Modules avx2

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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 8.4.4, 8.2.2, 8.10.2, 9.2.2, 9.2.1

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/ URL: http://www.abinit.org/ Keyword:chem

abyss bio 2.2.5, 2.0.2, 1.5.2, 1.9.0, 2.2.4, 2.1.5, 2.2.3

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

actc - 1.1

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

adol-c - 2.6.3, 2.7.0

Description: The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C. Homepage: https://projects.coin-or.org/ADOL-C

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 20.3.05, 20180404, 20190312

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

alamode chem 1.0.2

Description: ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. The binary alm is multi-threaded (OpenMP), add this command to your SLURM script: export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK Homepage: http://alamode.readthedocs.io/en/latest/index.html Keyword:chem

alberta phys 3.0.3

Description: ALBERTA is an Adaptive multiLevel finite element toolbox using Bisectioning refinement and Error control by Residual Techniques for scientific Applications. Currently, ALBERTA works without problems on Linux PCs, DEC, HP, SGI, and SUN workstations. OpenGL (e.g. Mesa) is a plus, BLAS is a must. ALBERTA is freely distributed for research and education. Homepage: http://www.alberta-fem.de/ Keyword:phys

allpaths-lg bio 52488

Description: ALLPATHS-LG, the new short read genome assembler. Homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/ 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: http://www.almabte.eu/

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

alpscore phys 2.2.0

Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys

amber chem 18.10-18.11, 18.14-18.17, 20.9-20.15

Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem

ambertools - 20

Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber20 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php

ampl-mp - 3.1.0

Description: An open-source library for mathematical programming. Homepage: https://github.com/ampl/mp URL: https://github.com/ampl/mp

angsd bio 0.918, 0.929

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

annovar bio 2017Jul16

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/ 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 2019R2, 2019R3, 16.2.3, 2020R2, 2020R1, 18.2, 2021R1, 18.1, 19.1, 19.2, 17.2

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

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/

ants vis 2.3.2, 2.2.0, 2.3.5

Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: https://stnava.github.io/ANTs/ URL: https://stnava.github.io/ANTs/ Keyword:vis

apbs chem 1.3

Description: APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Homepage: http://www.poissonboltzmann.org/apbs URL: http://www.poissonboltzmann.org/apbs Keyword:chem

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

arcs bio 1.0.6, 1.0.1, 1.2.1, 1.1.1

Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. Homepage: https://github.com/bcgsc/arcs URL: https://github.com/bcgsc/arcs Keyword:bio

argtable tools 2.13

Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ Keyword:tools

arks - 1.0.4

Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. Homepage: https://github.com/bcgsc/arcs URL: https://github.com/bcgsc/arcs

armadillo math 8.500.1, 9.850.1, 7.950.1, 9.900.2

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

arpack-ng math 3.5.0, 3.7.0, 3.4.0

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math

arrayfire - 3.7.3

Description: ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. Homepage: https://arrayfire.com/ URL: https://arrayfire.com/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: arrayfire-3.6.20181017

arrow tools 0.16.0, 0.11.1, 0.17.1, 1.0.0, 2.0.0, 0.8.0, 0.14.1, 0.15.1

Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.7.4 (default), python/3.6.3, python/3.5.4 Keyword:tools

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

aspect - 2.1.0, 2.2.0

Description: ASPECT: Advanced Solver for Problems in Earth's ConvecTion. An extensible code written in C++ to support research in simulating convection in the Earth's mantle and elsewhere to provide the geosciences with a well-documented and extensible code base for their research needs and to create an open, inclusive, participatory community providing users and developers with a state-of-the-art, comprehensive software that performs well while being simple to extend. Homepage: https://aspect.geodynamics.org/ URL: https://aspect.geodynamics.org/

assimp - 4.1.0

Description: Open Asset Import Library (short name: Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner. The most recent version also knows how to export 3d files and is therefore suitable as a general-purpose 3D model converter. Homepage: http://assimp.sourceforge.net/

atom chem 4.2.7_2

Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html URL: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem

atomicrex chem 1.0, 1.0.20181114

Description: atomicrex is a versatile tool for the construction of advanced atomistic models. It is written in C++ and Python. It was primarily developed to fit interatomic potential models. Thanks to its flexible generic structure its application range, however, is much larger. In a general sense, it allows one to develop models that describe a given property as a function of an atomic (or atom-like) configuration. The property in question can be scalar or vectorial in nature, and could represent e.g., total energies and forces, or eventually electronic eigen energies. It thus provides already the basic framework for constructing in the future for example tight binding models. Homepage: http://atomicrex.gitlab.io/atomicrex/ URL: http://atomicrex.gitlab.io/atomicrex/ Keyword:chem

atompaw - 4.1.0.6

Description: AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library. Homepage: http://users.wfu.edu/natalie/papers/pwpaw/man.html URL: http://users.wfu.edu/natalie/papers/pwpaw/man.html

augustus bio 3.3, 3.3.2, 3.3.3, 3.4.0, 3.2.3

Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: https://bioinf.uni-greifswald.de/augustus/ URL: https://bioinf.uni-greifswald.de/augustus/ Keyword:bio

autodock_vina - 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

bamm bio 2.5.0

Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/ Keyword:bio

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, 1.0.14

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

barrnap - 0.9

Description: Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new nhmmer tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. Homepage: https://github.com/tseemann/barrnap URL: https://github.com/tseemann/barrnap

bayesass bio 3.0.4

Description: BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes Homepage: http://www.rannala.org/?page_id=245 URL: http://www.rannala.org/?page_id=245 Keyword:bio

bayesass3-snps - 1.1

Description: Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols. This is an enhancement of the code produced by the Rannala Research Group: http://www.rannala.org/inference-of-recent-migration Most changes will not be obvious to the average user. However, the most important changes will now allow the user to input large SNP datasets that previously would have caused BayesAss to crash with a "segmentation fault" error. The upper limit of 420 loci has been removed. Homepage: https://github.com/stevemussmann/BayesAss3-SNPs URL: https://github.com/stevemussmann/BayesAss3-SNPs

bayescan bio 2.1

Description: BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. Homepage: http://cmpg.unibe.ch/software/BayeScan/ Keyword:bio

baypass bio 2.1

Description: The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics). Homepage: http://www1.montpellier.inra.fr/CBGP/software/baypass/ URL: http://www1.montpellier.inra.fr/CBGP/software/baypass/ 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 37.78, 37.36, 37.93, 38.44, 38.86

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 1.9, 1.4, 1.10.2, 1.11, 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

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 Keyword:bio

beagle-lib bio 2.1.2, 3.1.1, 3.1.2

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 BEAST 2.6.2, 2.4.0, 2.5.2, 1.8.2, 2.6.0, 2.6.3, 2.5.1

Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. - CC-Wiki: BEAST Homepage: http://beast2.org/ URL: http://beast2.org/ Keyword:bio

bedops - 2.4.35

Description: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. Homepage: http://bedops.readthedocs.io/en/latest/index.html URL: http://bedops.readthedocs.io/en/latest/index.html

bedtools bio 2.27.1, 2.26.0, 2.29.2, 2.28.0

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 URL: 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

berkeleygw phys 1.2.0, 2.1.0

Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org URL: http://www.berkeleygw.org Keyword:phys

bgcdist - 1.03

Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/ URL: https://sites.google.com/site/bgcsoftware/

bgen - 1.1.4

Description: Reference implementation of the bgen format Homepage: https://bitbucket.org/gavinband/bgen/src/default/ URL: https://bitbucket.org/gavinband/bgen/src/default/

bigdft chem 1.7.6, 1.8.3

Description: BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. Homepage: http://bigdft.org/Wiki/index.php?title=BigDFT_website URL: http://bigdft.org/Wiki/index.php?title=BigDFT_website Keyword:chem

biobloomtools - 2.3.2, 2.3.2-20200731

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, 1.7.1, 1.7.7

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

bismark - 0.22.1

Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

blacs math 1.1

Description: The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. Homepage: http://www.netlib.org/blacs/ URL: http://www.netlib.org/blacs/ Keyword:math

blasr bio 5.3.0, 5.3.3, 1.3.1

Description: BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. Homepage: https://github.com/PacificBiosciences/blasr Keyword:bio

blasr_libcpp bio 5.3.4, 20170426

Description: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences Homepage: https://github.com/PacificBiosciences/blasr_libcpp URL: https://github.com/PacificBiosciences/blasr_libcpp Keyword:bio

blast - 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/

blast+ bio 2.10.1, 2.11.0, 2.9.0, 2.4.0, 2.10.0, 2.6.0, 2.8.1, 2.7.1

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

blender vis 2.92.0, 2.79b

Description: Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. Homepage: https://www.blender.org/ URL: https://www.blender.org/ Compatible modules: python/3.7, python/3.8 Keyword:vis

blitz++ tools 1.0.1, 0.10

Description: Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface Homepage: https://github.com/blitzpp/blitz/ Keyword:tools

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

boltztrap - 1.2.5

Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ URL: http://www.icams.de/content/departments/cmat/boltztrap/

boost tools 1.60.0, 1.65.1, 1.63.0, 1.54.0, 1.68.0, 1.72.0, 1.66.0

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 1.65.1, 1.72.0, 1.60.0, 1.68.0

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 2.3.4.3, 2.3.0, 2.3.5.1, 2.3.4.1, 2.2.9, 2.3.3.1

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

bpp-core bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bpp-phyl bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bpp-phyl-omics bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bpp-popgen bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bpp-seq bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bpp-seq-omics bio 2.4.0

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio

bracken - 2.5

Description: Bracken is a companion program to Kraken 1.0 or Kraken 2.0. While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). Homepage: http://ccb.jhu.edu/software/bracken/index.shtml URL: http://ccb.jhu.edu/software/bracken/index.shtml

breakdancer bio 1.4.5

Description: BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads Homepage: http://gmt.genome.wustl.edu/packages/breakdancer Keyword:bio

breseq - 0.33.2

Description: breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. Homepage: https://github.com/barricklab/breseq

bufrlib geo 11.3.0.2, 10.2.3

Description: NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself. Homepage: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB URL: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB Keyword:geo

bullet - 2.89, 2.88

Description: Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics. Homepage: http://bulletphysics.org/ URL: http://bulletphysics.org/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: pybullet-2.9.8

busco bio 3.0.2

Description: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Homepage: http://busco.ezlab.org/ Keyword:bio

bustools - 0.40.0, 0.39.2

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, 0.7.17

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

cadmesh - 1.1

Description: Importing predefined CAD models into GEANT4 is not always possible or requires intermediate file format conversion to Geometry Description Markup Language (GDML) using commercial or third party software. CADMesh is a direct CAD model import interface for GEANT4 leveraging ASSIMP for reading the CAD files. Homepage: https://github.com/christopherpoole/CADMesh

caffe ai 1.0

Description: Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. Homepage: https://github.com/BVLC/caffe Keyword:ai

