcrypt-3.1.7, bitstring-3.1.7, bleach-3.1.4, blist-1.3.6, certifi-2020.4.5.1, cffi-1.14.0, chardet-3.0.4, cryptography-2.9.2, cycler-0.10.0, Cython-0.29.19, deap-1.3.1, defusedxml-0.6.0, dnspython-1.15.0, ecdsa-0.15, entrypoints-0.3, funcsigs-1.0.2, functools32-3.2.3.post2, future-0.17.1, idna-2.9, importlib-metadata-1.6.0, ipaddress-1.0.23, IPTest-0.1.1, ipywidgets-7.5.1, Jinja2-2.11.2, jsonschema-3.2.0, kiwisolver-1.1.0, lockfile-0.12.2, MarkupSafe-1.1.1, matplotlib-2.2.5, matplotlib-3.2.1, mistune-0.8.4, mock-3.0.5, mock-4.0.2, mpmath-1.1.0, nbconvert-5.6.1, nbformat-4.4.0, nbformat-5.0.6, netaddr-0.7.19, netifaces-0.10.9, nose-1.3.7, notebook-5.7.9, notebook-6.0.3, numpy-1.16.6, numpy-1.18.4, pandas-0.24.2, pandas-1.0.3, pandocfilters-1.4.2, paramiko-2.6.0, path-13.1.0, path.py-11.5.2, path.py-12.4.0, pathlib2-2.3.5, paycheck-1.0.2, pbr-5.4.3, prometheus-client-0.3.1, prometheus-client-0.7.1, pycparser-2.20, PyNaCl-1.2.1, PyNaCl-1.3.0, pyparsing-2.4.7, pyrsistent-0.16.0, pysqlite-2.8.3, pytz-2020.1, requests-2.23.0, scipy-1.2.3, scipy-1.4.1, Send2Trash-1.5.0, simplegeneric-0.8.1, singledispatch-3.4.0.3, subprocess32-3.5.2, sympy-1.5.1, terminado-0.8.3, testpath-0.4.4, urllib3-1.25.9, webencodings-0.5.1, widgetsnbextension-3.5.1, zipp-3.1.0 Keyword:math

scotch math 6.0.4, 6.0.6

Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: http://gforge.inria.fr/projects/scotch/ Keyword:math

scythe - 0.994

Description: Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. Homepage: https://github.com/ucdavis-bioinformatics/scythe URL: https://github.com/ucdavis-bioinformatics/scythe

sdsl - 2.1.1-20191211

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

seexpr vis 2.11

Description: SeExpr is a simple expression language that we use to provide artistic control and customization to our core software. We use it for procedural geometry synthesis, image synthesis, simulation control, and much more. Homepage: https://www.disneyanimation.com/technology/seexpr.html Keyword:vis

seqan-library - 2.4.0, 1.4.2

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

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/

seqtk bio 1.3

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

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

shengbte phys 1.1.1

Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/ Extensions: thirdorder-1.0.2 Keyword:phys

shotmap bio 1.1

Description: Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will: 1. Compared unassembled or assembled metagenomic sequences to a protein family database 2. Calculate metagenome functional abundance and diversity 3. Compare metagenomes using a variety of statistical and ecological tools 4. Identify protein families that differentiate metagenomes using robust statistical tests Shotmap can be run on a multicore computer or can optionally interface with an SGE-configured computing cluste (i.e., a cloud). Shotmap can also optionally manage the information and data associated with this workflow in a relational database. Homepage: https://github.com/sharpton/shotmap Keyword:bio

siesta chem 4.0

Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: http://departments.icmab.es/leem/siesta Keyword:chem

signalp bio 4.1f

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

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/

sip tools 4.19.2

Description: SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. Homepage: http://www.riverbankcomputing.com/software/sip/ Keyword:tools

slepc - 3.14.2

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 - 4.10.1, 4.11.20210226

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/

snappy tools 1.1.3

Description: Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. Homepage: https://github.com/google/snappy Keyword:tools

snpeff bio 4.3t, 5.0

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

soapdenovo2 bio r240

Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Homepage: http://soap.genomics.org.cn/index.html Keyword:bio

sortmerna bio 2.1

Description: SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/ Keyword:bio

spades bio 3.10.1

Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Keyword:bio

spark tools 2.2.1, 2.1.1, 2.4.4, 2.3.0, 2.1.0, 3.0.0, 2.2.0

Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools

sparsehash - 2.0.4

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

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

spglib chem 1.9.9

Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: https://github.com/atztogo/spglib Keyword:chem

sra-toolkit bio 2.9.6, 2.10.8, 2.8.2-1

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

sspace-longread bio 1-1

Description: SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Homepage: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread Keyword:bio

sspace_basic bio 2.1.1

Description: SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension Homepage: https://github.com/nsoranzo/sspace_basic Keyword:bio

stacks bio 1.46, 1.45, 2.53

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: https://catchenlab.life.illinois.edu/stacks/ URL: https://catchenlab.life.illinois.edu/stacks/ Keyword:bio

starccm phys 13.06.012-R8, 16.02.009-R8, 16.02.008-R8, 12.06.011-R8, 11.06.011-R8, 14.06.013-R8, 12.04.011-R8, 15.04.010-R8, 16.04.007-R8, 13.04.010-R8, 14.02.012-R8, 16.06.008-R8, 16.04.012-R8, 14.04.013-R8