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

cantera - 2.4.0

Description: Chemical kinetics, thermodynamics, and transport tool suite Homepage: https://github.com/Cantera/cantera URL: https://github.com/Cantera/cantera Compatible modules: python/3.6, python/3.7, python/3.8

canu bio 1.9, 1.8, 1.7, 1.7.1, 1.6, 2.0, 1.5

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

casm chem 0.2.1

Description: CASM is an open source software package designed to perform first-principles statistical mechanical studies of multi-component crystalline solids. CASM interfaces with first-principles electronic structure codes, automates the construction and parameterization of effective Hamiltonians and subsequently builds highly optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of freedom in crystalline solids. This includes cluster expansions for configurational disorder in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational degrees of freedom involved in structural phase transitions. Homepage: https://github.com/prisms-center/CASMcode Keyword:chem

casper bio 0.8.2

Description: CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads. Homepage: http://best.snu.ac.kr/casper/ URL: http://best.snu.ac.kr/casper/ 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

ccfits vis 2.5

Description: CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/CCfits/ Keyword:vis

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 4.6.8, 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/ Keyword:bio

cdo geo 1.7.2, 1.9.8, 1.9.5

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

cegma - 2.5

Description: CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. We use the KOGs database to build a set of these highly conserved ubiquitous proteins. We define a set of 458 core proteins, and the protocol, CEGMA, to find orthologs of the core proteins in new genomes and to determine their exon-intron structures. The procedure uses information from the core genes of six model organisms by first using TBLASTN to identify candidate regions in a new genome. It then proposes and redefines gene structures using a iterative combination of GeneWise, HMMER and geneid. The system includes the use of a profile for each core gene to ensure the reliability of the final predicted gene structure. CEGMA source code, compiled binaries and documentation are available under the GNU GENERAL PUBLIC LICENSE. Homepage: https://github.com/KorfLab/CEGMA_v2 URL: https://github.com/KorfLab/CEGMA_v2

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, 1.0.4-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, 1.2.2

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/

ceres-solver - 1.14.0

Description: Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010. Ceres Solver can solve two kinds of problems: - Non-linear Least Squares problems with bounds constraints. - General unconstrained optimization problems. Homepage: https://ceres-solver.googlesource.com/ceres-solver/ URL: https://ceres-solver.googlesource.com/ceres-solver/

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/

cfdem - 3.8.0

Description: CFDEM coupling provides an open source parallel coupled CFD-DEM framework combining the strengths of LIGGGHTS DEM code and the Open Source CFD package OpenFOAM(*) Homepage: https://www.cfdem.com/

cfitsio vis 3.48, 3.42

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

cfour chem 2.1

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

cfour-mpi chem 1.0, 2.1

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

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, 4.1.0, 4.1.2, 3.4.1

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/ URL: https://cgns.github.io/ Keyword:phys

chaiscript - 6.1.0

Description: ChaiScript is one of the only embedded scripting language designed from the ground up to directly target C++ and take advantage of modern C++ development techniques, working with the developer how they would expect it to work. Being a native C++ application, it has some advantages over existing embedded scripting languages: - It uses a header-only approach, which makes it easy to integrate with existing projects. - It maintains type safety between your C++ application and the user scripts. - It supports a variety of C++ techniques including callbacks, overloaded functions, class methods, and stl containers. Homepage: http://chaiscript.com/

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

chemps2 chem 1.8.9

Description: CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. Homepage: https://github.com/SebWouters/CheMPS2 URL: https://github.com/SebWouters/CheMPS2 Keyword:chem

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, 2.4.1.3, 2.4.1.0, 2.4.1.2, 2.1.3.1, 2.3.4.3

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

clustal-omega bio 1.2.4

Description: Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Homepage: http://www.clustal.org/omega/ URL: http://www.clustal.org/omega/ Keyword:bio

cmake tools 3.16.3, 3.18.4, 3.12.3

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, 0.4.1

Description: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing Homepage: https://github.com/abyzovlab/CNVnator URL: https://github.com/abyzovlab/CNVnator Keyword:bio

code-server - 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

colmap - 3.5, 3.6

Description: COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for reconstruction of ordered and unordered image collections. The software is licensed under the new BSD license. Homepage: https://github.com/colmap/colmap URL: https://github.com/colmap/colmap

combblas - 1.6.2

Description: The Combinatorial BLAS (CombBLAS) is an extensible distributed-memory parallel graph library offering a small but powerful set of linear algebra primitives specifically targeting graph analytics. Homepage: https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/

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 1.07, 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, 5.1, 6.1, 7.1

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: https://www.cp2k.org/ URL: https://www.cp2k.org/ Keyword:chem

cpmd chem 3.17.1, 4.3

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 URL: http://cpmd.org Keyword:chem

cppunit tools 1.12.1

Description: CppUnit is the C++ port of the famous JUnit framework for unit testing. Homepage: http://sourceforge.net/projects/cppunit/ Keyword:tools

crest - 2.10.1

Description: Conformer-Rotamer Ensemble Sampling Tool Homepage: https://github.com/grimme-lab/crest URL: https://github.com/grimme-lab/crest

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

cslib - 20180813, 13Aug18

Description: The client/server model is a messaging paradigm, used ubiquitously by web-based applications, where one or more clients (e.g. your phone) communicate with a server (e.g. a website). In the context of the CSlib, it can used to couple two scientific applications (apps) together where one app acts as the client and the other as the server. The client sends messages to the server requesting it perform specific computations and return the results. Homepage: https://cslib.sandia.gov/index.html URL: https://cslib.sandia.gov/index.html

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

ctffind chem 4.1.8, 4.1.10

Description: program for finding CTFs of electron micrographs Homepage: http://grigoriefflab.janelia.org/ctffind4 Keyword:chem

cuda tools 11.0, 7.5.18, 10.0.130, 10.1, 10.2, 8.0.44, 9.2.148, 9.0.176

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

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

cwp_su geo 44R11

Description: Seismic Unix is a seismic processing and research environment developed at the Center for Wave Phenomena. Homepage: http://www.cwp.mines.edu/cwpcodes/ Keyword:geo

dakota tools 6.8, 6.13

Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools

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

dalton chem 2017-alpha, 2020, 2018

Description: The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements.. Homepage: http://daltonprogram.org/ URL: http://daltonprogram.org/ Keyword:chem

damask - 2.0.3

Description: DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of elastoplastic boundary value problems along with damage and thermal physics. Homepage: https://damask.mpie.de/Home/WebHome URL: https://damask.mpie.de/Home/WebHome

dcm2niix bio 1.0.20200331, 1.0.20180622

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, 9.2.0, 8.4.2, 9.0.1

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/ URL: http://www.dealii.org/ Keyword:math

dealii-petsc 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/ URL: http://www.dealii.org/ Keyword:math

delft3d - 62441, 7565

Description: Delft3D is a powerful modelling suite focusing primarily on coastal, estuarine, river, rural and urban environments Delft3D FM Suite can simulate storm surges, hurricanes, tsunamis, detailed flows and water levels, waves, sediment transport and morphology, water quality and ecology, and is capable of handling the interactions between these processes. Homepage: https://svn.oss.deltares.nl URL: https://svn.oss.deltares.nl

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

demon2k chem 4.4.4

Description: deMon (density of Montreal) is a software package for density functional theory (DFT) [1-3] calculations. It uses the linear combination of Gaussian-type orbital (LCGTO) approach for the self-consistent solution of the Kohn-Sham (KS) DFT equations. The calculation of the four-center electron repulsion integrals is avoided by introducing an auxiliary function basis for the variational fitting of the Coulomb potential [4-6]. Homepage: http://www.demon-software.com/public_html/index.html Keyword:chem

detonate bio 1.11

Description: DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences. Homepage: http://deweylab.biostat.wisc.edu/detonate/ Keyword:bio

dftbplus - 19.1, 18.2

Description: DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. Homepage: https://www.dftb-plus.info URL: https://www.dftb-plus.info

dftd3-lib - 0.9

Description: This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. Homepage: https://github.com/dftbplus/dftd3-lib URL: https://github.com/dftbplus/dftd3-lib

diamond bio 0.9.8, 0.9.14, 0.8.38, 0.9.32, 0.9.22, 2.0.2

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

discosnp bio 2.3.X

Description: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is needed. Homepage: https://github.com/GATB/DiscoSnp Keyword:bio

discovardenovo bio 52488

Description: DISCOVAR de novo is a short read genome assembly developed by the Broad Institute. It can generate high quality assemblies from the latest 250 base Illumina paired-end PCR-free fragment read' Homepage: https://software.broadinstitute.org/software/discovar/blog/?page_id=98 Keyword:bio

dl_poly4 chem 4.10.0, 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 URL: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem

dmalloc tools 5.5.2

Description: The debug memory allocation or dmalloc library has been designed as a drop in replacement for the system s malloc, realloc, calloc, free and other memory management routines while providing powerful debugging facilities configurable at runtime. These facilities include such things as memory-leak tracking, fence-post write detection, file/line number reporting, and general logging of statistics. The library is reasonably portable having been run successfully on at least the following operating systems: AIX, BSD/OS, DG/UX, Free/Net/OpenBSD, GNU/Hurd, HPUX, Irix, Linux, MS-DOG, NeXT, OSF, SCO, Solaris, SunOS, Ultrix, Unixware, Windoze, and even Unicos on a Cray T3E. It also provides support for the debugging of threaded programs. The package includes the library, configuration scripts, debug utility application, test program, and documentation. Homepage: http://dmalloc.com/ URL: http://dmalloc.com/ Keyword:tools

dotnet-core - 3.0.0, 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

dssp - 2.3.0

Description: The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. If you use DSSP, please quote these two articles: 1) A series of PDB related databases for everyday needs. Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Research 2015 January; 43(Database issue): D364-D368. 2) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824. Homepage: https://swift.cmbi.umcn.nl/gv/dssp/ URL: https://swift.cmbi.umcn.nl/gv/dssp/

dtiprep bio 1.2.9

Description: DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. Homepage: https://www.nitrc.org/projects/dtiprep/ Keyword:bio

eccodes geo 2.15.0, 2.18.0, 2.8.2, 2.19.0

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 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

eems bio 20171011

Description: This repository contains an implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples. EEMS uses the concept of effective migration to model the relationship between genetics and geography, and it outputs an estimated effective migration surface (hence, EEMS) - a visual representation of population structure that can highlight potential regions of higher-than-average and lower-than-average historic gene flow. Homepage: https://github.com/dipetkov/eems Keyword:bio

eigen math 3.2.2, 3.3.7, 3.2.10, 3.3.2, 3.3.5

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

eigensoft bio 7.2.1

Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Homepage: http://www.hsph.harvard.edu/alkes-price/software/ URL: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio

elixir tools 1.5

Description: Elixir is a dynamic, functional language designed for building scalable and maintainable applications. Homepage: https://elixir-lang.org/ Keyword:tools

elk chem 5.2.10, 5.2.14

Description: An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universitt Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. Homepage: http://elk.sourceforge.net/ Keyword:chem

elmerfem - scc20, 9.0, 8.4

Description: Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After it's open source publication in 2005, the use and development of Elmer has become international. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). Homepage: https://www.csc.fi/web/elmer URL: https://www.csc.fi/web/elmer

elpa math 2018.11.001, 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

elsi - 2.2.1

Description: ELSI: ELectronic Structure Infrastructure is a software bundle and unified interface for methods that solve or circumvent eigenvalue problems in the self-consistent field cycle of density-functional theory. Homepage: https://wordpress.elsi-interchange.org/

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: http://emboss.sourceforge.net/ Keyword:bio

embree - 3.11.0

Description: Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. Homepage: https://github.com/embree/embree URL: https://github.com/embree/embree

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

epacts - 3.4.2

Description: EPACTS - Efficient and Parallelizable Association Container Toolbox Homepage: https://github.com/statgen/EPACTS URL: https://github.com/statgen/EPACTS

erds bio 1.1

Description: ERDS is an open-source software free to academia and nor-profit organization, designed for inferring copy number variants (CNVs) in high-coverage human genomes using next generation sequence (NGS) data. When a CNV presents in a test genome, multiple signatures, weak or strong, would present in the alignment data. ERDS starts from read depth (RD) information, and integrates other information including paired end mapping (PEM) and soft-clip signature to call CNVS sensitively and accurately. Homepage: http://www.utahresearch.org/mingfuzhu/erds/ Keyword:bio

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 7.1.0r, 7.0.1, 8.0.1

Description: The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Homepage: https://www.earthsystemcog.org/projects/esmf/ URL: https://www.earthsystemcog.org/projects/esmf/ Keyword:geo

etsf_io io 1.0.4

Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools Keyword:io

etsf_io-mpi - 1.0.4

Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools

exonerate bio 2.4.0

Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate URL: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Keyword:bio

expat tools 2.2.6, 2.2.9, 2.2.5

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

express - 1.5.1

Description: Streaming quantification for high-throughput sequencing Homepage: https://pachterlab.github.io/eXpress URL: https://pachterlab.github.io/eXpress

faiss - 1.6.2, 1.6.5

Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.6.3, python/3.7.4, python/3.8.0

falcon bio 1.8.8

Description: Falcon: a set of tools for fast aligning long reads for consensus and assembly Homepage: https://github.com/PacificBiosciences/FALCON Extensions: FALCON-1.8.8, networkx-1.10, pypeFLOW-20170504 Keyword:bio

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 36.3.8g, 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

fastani - 1.2, 1.32

Description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Homepage: https://github.com/ParBLiSS/FastANI URL: https://github.com/ParBLiSS/FastANI

fastme bio 2.1.6.1

Description: FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. Homepage: http://www.atgc-montpellier.fr/fastme/ Keyword:bio

fastp bio 0.19.5, 0.20.0, 0.12.4

Description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Homepage: https://github.com/OpenGene/fastp Keyword:bio

fastq_screen bio 0.11.4

Description: FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ 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

fastqtl - 2.184

Description: FastQTL is a QTL mapper Homepage: http://fastqtl.sourceforge.net/ URL: http://fastqtl.sourceforge.net/

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/ Extensions: GD-2.67, GD::Graph-1.43, GD::Text-0.86, PerlIO::gzip-0.20 Keyword:bio

fds - 6.7.5

Description: Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Homepage: https://pages.nist.gov/fds-smv/ URL: https://pages.nist.gov/fds-smv/

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

ferret vis 7.3

Description: Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. Homepage: http://ferret.pmel.noaa.gov/ URL: http://ferret.pmel.noaa.gov/ Keyword:vis

ffmpeg - 4.2.1

Description: A complete, cross-platform solution to record, convert and stream audio and video. Homepage: https://www.ffmpeg.org/ URL: https://www.ffmpeg.org/

fftw math 3.3.8, 3.3.6, 3.3.7, 3.3.4

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, 3.3.8, 2.1.5

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

fgsl - 1.2.0

Description: FGSL: A Fortran interface to the GNU Scientific Library Homepage: https://doku.lrz.de/display/PUBLIC/FGSL+-+A+Fortran+interface+to+the+GNU+Scientific+Library

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 Keyword:bio

fineradstructure - 0.3.2r109

Description: The fineSTRUCTURE package represents a powerful model-based approach to investigating population structure using genetic data. Homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html URL: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

flashpca2 - d891160a

Description: FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA is based on the Spectra library. Homepage: http://www.flapw.de/ URL: http://www.flapw.de/

fleur - MaX-R4

Description: FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory. Homepage: http://www.flapw.de/ URL: http://www.flapw.de/

flexbar - 3.5.0

Description: Flexbar flexible barcode and adapter removal: The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided, e.g. trimming of homopolymers at read ends. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The software supports data in fasta and fastq format from multiple sequencing platforms. Homepage: https://github.com/seqan/flexbar URL: https://github.com/seqan/flexbar

flint math 2.5.2

Description: FLINT is a C library for doing number theory, maintained by William Hart. FLINT supports arithmetic with numbers, polynomials, power series and matrices over many base rings, including: - Multiprecision integers and rationals - Integers modulo n - p-adic numbers - Finite fields (prime and non-prime order) - Real and complex numbers (via the Arb extension library) Homepage: http://www.flintlib.org/ Keyword:math

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/

fpa - nov.23.2016

Description: FPA the four-point aligner Homepage: https://github.com/ariloytynoja/fpa

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

fpocket - 3.1.4.2

Description: fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. Homepage: https://github.com/Discngine/fpocket URL: https://github.com/Discngine/fpocket

fraggenescan bio 1.31, 1.30, 1.19

Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/ URL: http://omics.informatics.indiana.edu/FragGeneScan/ Keyword:bio

frealign chem 9.11

Description: Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Homepage: http://grigoriefflab.janelia.org/frealign Keyword:chem

freebayes bio 1.1.0, 1.2.0

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 1.0.3

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 Keyword:tools

fsl bio 5.0.10, 6.0.3, 5.0.11, 6.0.1, 5.0.9

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio

fusioncatcher bio 0.99.7c-beta

Description: Finder of somatic fusion-genes in RNA-seq data. The database is installed in $EBROOTFUSIONCATCHER/data/current. Homepage: https://github.com/ndaniel/fusioncatcher Keyword:bio

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: http://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

g_mmpbsa chem GROMACS 2016-04-19

Description: G_MMPBSA calculates components of binding energy using MM-PBSA method except the entropic term and energetic contribution of each residue to the binding using energy decomposition scheme. - CC-Wiki: GROMACS Homepage: https://rashmikumari.github.io/g_mmpbsa/ Keyword:chem

ga tools 5.7.2

Description: Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency. I8 version. Homepage: http://hpc.pnl.gov/globalarrays/ URL: http://hpc.pnl.gov/globalarrays/ Keyword:tools

gamess-us chem 20170420-R1, 20180920-R3, 20190630-R1, 2020.2

Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS is built with Intel compilers and IntelMPI. It includes experimental MU CoupledCluster theory code. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem

gapfiller bio 2.1.1

Description: GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. Homepage: https://sourceforge.net/projects/gapfiller Keyword:bio

gate bio 8.2, 8.0

Description: GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography Homepage: http://www.opengatecollaboration.org/ URL: http://www.opengatecollaboration.org/ Keyword:bio

gatk bio 4.0.8.1, 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

gcc tools 5.4.0, 7.3.0, 8.3.0, 9.1.0, 9.3.0, 10.2.0, 6.4.0, 4.9.4, 8.4.0, 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 - 7.3.0, 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/

gcta bio 1.26.0

Description: GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following analyses. Homepage: http://cnsgenomics.com/software/gcta/ URL: http://cnsgenomics.com/software/gcta/ Keyword:bio

gctf chem 1.18, 1.06

Description: Gctf: real-time CTF determination and correction Homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/ Keyword:chem

gdal geo 2.4.1, 2.2.1, 3.0.4, 2.1.3, 3.0.1, 2.2.2

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

gdal-mpi geo 1.10.1, 1.11.5

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/ Keyword:geo

gdcm - 3.0.8

Description: Grassroots DICOM: Cross-platform DICOM implementation Homepage: https://sourceforge.net/projects/gdcm URL: https://sourceforge.net/projects/gdcm

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 10.06, 10.05.p01, 9.6.p04, 10.04.p02, 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/ URL: http://geant4.cern.ch/ Keyword:phys

geant4-seq - 10.05.p01

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/

gemma bio 0.97, 0.98.3

Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio

geneid - 1.4.5

Description: program to predict genic elements as splice sites, exons or genes, along eukaryotic DNA sequences. geneid offers also some rudimentary support to integrate predictions for multiple sources. The program is written in ANSI C, and runs on UNIX operating systems. Installation, setup and usage of geneid is very easy, and there is a range of options to configure output predictions and program behaviour. Homepage: https://github.com/guigolab/geneid URL: https://github.com/guigolab/geneid

genewise - 2.4.1

Description: Package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. It is a collection of algorithms which generally differ from the usualy, **standard** bioinformatics comparison methods. Probably the most used algorithm in Wise2 is **genewise**, which is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment Homepage: http://www.ebi.ac.uk/~birney/wise2 URL: http://www.ebi.ac.uk/~birney/wise2

genometools bio 1.6.1, 1.5.10

Description: The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software. Homepage: https://github.com/genometools/genometools Keyword:bio

geos geo 3.6.1, 3.7.2, 3.4.3, 3.8.1

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

gerris - 20131206

Description: Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow Homepage: http://gfs.sourceforge.net/wiki/index.php/Main_Page URL: http://gfs.sourceforge.net/wiki/index.php/Main_Page

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

glimmerhmm - 3.0.4

Description: GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models. Homepage: https://ccb.jhu.edu/software/glimmerhmm URL: https://ccb.jhu.edu/software/glimmerhmm