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 verison 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 14.06.013, 15.04.010, 14.02.012, 16.04.012, 12.06.011, 16.06.008, 13.04.010, 11.06.011, 16.02.008, 14.04.013, 16.02.009, 13.06.012, 16.04.007, 12.04.011

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

su2 math 5.0.0, 6.0.1

Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu Keyword:math

subread bio 1.5.2

Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ Keyword:bio

suitesparse math 4.5.4, 5.7.1

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

sumaclust bio 1.0.20

Description: SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Homepage: http://metabarcoding.org/sumatra Keyword:bio

superlu math 5.1.1

Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. - Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math

supernova bio 2.1.1, 2.0.0

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

swig - 4.0.1, 3.0.12

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/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0

tabix bio 0.2.6

Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net Keyword:bio

taxonkit - 0.6.2

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 2018_U5, 2020.2, 2017.2.132

Description: Intel Threading Building Blocks 2017 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. Homepage: http://software.intel.com/en-us/articles/intel-tbb/ Keyword:tools

tcl tools 8.5.19, 8.6.8

Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools

tensorrt - 6.0.1.5

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/3.6.3 (default), python/3.7.4

tktable tools 2.10

Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877 Keyword:tools

tmhmm bio 2.0c

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

tophat bio 2.1.1

Description: TopHat is a fast splice junction mapper for RNA-Seq reads. Homepage: http://ccb.jhu.edu/software/tophat/ Keyword:bio

torch ai 20170530, 20170731

Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai

trans-abyss bio 1.5.5

Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio

transdecoder bio 3.0.1, 5.5.0

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

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

trf bio 4.09

Description: Tandem repeats finder: a program to analyze DNA sequences. Legacy version. Homepage: https://tandem.bu.edu/trf/trf.html Keyword:bio

trilinos tools 12.10.1

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: http://trilinos.sandia.gov/ Keyword:tools

trimal bio 1.4

Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ Keyword:bio

trimmomatic bio 0.36, 0.39

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

trinity bio 2.4.0

Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. - Homepage: http://trinityrnaseq.github.io/ Keyword:bio

trinotate bio 3.0.2

Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ Keyword:bio

ucx - 1.9.0, 1.5.2, 1.8.0

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 2.2.24, 2.2.26

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, 2.3.7

Description: unixODBC provides a uniform interface between application and database driver Homepage: https://www.unixodbc.org URL: https://www.unixodbc.org

valgrind-mpi tools 3.13.0

Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org/downloads/ Keyword:tools

varscan - 2.4.2, 2.4.1

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

vault - 1.0.3

Description: Manage Secrets and Protect Sensitive Data Secure, store and tightly control access to tokens, passwords, certificates, encryption keys for protecting secrets and other sensitive data using a UI, CLI, or HTTP API. Homepage: https://www.vaultproject.io/

vcftools bio 0.1.14

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 Keyword:bio

verifybamid bio 1.1.3

Description: verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps. Homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html Keyword:bio

viennacl math 1.7.1

Description: ViennaCL is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports CUDA, OpenCL, and OpenMP (including switches at runtime). Homepage: http://viennacl.sourceforge.net/ Keyword:math

visit vis 2.13.3

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

vmd vis 1.9.3

Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: http://www.ks.uiuc.edu/Research/vmd Keyword:vis

voro++ math 0.4.6

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++/ Keyword:math

vsearch bio 2.4.3

Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio

vtk vis 6.3.0, 8.0.0

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: http://www.vtk.org Keyword:vis

vtune tools 2018.3, 2020.1, 2019.3

Description: Intel VTune Profiler is a performance analysis tool for C, C++, C#, Fortran, Java, Python, Go, DPC++, and OpenCL. Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html Keyword:tools

wildmagic - 5.0

Description: Geometric Tools Wild Magic is a C++ library for real-time computer graphics and physics, mathematics, geometry, numerical analysis, and image analysis. Homepage: https://www.geometrictools.com/ URL: https://www.geometrictools.com/

wps geo 3.8.0, 3.8.1

Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo

wrf geo 3.8.0, 3.8.1

Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo

wrf-fire geo 20170625

Description: WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method. Homepage: http://www.openwfm.org/wiki/WRF-SFIRE Keyword:geo

xcrysden vis 1.5.60

Description: XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Homepage: http://www.xcrysden.org/ URL: http://www.xcrysden.org/ Keyword:vis

xerces-c++ tools 3.1.1

Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. Homepage: http://xerces.apache.org/xerces-c/ Keyword:tools

xml-libxml - 2.0205

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

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

yaxt tools 0.9.0, 0.5.1, 0.9.1

Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools

zeromq tools 4.2.5

Description: ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. Homepage: http://www.zeromq.org/ Keyword:tools