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

globalarrays - 5.7.2, 5.8

Description: Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model Homepage: https://hpc.pnl.gov/globalarrays URL: https://hpc.pnl.gov/globalarrays

glost tools 0.3.1

Description: This is GLOST, the Greedy Launcher Of Small Tasks. Homepage: https://github.com/cea-hpc/glost URL: https://github.com/cea-hpc/glost Keyword:tools

glpk math 4.65, 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 2018-07-04, 2019-09-12, 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/ URL: 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)

gmsh phys 4.0.7, 3.0.6, 4.7.0

Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys

gmt geo 5.4.2

Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: http://gmt.soest.hawaii.edu/ Keyword:geo

gmtk - 1.4.4

Description: GMTK: The Graphical Models Toolkit Homepage: http://melodi.ee.washington.edu/ URL: http://melodi.ee.washington.edu/

gnuplot vis 5.2.5, 5.2.2

Description: Portable interactive, function plotting utility Homepage: 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

googletest tools 1.8.0

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

gossamer bio 0.1

Description: Gossamer bioinformatics suite Homepage: https://github.com/data61/gossamer Keyword:bio

gptl - 8.0.2

Description: General Purpose Timing Library Homepage: https://github.com/jmrosinski/GPTL URL: https://github.com/jmrosinski/GPTL

grace vis 5.99.0, 5.1.25

Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace URL: http://freecode.com/projects/grace Keyword:vis

grackle phys 2.1, 3.1

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

graph-tool - 2.37

Description: Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. Homepage: https://graph-tool.skewed.de/ URL: https://graph-tool.skewed.de/ Compatible modules: python/3.6, python/3.7, python/3.8

grass geo 7.4.0, 7.8.4

Description: GRASS: Geographic Resources Analysis Support System, commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. Homepage: https://grass.osgeo.org/download/software/sources/ URL: https://grass.osgeo.org/download/software/sources/ Keyword:geo

grib_api - 1.28.0

Description: The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages. Homepage: https://software.ecmwf.int/wiki/display/GRIB/Home

grnboost bio 20171009

Description: GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. Inferring a gene regulatory network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology. GRNBoost was inspired by GENIE3, a popular algorithm for GRN inference. GENIE3 breaks up the inference problem into a number of tree-based ensemble (Random Forest) nonlinear regressions, building a predictive model for the expression profile of each gene in the dataset in function of the expression profiles of a collection of candidate regulatory genes (transcription factors). The regression models act as a feature selection mechanism, they yield the most predictive regulators for the target genes as candidate links in the resulting gene regulatory network.. Homepage: https://github.com/aertslab/GRNBoost Keyword:bio

gromacs chem GROMACS 2020.4, 2020.2, 2018.3, 2019.6, 2016.3, 4.6.7, 5.1.4, 5.0.7, 5.1.5, 2016.5, 2018.2, 2018.7, 2019.3, 2018.1

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, 4.6.7, 2019.6, 2018.1, 2019.5

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 URL: http://www.gromacs.org Keyword:chem

gsl math 2.6, 1.16, 2.3, 2.2.1, 2.5, 2.4

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

gts - 0.7.6

Description: GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Homepage: http://gts.sourceforge.net/ URL: http://gts.sourceforge.net/

gudhi - 3.4.1

Description: The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology. The library comes with data sets, demos, examples and test suites. Homepage: https://gudhi.inria.fr/ URL: https://gudhi.inria.fr/ Compatible modules: python/3.6, python/3.7, python/3.8

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 - 9.0.2, 9.1.0, 9.0.1, 8.1.1, 9.0.3

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: http://www.gurobi.com URL: http://www.gurobi.com

h4toh5 io 2.2.2, 2.2.5

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/ URL: http://www.hdfgroup.org/h4toh5/ Keyword:io

hal bio 20180814

Description: Hierarchical Alignment (HAL) is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. Homepage: https://github.com/ComparativeGenomicsToolkit/hal Keyword:bio

hapgen2 - 2.2.0
harminv math 1.4

Description: Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. Homepage: http://ab-initio.mit.edu/wiki/index.php/Harminv Keyword:math

hdf io 4.2.12

Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: http://www.hdfgroup.org/products/hdf4/ Keyword:io

hdf-eos5 - 5.1.16

Description: HDF is the prescribed format for standard data products that are derived from EOS missions. HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self-describing file format for transfer of various types of data between different machines based upon HDF. HDF-EOS is a standard format to store data collected from EOS satellites: Terra, Aqua and Aura. Two versions of HDF-EOS libraries: HDF-EOS2 (v2.20) based on HDF4 and HDF-EOS5 (v5.1.16) based on HDF5 are developed. Homepage: https://hdfeos.org URL: https://hdfeos.org

hdf5 io 1.10.6, 1.8.18, 1.8.20, 1.10.3, 1.10.5, 1.8.22, 1.10.1, 1.8.21

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 1.8.18, 1.10.6, 1.10.3

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, 6.22.1

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 3.0-beta.3, 2.0.16

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: http://en.wikipedia.org/wiki/HH-suite Keyword:bio

hisat2 bio 2.2.0, 2.1.0

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, 3.2.1, 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/ URL: http://hmmer.org/ Keyword:bio

hoomd-blue - 2.9.3

Description: HOOMD-blue is a general-purpose particle simulation toolkit for both GPUs and CPUs, with a Python interface. Homepage: http://glotzerlab.engin.umich.edu/hoomd-blue/ URL: http://glotzerlab.engin.umich.edu/hoomd-blue/

hpl tools 2.2, 2.3

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: https://www.netlib.org/benchmark/hpl/ URL: https://www.netlib.org/benchmark/hpl/ Keyword:tools

htslib bio 1.5, 1.9, 1.4

Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix - Homepage: http://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/

hyphy bio 2.3.14, 2.5.26, 2.3.13

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

hypre math 2.15.1, 2.10.0b, 2.20.0

Description: Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. Homepage: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods URL: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods Keyword:math

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/

idba-ud - 1.1.3

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

igblast bio 1.16.0, 1.8.0, 1.17.0, 1.9.0, 1.7.0

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/

ima3 - 20210120

Description: IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models. For a given phylogenetic tree IMa3 addresses the same model as IMa2. Like IMa2-p, IMa3 can run on multiple processors. Homepage: https://github.com/jodyhey/IMa3 URL: https://github.com/jodyhey/IMa3

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, 2018.1.163, 2019.2.187, 11.3.4.258, 2020.1.217, 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, 2018.3.222

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, 1.0.2, 1.1.3

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 2014.6, 2020.1.217, 2018.3, 2017.5, 2019.3, 2017.1, 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/ Keyword:tools

intelmpi mpi 2018.3.222, 2019.3.199, 2019.7.217

Description: Intel MPI Library, compatible with MPICH ABI. Note: like Open MPI, this module's mpicc calls the toolchain compiler. mpiicc calls icc, and mpigcc calls gcc, and similar for C++ and Fortran. Homepage: http://software.intel.com/en-us/intel-mpi-library/

interproscan bio 5.50-84.0, 5.40-77.0, 5.23-62.0

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

ioapi - 3.2-2020111

Description: The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems. Homepage: https://www.cmascenter.org/ioapi/ URL: https://www.cmascenter.org/ioapi/

ipopt - 3.12.13

Description: IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. Homepage: https://projects.coin-or.org/Ipopt URL: https://projects.coin-or.org/Ipopt

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

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

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

iq-tree bio 1.6.12, 1.5.5, 2.0.7

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

irfinder - 1.2.6, 1.2.5

Description: Basic STAR (Spliced Transcripts Alignment to a Reference) STAR workflow consists of 2 steps: Generating genoms indexes files and mapping reads to the genomes. Homepage: https://github.com/williamritchie/IRFinder/ URL: https://github.com/williamritchie/IRFinder/ Extensions: Data::Dumper-2.173

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 5.0.1, 4.12.2, 4.13.1, 4.13.3

Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis

jags math 4.3.0, 4.2.0

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

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: http://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis

java tools 13.0.2, 13.0.1, 1.7.0_80, 1.8.0_121, 1.8.0_192, 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

jdftx chem 1.4.2

Description: JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. It is distributed under the GPL license (version 3 or higher) and publications resulting from its use must cite: R. Sundararaman, K. Letchworth-Weaver, K.A. Schwarz, D. Gunceler, Y. Ozhabes and T.A. Arias, 'JDFTx: software for joint density-functional theory Homepage: http://jdftx.org/index.html Keyword:chem

jellyfish bio 2.3.0, 2.2.6, 2.2.10, 1.1.11

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

julia tools 1.1.1, 1.2.0, 0.5.1, 1.3.0, 1.4.1, 0.6.0, 0.6.2, 1.0.0, 1.4.0, 1.0.2, 1.1.0

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

kaiju bio 1.7.4, 1.6.2

Description: Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Homepage: http://kaiju.binf.ku.dk/ URL: http://kaiju.binf.ku.dk/ Keyword:bio

kallisto bio 0.44.0, 0.46.0, 0.45.0, 0.46.1

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: https://pachterlab.github.io/kallisto/ URL: https://pachterlab.github.io/kallisto/ Keyword:bio

kentutils bio 20180716

Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ URL: http://genome.cse.ucsc.edu/ Keyword:bio

kim chem 1.8.2, 1.9.7, 2.1.3

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/ URL: 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/

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/

kokkos tools 2.7.24

Description: Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources. It currently can use OpenMP, Pthreads and CUDA as backend programming models. Homepage: https://github.com/kokkos/ Keyword:tools

kraken bio 1.1, 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

kraken2 bio 2.0.8-beta, 2.0.7-beta, 2.1.1

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/ URL: 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, 20190807, 20181212, 20201029

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

lammps-user-intel 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-VTK, -QEQ, -USER-ATC, -MANYBODY Homepage: http://lammps.sandia.gov/ Keyword:chem

last bio 1145, 959

Description: LAST finds similar regions between sequences. Homepage: http://last.cbrc.jp/ URL: http://last.cbrc.jp/ Keyword:bio

lastz - 1.04.03

Description: LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. Homepage: https://www.bx.psu.edu/~rsharris/lastz/ URL: https://www.bx.psu.edu/~rsharris/lastz/

latte chem 1.2.1

Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE URL: https://github.com/lanl/LATTE Keyword:chem

leveldb tools 1.20, 1.18

Description: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. Homepage: https://github.com/google/leveldb Keyword:tools

libbeef - 0.1.2

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: https://github.com/vossjo/libbeef URL: https://github.com/vossjo/libbeef

libcerf math 1.5

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: http://apps.jcns.fz-juelich.de/src/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

libctl tools 3.2.2

Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations. Homepage: http://ab-initio.mit.edu/libctl Keyword:tools

libevent - 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

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 2.2.5

Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/ Keyword:vis

libgeotiff - 1.5.1

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, 0.7.5

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

libgridxc chem 0.8.0

Description: A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. Homepage: https://launchpad.net/libgridxc URL: https://launchpad.net/libgridxc Keyword:chem

libgridxc-mpi - 0.8.0

Description: A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. Homepage: https://launchpad.net/libgridxc URL: https://launchpad.net/libgridxc

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: http://libharu.org/ URL: http://libharu.org/

libint chem 2.6.0, 1.1.6, 2.2.0, 2.4.2, 2.3.1, 2.0.3

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

libmatheval math 1.1.11

Description: GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. Homepage: http://www.gnu.org/software/libmatheval/ Keyword:math

libmaus2 bio 2.0.499

Description: libmaus2 is a collection of data structures and algorithms. Homepage: https://github.com/gt1/libmaus2 URL: https://github.com/gt1/libmaus2 Keyword:bio

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

libomm - 2015-06-05

Description: libOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. Homepage: https://bazaar.launchpad.net/~libomm-team/libomm/trunk/

libplinkio bio 0.9.5

Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio Keyword:bio

libpsml - 1.1.8

Description: LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. Homepage: https://launchpad.net/libpsml URL: https://launchpad.net/libpsml

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/

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: http://libspatialindex.github.io Keyword:phys

libspatialite phys 4.3.0a

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 Keyword:phys

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/

libtricubic math 1.0

Description: Library implementing tricubic interpolation. Homepage: https://github.com/nbigaouette/libtricubic Keyword:math

libxc chem 3.0.0, 4.2.1, 4.2.3, 3.0.1, 5.0.0, 4.3.4, 2.2.1, 2.2.2

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 - 1.1.29

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, 1.8.2, 1.16.1

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

links bio 1.8.6

Description: LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer). Homepage: http://www.bcgsc.ca/platform/bioinfo/software/links URL: http://www.bcgsc.ca/platform/bioinfo/software/links Keyword:bio

lis math 2.0.10

Description: Lis, a Library of Iterative Solvers for linear systems, is a parallel library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. The installation of Lis requires a C compiler. The Fortran interface requires a Fortran compiler, and the algebraic multigrid preconditioner requires a Fortran 90 compiler. For parallel computing environments, an OpenMP or MPI-1 library is used. Both the Harwell-Boeing and Matrix Market formats are supported to import and export user data. Homepage: http://www.netlib.org/misc/lis/ Keyword:math

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 7.0.0, 6.0.1, 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

lobstr bio 4.0.6

Description: lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data. Homepage: http://lobstr.teamerlich.org/ Keyword:bio

locarna bio 1.9.2.1

Description: LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure. Homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ Keyword:bio

lpsolve math 5.5.2.5

Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ URL: https://sourceforge.net/projects/lpsolve/ Keyword:math

ls-dyna phys 12.0, 11.1, 9.2, 9.3, 9.1, 10.2, 10.1, 10.0, 11.0, 7.1.2, 8.1, 7.1.3

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna URL: http://www.lstc.com/products/ls-dyna Keyword:phys

ls-dyna-mpi phys 9.1, 7.1.3, 9.2, 9.3, 7.1.2, 10.1, 11.1, 10.0, 8.1, 12.0

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna URL: http://www.lstc.com/products/ls-dyna Keyword:phys

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

ltr_retriever - 2.9.0

Description: LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations. By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Homepage: https://github.com/oushujun/LTR_retriever URL: https://github.com/oushujun/LTR_retriever

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

maffilter - 2020.11

Description: Genome Alignment Processor Homepage: https://jydu.github.io/maffilter/ URL: https://jydu.github.io/maffilter/

mafft bio 7.310, 7.397

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

mafft-mpi - 7.471

Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences), etc. Homepage: https://mafft.cbrc.jp/alignment/software/source.html URL: https://mafft.cbrc.jp/alignment/software/source.html

magma math 2.4.0, 2.5.4, 2.2.0, 2.5.0

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

maker bio 3.01.03, 2.31.9, 2.31.10

Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. Homepage: http://www.yandell-lab.org/software/maker.html URL: http://www.yandell-lab.org/software/maker.html Extensions: Acme::Damn-0.08, Bit::Vector-7.4, DBD::Pg-3.14.2, Devel::Symdump-2.18, forks-0.36, Inline-0.86, Inline::C-0.81, IO::All-0.87, IO::Prompt-0.997004, Pegex-0.75, Perl::Unsafe::Signals-0.03, Sys::SigAction-0.23, YAML::PP-0.026, YAML::XS-0.82 Keyword:bio

manta bio 1.6.0, 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

marginpolish - 1.3.0

Description: MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly. Homepage: https://github.com/UCSC-nanopore-cgl/MarginPolish URL: https://github.com/UCSC-nanopore-cgl/MarginPolish

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/

marvel bio 1.0

Description: MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. Homepage: https://github.com/schloi/MARVEL Keyword:bio

masurca bio 3.2.4, 3.3.0, 3.2.8, 3.2.7, 3.2.6, 3.4.1, 4.0.1

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html URL: http://www.genome.umd.edu/masurca.html Keyword:bio

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, 2020a, 2016b, 2014a, 2017a, 2020b, 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, 2.2.7

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

mcl math 14.137

Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math

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

meep phys 1.3, 1.16.1

Description: Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications. Homepage: https://meep.readthedocs.io/en/latest/ URL: https://meep.readthedocs.io/en/latest/ Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:phys

mefit bio 1.0

Description: MeFiT (Merging and Filtering Tool for Paired-End Reads): This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality. Homepage: https://github.com/nisheth/MeFiT Extensions: HTSeq-0.9.1, pysam-0.14 Keyword:bio

megahit bio 1.2.7, 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 URL: https://github.com/voutcn/megahit Keyword:bio

meme - 5.0.5, 4.11.2, 5.2.0, 5.0.3

Description: The MEME Suite allows you to: - discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, - search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, - compare a motif to all motifs in a database of motifs, - associate motifs with Gene Ontology terms via their putative target genes, - analyse motif enrichment using SpaMo or CentriMo. Homepage: http://meme-suite.org URL: http://meme-suite.org

meraculous bio 2.2.5.1-1-ga103cd6, 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, 18.0.0

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

mesa-astrophysics phys r10108

Description: MESA Modules for Experiments in Stellar Astrophysics, Homepage: http://mesa.sourceforge.net/ Keyword:phys

mesquite math 2.3.0

Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/ Keyword:math

met phys 8.0_bugfix, 9.0.2, 9.1.1

Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: ihttps://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php URL: ihttps://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php Keyword:phys

metabat bio 2.14, 2.12.1

Description: An efficient tool for accurately reconstructing single genomes from complex microbial communities Homepage: https://bitbucket.org/berkeleylab/metabat URL: https://bitbucket.org/berkeleylab/metabat Compatible modules: Keyword:bio

metaeuk - 4-a0f584d

Description: MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homepage: metaeuk.soedinglab.org URL: metaeuk.soedinglab.org

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/

metagenome-atlas - 2.4.3

Description: Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation. Homepage: https://github.com/metagenome-atlas/atlas URL: https://github.com/metagenome-atlas/atlas

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/ URL: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio

metamaps - 2020.03.11

Description: MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality. The approximate mapping algorithm employed by MetaMaps is based on MashMap. MetaMaps adds a mapping quality model and EM-based estimation of sample composition. Homepage: https://github.com/DiltheyLab/MetaMaps URL: https://github.com/DiltheyLab/MetaMaps

metaphlan bio 2.2.0, 2.8

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://github.com/biobakery/MetaPhlAn URL: https://github.com/biobakery/MetaPhlAn Keyword:bio

metaxa2 - 2.2

Description: Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically Homepage: https://microbiology.se/software/metaxa2/ URL: https://microbiology.se/software/metaxa2/

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

mf2005 - 1.12.0

Description: is the U.S. Geological Survey modular finite-difference flow model, which is a computer code that solves the groundwater flow equation. The program is used by hydrogeologists to simulate the flow of groundwater through aquifers. Homepage: https://en.wikipedia.org/wiki/MODFLOW URL: https://en.wikipedia.org/wiki/MODFLOW

mfem phys 3.4

Description: MFEM is a free, lightweight, scalable C++ library for finite element methods. Homepage: http://mfem.org/ Keyword:phys

micmac - 1.0.beta13

Description: MicMac is a photogrammetry software developped at the IGN (French National Geographic Institute) and ENSG (French national school for geographic sciences). This installation also includes ExifTool perl modules. Homepage: https://micmac.ensg.eu/

minc-toolkit bio 1.9.16, 1.9.18.1

Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/ URL: http://bic-mni.github.io/ Keyword:bio

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

miniasm bio 0.3

Description: Ultrafast de novo assembly for long noisy reads (though having no consensus step). Homepage: https://github.com/lh3/miniasm 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

minimac4 - 1.0.2

Description: Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality. Homepage: https://genome.sph.umich.edu/wiki/Minimac4 URL: https://genome.sph.umich.edu/wiki/Minimac4

minimap2 bio 2.13

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 Keyword:bio

mira bio 4.0.2

Description: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). Homepage: https://sourceforge.net/projects/mira-assembler/ Keyword:bio

mitobim bio 1.9

Description: This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article c an be found [here](http://nar.oxfordjournals.org/content/41/13/e129 "MITObim full article at NAR"). Kindly cite the arti cle if you are using MITObim in your work. Homepage: https://github.com/chrishah/MITObim/ Keyword:bio

mitsuba vis 0.1.1

Description: Mitsuba is a research-oriented rendering system in the style of PBRT, from which it derives much inspiration. It is written in portable C++, implements unbiased as well as biased techniques, and contains heavy optimizations targeted towards current CPU architectures. Mitsuba is extremely modular: it consists of a small set of core libraries and over 100 different plugins that implement functionality ranging from materials and light sources to complete rendering algorithms. Homepage: https://www.mitsuba-renderer.org/index.html Keyword:vis

mixcr bio 3.0.13, 2.1.10, 2.1.5

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, 0.14

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

mmseqs2 - 10-6d92c

Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com

molden chem 5.7, 6.5

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/ URL: http://www.cmbi.ru.nl/molden/ Keyword:chem

mono tools 5.4.0.56, 4.6.2.7, 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/ Keyword:tools

mothur bio 1.40.4, 1.41.3, 1.39.4, 1.41.0, 1.41.1, 1.44.3

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/ URL: http://www.mothur.org/ Keyword:bio

motioncor2 bio 1.0.5

Description: Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. Based on observations that the electron beam induces doming of the thin vitreous ice layer, we developed an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Homepage: http://msg.ucsf.edu/em/software/motioncor2.html Keyword:bio

mpb - 1.11.1

Description: MPB is a software package to compute definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. It can compute optical dispersion relations and eigenstates for structures such as strip waveguides and optical fibers. MPB is well suited for the study of photonic crystals: periodic dielectric structures exhibiting a band gap in their optical modes, prohibiting propagation of light in that frequency range. Homepage: https://mpb.readthedocs.io/en/latest URL: https://mpb.readthedocs.io/en/latest

mpe2 mpi 2.4.9b

Description: MPE is a software package for MPI (Message Passing Interface) programmers. The package provides users with a number of useful tools for their MPI programs. The latest version is called MPE2. Current available tools under MPE2 are the following: 1. A set of profiling libraries to collect information about the behavior of MPI programs. Linking the user MPI program with the libraries will generate logfile for postmortem visualization when the user program is executed. 2. Convenient compiler wrapper, mpecc and mpefc, are provided to compile/link with the related profiled libraries, e.g. "mpecc -mpilog" enables automatic MPI and user-defined MPE logging, "mpecc -mpicheck" enables collective and datatype checking of the user MPI program, and "mpecc -help" shows available options. 3. A SLOG-2 viewer, Jumpshot, for the various logfiles. 4. A set of CLOG-2 and SLOG-2 utilities programs. 5. An MPI collective and datatype checking library. 6. A shared-display parallel X graphics library. 7. A profiling wrapper generator for MPI interface. 8. Routines for sequentializing a section of code being executed in parallel. 9. Debugger setup routines. Homepage: http://www.mcs.anl.gov/research/projects/perfvis/download/index.htm Keyword:mpi

mpfi math 1.5.1

Description: MPFI, a multiple precision interval arithmetic library based on MPFR MPFI stands for Multiple Precision Floating-point Interval library. Homepage: http://perso.ens-lyon.fr/nathalie.revol/software.html Keyword:math

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 3.0.3, 3.0.0

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

mpich - 3.2.1

Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). Homepage: http://www.mpich.org/

mrbayes bio 3.2.7a, 3.2.6

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

mrtrix bio 3.0.1, 3.0_RC3

Description: MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. Homepage: http://www.brain.org.au/software/index.html#mrtrix URL: http://www.brain.org.au/software/index.html#mrtrix Keyword:bio

mscg chem 1.7.3.1

Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release URL: https://github.com/uchicago-voth/MSCG-release Keyword:chem

msmc bio 1.0.1

Description: This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences (Schiffels and Durbin, 2014, Nature Genetics, or Preprint). In short, msmc can infer the scaled population size of a single population as a function of time the timing and nature of population separations between two populations from multiple phased haplotypes. When only two haplotypes are given, MSMC is similar to PSMC, and we call it PSMC' because of subtle differences in the method and the underlying model, which allows PSMC' to infer more accurately the recombination rate. Homepage: https://github.com/stschiff/msmc Keyword:bio

msmc2 - 2.0.0

Description: This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data. For a general guide, please refer to version 1: https://github.com/stschiff/msmc Binaries are attached to the releases (under the "Releases" tab within github). Homepage: https://github.com/stschiff/msmc URL: https://github.com/stschiff/msmc

multiwfn chem 3.6, 3.5

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

multovl bio 1.3.8203e7d

Description: The MULTOVL suite of programs finds multiple overlaps among genomic regions. The MULTOVL algorithm can detect several kinds of region overlaps. In addition to the N-fold overlaps you can detect solitary regions which are the input regions that do not overlap with any other region in the input data set, and union overlaps that is the union of the input regions that overlap at least once somewhere. Homepage: https://sourceforge.net/projects/multovl/ Keyword:bio

mummer bio 3.23, 4.0.0beta2

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

mumps-metis tools 5.2.1, 5.1.2

Description: A parallel sparse direct solver Homepage: https://graal.ens-lyon.fr/MUMPS/ URL: https://graal.ens-lyon.fr/MUMPS/ Keyword:tools

mumps-parmetis tools 5.1.2, 5.3.5

Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/ URL: http://graal.ens-lyon.fr/MUMPS/ Keyword:tools

muparser math 2.2.6, 2.2.5

Description: muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. Homepage: http://beltoforion.de/article.php?a=muparser Keyword:math

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: http://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 2.13, 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 2.13, 2.12, 2.14

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-ofi - 2.14

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/

namd-ofi-smp - 2.14

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/

namd-ucx - 2.13, 2.14

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/

namd-ucx-smp - 2.14

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/

namd-verbs chem 2.13, 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 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/ Keyword:chem

nanopolish bio 0.11.2, 0.13.2, 0.8.5

Description: Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Homepage: https://github.com/jts/nanopolish URL: https://github.com/jts/nanopolish Keyword:bio

nccl tools 2.3.5, 2.4.2, 2.5.6, 2.7.8

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

nccmp - 1.8.7.0

Description: nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment. Homepage: https://gitlab.com/remikz/nccmp URL: https://gitlab.com/remikz/nccmp

nciplot - 4.0-20200624

Description: NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. Homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html URL: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html

ncl vis 6.6.2, 6.4.0

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

nco io 4.6.6, 4.9.5

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

ncview vis 2.1.7, 2.1.8

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 URL: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis

nektar++ math 4.4.1, 5.0.1

Description: Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Homepage: https://www.nektar.info/ URL: https://www.nektar.info/ Keyword:math

neper chem 3.3.0, 3.4.0

Description: Neper is a software package for polycrystal generation and meshing. It can deal with 2D and 3D polycrystals with very large numbers of grains. Homepage: http://neper.sourceforge.net/index.html Keyword:chem

nest - 2.16.0

Description: NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. Homepage: http://www.nest-simulator.org/

netcdf io 4.6.1, 4.7.3, 4.7.0, 4.7.4, 4.4.1.1

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

netcdf-c++4 io 4.3.1, 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: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io

netcdf-c++4-mpi io 4.3.0, 4.3.1

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

netcdf-fortran io 4.4.4, 4.4.5, 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, 4.5.1, 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 4.6.1, 4.1.3, 4.7.4, 4.4.1.1

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

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: NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Homepage: https://pypi.python.org/pypi/networkx Keyword:tools

neuron bio 7.6.3, 7.8.2, 7.5

Description: Empirically-based simulations of neurons and networks of neurons. Homepage: http://www.neuron.yale.edu/neuron URL: http://www.neuron.yale.edu/neuron Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:bio

newmat - 10, 11

Description: Newmat C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues. Homepage: http://www.robertnz.net/index.html URL: http://www.robertnz.net/index.html

nextflow - 20.04.1, 19.10.0, 19.04.0, 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 0.5.0, 0.5.5, 0.5.4

Description: NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. Homepage: http://cibiv.github.io/NextGenMap/ URL: http://cibiv.github.io/NextGenMap/ Keyword:bio

ngs-bits bio 2018_10

Description: ngs-bits contains a lot of tools that are used for NGS-based diagnostics Homepage: https://github.com/imgag/ngs-bits Extensions: kiwisolver-1.0.1, matplotlib-3.0.2, pyparsing-2.3.0, subprocess32-3.5.3 Keyword:bio

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 2.7.0, 2.6.1, 2.4.2, 2.6.2

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 URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.6, python/3.6, python/3.7, python/3.7, python/3.8, python/3.8, python/3.6, python/3.6, python/3.7, python/3.7, python/3.8, python/3.8 Keyword:math

nodejs tools 11.1.0, 14.4.0

Description: Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: http://nodejs.org URL: http://nodejs.org Keyword:tools

nspr - 4.21

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 - 3.45

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 11.3.0, 11.4.3

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

ntpoly - 2.2

Description: NTPoly is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. Homepage: https://william-dawson.github.io/NTPoly/

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/

nvptx-tools - 0.20180301

Description: A collection of tools for use with nvptx-none GCC toolchains: https://gcc.gnu.org/wiki/nvptx Homepage: https://github.com/MentorEmbedded/nvptx-tools URL: https://github.com/MentorEmbedded/nvptx-tools

nwchem chem 6.6.revision27746, 7.0.0, 7.0.2, 6.8.1

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 URL: 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 4.4.1, 5.2.0, 4.2.2, 4.2.1

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

octopus chem 7.2, 9.1, 10.1, 8.4

Description: Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page URL: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page Keyword:chem

oligoarrayaux - 3.8

Description: OligoArrayAux is a subset of the UNAFold package for use with OligoArray. Homepage: http://unafold.rna.albany.edu/?q=DINAMelt/OligoArrayAux

one-dnn - 1.8

Description: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) ONE-DNN) Homepage: https://01.org/onednn URL: https://01.org/onednn

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/

open3dqsar chem 2.3

Description: Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID, CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script), and MOE grid interaction fields (exported from and MOE with the aid of a small SVL script). Homepage: http://open3dqsar.sourceforge.net/?Home Keyword:chem

openbabel chem 2.4.1, 3.0.0, 3.1.1

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: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: openbabel-3.1.1.1 Keyword:chem

openbabel-omp - 3.1.1

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: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: openbabel-3.1.1.1

openblas math 0.2.20, 0.3.4, 0.3.6, 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

openblas-64bits - 0.3.9, 0.3.6

Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. This build is for ILP64 (64bit integer ingexes). Homepage: http://xianyi.github.com/OpenBLAS/ URL: http://xianyi.github.com/OpenBLAS/

opencarp - 4.0

Description: openCARP is an open cardiac electrophysiology simulator for in-silico experiments. Homepage: https://opencarp.org URL: https://opencarp.org

opencascade - 7.5.0

Description: Open CASCADE Technology (OCCT) is a world-known 3D modeling kernel, freely available in open source. It's a software development kit (SDK) intended for the development of applications dealing with 3D CAD data. OCCT includes a set of C++ class libraries providing services for 3D surface and solid modeling, visualization, data exchange and rapid application development. Homepage: https://www.opencascade.com/open-cascade-technology/ URL: https://www.opencascade.com/open-cascade-technology/

opencoarrays - 2.9.2

Description: OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran. Homepage: https://github.com/sourceryinstitute/opencoarrays URL: https://github.com/sourceryinstitute/opencoarrays

opencolorio vis 1.0.9, 1.1.1

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/ URL: http://opencolorio.org/ Keyword:vis

opencv vis 4.4.0, 2.4.13.3, 4.1.0, 3.3.0, 4.5.1, 4.2.0, 3.4.3

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/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Keyword:vis

opencv_contrib vis 3.4.3

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/ 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 2.3.1, v2012, v1712, 6.20180813, 4.1, v1906, 3.0.1, 5.0, v1812, v2006, 2.4.0, v1706, 2.2.2, v1912

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: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys

openfoam-extend phys 4.0, 4.1

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.extend-project.de/ URL: http://www.extend-project.de/ Keyword:phys

openimagedenoise - 1.2.2

Description: Intel Open Image Denoise is an open source library of high-performance, high-quality denoising filters for images rendered with ray tracing. Homepage: https://github.com/OpenImageDenoise/oidn URL: https://github.com/OpenImageDenoise/oidn

openimageio vis 2.1.17.0, 1.8.15, 1.8.7

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

openmm chem OpenMM 7.1.1, 7.5.0, 7.4.1

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 (default), python/3.5.4, python/3.6.3, python/3.7.4 Keyword:chem

openmolcas chem 20.10, 20.07, 18.9

Description: OpenMolcas is a quantum chemistry software package. The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure. This module does include WFA and GRID-IT and EFP but does NOT include DMRG and NECI modules. Homepage: https://gitlab.com/Molcas/OpenMolcas URL: https://gitlab.com/Molcas/OpenMolcas Keyword:chem

openmpi mpi 2.1.1, 3.1.2, 4.0.1, 1.6.5, 1.8.8, 2.0.2, 4.0.3, 3.1.4, 1.10.7, 4.0.5

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

openms - 2.5.0

Description: OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. Homepage: https://github.com/OpenMS/OpenMS URL: https://github.com/OpenMS/OpenMS

openmx - 3.9, 3.8

Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/

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, 3.1.0, 3.0.0, 3.2.0

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/ URL: http://opensees.berkeley.edu/

openslide vis 3.4.1

Description: OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Homepage: http://openslide.org/ Keyword:vis

openvdb - 7.0.0

Description: OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. Homepage: https://github.com/AcademySoftwareFoundation/openvdb URL: https://github.com/AcademySoftwareFoundation/openvdb

openvkl - 0.10.0

Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKLs performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl

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 4.1.1, 4.2.0, 4.0.0.2, 3.0.3, 4.2.1, 4.1.2, 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/ Extensions: DBD::mysql-4.050, Devel::CheckLib-1.13, IO::CaptureOutput-1.1104, Mock::Config-0.03 Keyword:bio

osl vis 1.9.6

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

ospray - 1.8.5, 2.2.0

Description: Intel OSPRay is an open source, scalable, and portable ray tracing engine for high-performance, high-fidelity visualization on Intel Architecture CPUs. Homepage: https://github.com/ospray/ospray URL: https://github.com/ospray/ospray

osu-micro-benchmarks tools 5.3.2, 5.6.1, 5.6.2, 5.6.3

Description: OSU Micro-Benchmarks Homepage: https://mvapich.cse.ohio-state.edu/benchmarks/ URL: https://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 1.1, 2.2, 2.0

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

p4vasp chem 0.3.30

Description: p4vasp is the VASP Visualization Tool that can be used to display structure, unitcell, supercell, charge/probability/spin density, local potential, forces, velocities, dynamics, measure distances and angles, .... It can be used also to analyze electronic properties, total and local DOS and band structure Homepage: http://www.p4vasp.at Keyword:chem

packmol - 18.013

Description: Packing Optimization for Molecular Dynamics Simulations Homepage: http://m3g.iqm.unicamp.br/packmol URL: http://m3g.iqm.unicamp.br/packmol

pairedbamtobed12 - 1.2

Description: pairedBamToBed12 converts properly paired BAM alignments to BED12 format. Typical proper pairs will be represented by a 2 blocks BED12 entry. Additional blocks are produced when an alignment contains long deletion (CIGAR N-op). Thickness indicates the first read of the pair. The BAM input file must be grouped/sorted by query name (not alignment position). Homepage: https://github.com/Population-Transcriptomics/pairedBamToBed12 URL: https://github.com/Population-Transcriptomics/pairedBamToBed12

paml bio 4.9j, 4.9h

Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio

panarray - 1.0

Description: PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on a single microarray chip. These unique pan-genome tiling arrays provide maximum flexibility for the analysis of both known and uncharacterized strains. Homepage: https://www.cbcb.umd.edu/software/panarray

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 20170622, 20160722

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

paraview vis 5.5.2, 5.3.0, 5.8.0

Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis

paraview-offscreen vis 5.8.0, 5.3.0, 5.5.2

Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis

paraview-offscreen-gpu vis 5.4.0, 5.4.1, 5.8.0

Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis

pari-gp - 2.13.0

Description: PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. Homepage: http://pari.math.u-bordeaux.fr URL: http://pari.math.u-bordeaux.fr

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 URL: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math

parmgridgen math 1.0

Description: ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. Homepage: http://www-users.cs.umn.edu/~moulitsa/software.html URL: http://www-users.cs.umn.edu/~moulitsa/software.html Keyword:math

pbbam bio 20170508, 1.0.7

Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ URL: http://pbbam.readthedocs.io/ Keyword:bio

pbcopper - 1.4.0

Description: The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications. Homepage: https://github.com/PacificBiosciences/pbcopper URL: https://github.com/PacificBiosciences/pbcopper

pbdagcon bio 20170330

Description: pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. Homepage: https://github.com/PacificBiosciences/pbdagcon Keyword:bio

pbsuite bio 15.8.24

Description: PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. Homepage: https://sourceforge.net/p/pb-jelly/wiki/Home/ URL: https://sourceforge.net/p/pb-jelly/wiki/Home/ Extensions: networkx-1.10 Keyword:bio

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

pcmsolver chem 1.2.1, 1.1.10

Description: An API for the Polarizable Continuum Model. Homepage: https://pcmsolver.readthedocs.org Keyword:chem

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 - 10.31

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: http://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 0.9.10

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: http://sco.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

percolator bio 3-02

Description: Semi-supervised learning for peptide identification from shotgun proteomics datasets Homepage: https://github.com/percolator Keyword:bio

peridigm phys 2019-01-08

Description: Peridigm is an open-source computational peridynamics code developed at Sandia National Laboratories for massively-parallel multi-physics simulations. It has been applied primarily to problems in solid mechanics involving pervasive material failure. Homepage: https://peridigm.sandia.gov/ Keyword:phys

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 3.8.2, 2.3.3, 3.7.5, 3.12.0, 3.13.3, 3.12.4, 3.13.6, 3.11.3, 3.9.0, 3.14.1, 3.10.2, 3.1-p8, 3.10.5

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 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, 3.10.2

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

petsc-complex tools 3.10.4, 3.9.0, 3.10.2, 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 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

pexsi - 1.2.0

Description: The Pole EXpansion and Selected Inversion (PEXSI) method is a fast method for electronic structure calculation based on Kohn-Sham density functional theory. It efficiently evaluates certain selected elements of matrix functions, e.g., the Fermi-Dirac function of the KS Hamiltonian, which yields a density matrix. Homepage: https://pexsi.readthedocs.io/

pfamscan - 1.6

Description: PfamScan is used to search a FASTA sequence against a library of Pfam HMM. Homepage: http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ URL: http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ Extensions: B::Hooks::EndOfScope-0.24, Carp-1.50, Class::Load-0.25, Class::Load::XS-0.10, CPAN::Meta::Check-0.014, Data::OptList-0.110, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.005, Devel::StackTrace-2.04, Dist::CheckConflicts-0.11, Eval::Closure-0.14, File::pushd-1.016, IPC::Run-20180523.0, List::Util-1.53, Module::Runtime-0.016, Module::Runtime::Conflicts-0.003, Moose-2.2012, MRO::Compat-0.13, namespace::clean-0.27, Package::DeprecationManager-0.17, Package::Stash-0.38, Package::Stash::XS-0.29, Params::Util-1.07, parent-0.237, Role::Tiny-2.001004, Sub::Exporter-0.987, Sub::Identify-0.14, Sub::Name-0.26, Test::CleanNamespaces-0.24, Test::Needs-0.002006, Try::Tiny-0.30, Variable::Magic-0.62

pfft math 1.0.8-alpha

Description: PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. Homepage: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en URL: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en Keyword:math

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/

pgplot vis 5.2

Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: http://www.astro.caltech.edu/~tjp/pgplot/ URL: http://www.astro.caltech.edu/~tjp/pgplot/ Keyword:vis

phana chem 20150831

Description: This program reads the binary file created by fix_phonon and helps to analyse the phonon related info. Homepage: https://github.com/lingtikong/phana Keyword:chem

phylip bio 3.697, 3.698

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

phylobayes bio 4.1c

Description: A Bayesian software for phylogenetic reconstruction using mixture models Homepage: http://megasun.bch.umontreal.ca/People/lartillot/www/download.html URL: http://megasun.bch.umontreal.ca/People/lartillot/www/download.html Keyword:bio

phylobayes-mpi bio 20180420, 20201026

Description: A Bayesian software for phylogenetic reconstruction using mixture models Homepage: https://github.com/bayesiancook/pbmpi URL: https://github.com/bayesiancook/pbmpi Keyword:bio

phyml - 3.3.20190321

Description: Phylogenetic estimation using (Maximum) Likelihood Homepage: https://github.com/stephaneguindon/phyml URL: https://github.com/stephaneguindon/phyml

phyx bio 1.1, 0.999

Description: phyx performs phylogenetics analyses on trees and sequences. Homepage: https://github.com/FePhyFoFum/phyx URL: https://github.com/FePhyFoFum/phyx Keyword:bio

picard bio 2.23.2, 2.20.6, 2.10.7, 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

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

pindel bio 0.2.5b8

Description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. Homepage: http://gmt.genome.wustl.edu/packages/pindel/ Keyword:bio

plast bio 2.3.2

Description: PLAST is a parallel alignment search tool for comparing large protein banks Homepage: http://www.irisa.fr/symbiose/projects/plast/ Keyword:bio

platanus bio 1.2.4

Description: PLATform for Assembling NUcleotide Sequences Homepage: http://platanus.bio.titech.ac.jp/ Keyword:bio

platypus bio 0.8.1

Description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Homepage: http://www.well.ox.ac.uk/platypus Keyword:bio

plink bio 1.9b_4.1-x86_64, 1.07, 1.9b_5.2-x86_64, 2.00-10252019-avx2, 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 2.7.0, 2.6.1, 2.6.2, 2.1.5, 2.4.2, 2.3.0, 2.5.3, 2.3.7, 2.5.4, 2.3.2, 2.5.2, 2.4.3

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. This module has been compiled with additional modules, and support for XDR-files (GROMACS XTC/TRR), Python, GSL, Boost-serialization, Boost-Graph and other optional features. To find out more, run 'plumed config show' after loading this module. Homepage: http://www.plumed-code.org URL: http://www.plumed-code.org Keyword:chem

pmix - 1.2.5

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 1.9.0, 1.8.1, 1.10.0

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 URL: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io

postgresql tools 12.1, 10.3, 11.6, 10.2, 9.6.6

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/ Keyword:tools

pov-ray - 3.8.0-x.10064738

Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: http://www.povray.org/ URL: http://www.povray.org/

povray vis 3.7.0.7

Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: http://www.povray.org/ Keyword:vis

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

prank bio 140603, 170427, 140110

Description: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Homepage: http://wasabiapp.org/software/prank/ URL: http://wasabiapp.org/software/prank/ 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, 4.9.3, 5.1.0, 6.0.0, 5.2.0, 6.3.0

Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: http://trac.osgeo.org/proj/ URL: http://trac.osgeo.org/proj/ Keyword:geo

proj4-fortran geo 1.0

Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran Keyword:geo

proovread bio 2.14.1

Description: PacBio hybrid error correction through iterative short read consensus Homepage: https://github.com/BioInf-Wuerzburg/proovread Keyword:bio

protobuf tools 3.7.1, 3.6.1, 3.9.1, 3.11.1, 3.3.0

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

psfex - 3.21.1

Description: A computer program that extracts precise models of the Point Spread Functions (PSFs) from images processed by SExtractor and measures the quality of images. The generated PSF models can be used for model-fitting photometry or morphological analyses. Homepage: https://psfex.readthedocs.io/en/latest/index.html URL: https://psfex.readthedocs.io/en/latest/index.html

psi4 chem 1.1, 1.3.2

Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ URL: http://www.psicode.org/ Compatible modules: python/3.7, python/3.8 Extensions: Pint-0.16.1, pydantic-1.7.3 Keyword:chem

psmc bio 0.6.5

Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc Keyword:bio

pwrf geo 3.9.1, 3.8.1

Description: Based on extensive experience with mesoscale modeling in the polar regions by the Polar Meteorology Group of the Byrd Polar and Climate Research Center at The Ohio State University, the Weather Research and Forecasting model (WRF) has been modified for use in the Polar Regions (referred to as the Polar WRF). Compiled with -DNO_LEAP_CALENDAR Homepage: http://polarmet.osu.edu/hines/PWRF/ Keyword:geo

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

pyqt - 4.12

Description: PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. Homepage: http://www.riverbankcomputing.co.uk/software/pyqt

python tools 3.5.4, 3.7.0, 3.7.4, 2.7.14, 3.5.2, 3.6.3, 3.8.2, 2.7.13, 3.8.0

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ URL: http://python.org/ Extensions: gnureadline-8.0.0, pip-19.3.1, setuptools-41.6.0, virtualenv-16.7.7, wheel-0.33.6 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 2.1.3

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/ Keyword:geo

qgis geo 2.18.24, 3.10.6

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/3.6, python/3.7, python/3.8 Extensions: OWSLib-0.20.0, psycopg2-2.8.5, pyproj-2.6.1.post1, PyYAML-5.3.1 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/ 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

Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla Keyword:tools

qt tools 5.9.6, 4.8.7, 5.12.3, 5.6.1, 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/ Keyword:tools

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 6.4.1, 6.7, 6.5, 6.0, 6.3, 6.6, 6.2.2, 6.1

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

quast - 5.0.2

Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Extensions: joblib-0.17.0, path-15.0.0, QUAST-5.0.2, simplejson-3.17.0

quorum bio 1.1.1

Description: QuorUM is an error corrector for Illumina reads Homepage: http://www.genome.umd.edu/quorum.html Keyword:bio

qwt tools 6.1.3

Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://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/ Keyword:tools

r tools 3.5.2, 3.4.3, 3.5.0, 3.3.3, 3.4.0, 3.4.4, 4.0.0, 3.5.1, 4.0.2, 3.6.1, 3.6.0

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 3.12, 3.8, 3.9, 3.4

Description: Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. Homepage: https://bioconductor.org URL: https://bioconductor.org Extensions: abind-1.4-5, ade4-1.7-16, admisc-0.11, affxparser-1.62.0, affy-1.68.0, affycoretools-1.62.0, affyio-1.60.0, AgiMicroRna-2.40.0, ALDEx2-1.22.0, ALL-1.32.0, annaffy-1.62.0, annotate-1.68.0, AnnotationDbi-1.52.0, AnnotationFilter-1.14.0, AnnotationForge-1.32.0, AnnotationHub-2.22.0, ape-5.4-1, aroma.affymetrix-3.2.0, aroma.apd-0.6.0, aroma.core-3.2.1, aroma.light-3.20.0, ash-1.0-15, askpass-1.1, assertthat-0.2.1, ATACseqQC-1.14.4, aws-2.5, aws.s3-0.3.21, aws.signature-0.6.0, awsMethods-1.1-1, backports-1.2.1, ballgown-2.22.0, base64-2.0, base64enc-0.1-3, batchelor-1.6.2, baySeq-2.24.0, beachmat-2.6.3, beanplot-1.2, beeswarm-0.2.3, BH-1.72.0-3, BiasedUrn-1.07, Biobase-2.50.0, BiocFileCache-1.14.0, BiocGenerics-0.36.0, BiocManager-1.30.10, BiocNeighbors-1.8.2, BiocParallel-1.24.1, BiocSingular-1.6.0, BiocVersion-3.12.0, biomaRt-2.46.0, biomformat-1.18.0, Biostrings-2.58.0, biovizBase-1.38.0, bit-4.0.4, bit64-4.0.5, bitops-1.0-6, blme-1.0-4, blob-1.2.1, bluster-1.0.0, boot-1.3-25, brio-1.1.0, broom-0.7.2, BSgenome-1.58.0, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.3, BSgenome.Mmusculus.UCSC.mm10-1.4.0, bumphunter-1.32.0, Cairo-1.5-12.2, callr-3.5.1, CAMERA-1.46.0, caret-6.0-86, Category-2.56.0, caTools-1.18.0, ccdata-1.16.0, ccmap-1.16.0, cellranger-1.1.0, CGHbase-1.50.0, checkmate-2.0.0, ChIPpeakAnno-3.24.1, circlize-0.4.11, class-7.3-17, cli-2.2.0, clipr-0.7.1, clue-0.3-58, cluster-2.1.0, coda-0.19-4, codetools-0.2-18, colorRamps-2.3, colorspace-2.0-0, colourpicker-1.1.0, commonmark-1.7, ComplexHeatmap-2.6.2, conquer-1.0.2, ConsensusClusterPlus-1.54.0, conumee-1.24.0, corpcor-1.6.9, cowplot-1.1.0, cpp11-0.2.4, crayon-1.3.4, crossmeta-1.16.1, crosstalk-1.1.0.1, cummeRbund-2.32.0, curl-4.3, cytolib-2.2.0, CytoML-2.2.1, dada2-1.18.0, data.table-1.13.4, DBI-1.1.0, dbplyr-2.0.0, DeconRNASeq-1.32.0, DEGseq-1.44.0, DelayedArray-0.16.0, DelayedMatrixStats-1.12.1, deldir-0.2-3, dendextend-1.14.0, DEoptimR-1.0-8, derfinder-1.24.0, derfinderHelper-1.24.0, desc-1.2.0, DESeq2-1.30.0, dichromat-2.0-0, diffcyt-1.10.0, diffobj-0.3.2, digest-0.6.27, diptest-0.75-7, DNAcopy-1.64.0, doParallel-1.0.16, doRNG-1.8.2, dplyr-1.0.2, dqrng-0.2.1, DRIMSeq-1.18.0, DropletUtils-1.10.1, DT-0.16, dupRadar-1.20.0, DynDoc-1.68.0, e1071-1.7-4, EBImage-4.32.0, edgeR-3.32.0, ellipse-0.4.2, ellipsis-0.3.1, ensembldb-2.14.0, evaluate-0.14, ExperimentHub-1.16.0, fansi-0.4.1, farver-2.0.3, fastcluster-1.1.25, fastICA-1.2-2, fastmap-1.0.1, fastmatch-1.1-0, fda-5.1.7, FDb.InfiniumMethylation.hg19-2.2.0, fdrtool-1.2.15, fds-1.8, ff-4.0.4, fftwtools-0.9-9, fgsea-1.16.0, fitdistrplus-1.1-3, flexmix-2.3-17, flowClust-3.28.0, flowCore-2.2.0, FlowSOM-1.22.0, FlowSorted.Blood.EPIC-1.8.0, FlowSorted.CordBloodCombined.450k-1.6.0, flowStats-4.2.0, flowViz-1.54.0, flowWorkspace-4.2.0, FNN-1.1.3, foreach-1.5.1, foreign-0.8-80, formatR-1.7, Formula-1.2-4, formula.tools-1.7.1, fpc-2.2-9, fs-1.5.0, futile.logger-1.4.3, futile.options-1.0.1, future-1.21.0, future.apply-1.6.0, gbm-2.1.8, gbRd-0.4-11, gcrma-2.62.0, gdata-2.18.0, gdsfmt-1.26.0, genefilter-1.72.0, geneLenDataBase-1.26.0, geneplotter-1.68.0, generics-0.1.0, GENESIS-2.20.0, GENIE3-1.12.0, GenomeInfoDb-1.26.2, GenomeInfoDbData-1.2.4, GenomicAlignments-1.26.0, GenomicFeatures-1.42.1, GenomicFiles-1.26.0, GenomicRanges-1.42.0, GenomicScores-2.2.0, genoset-1.45.1, GEOquery-2.58.0, GetoptLong-1.0.5, GGally-2.0.0, ggbeeswarm-0.6.0, ggbio-1.38.0, ggcyto-1.18.0, ggplot2-3.3.2, ggrepel-0.8.2, ggridges-0.5.2, ggvis-0.4.7, GLAD-2.54.0, Glimma-2.0.0, glmmTMB-1.0.2.1, glmnet-4.0-2, GlobalAncova-4.8.0, GlobalOptions-0.1.2, globals-0.14.0, globaltest-5.44.0, glue-1.4.2, GO.db-3.12.1, goftest-1.2-2, goseq-1.42.0, GOstats-2.56.0, gower-0.2.2, gplots-3.1.1, graph-1.68.0, gridExtra-2.3, GSA-1.03.1, GSEABase-1.52.1, gsl-2.1-6, gsmoothr-0.1.7, GSVA-1.38.0, gtable-0.3.0, gtools-3.8.2, Gviz-1.34.0, GWASExactHW-1.01, GWASTools-1.36.0, HDF5Array-1.18.0, hdrcde-3.3, hexbin-1.28.1, hgu133plus2.db-3.2.3, highr-0.8, Hmisc-4.4-2, HMMcopy-1.32.0, hms-0.5.3, Homo.sapiens-1.3.1, htmlTable-2.1.0, htmltools-0.5.0, htmlwidgets-1.5.3, httpuv-1.5.4, httr-1.4.2, hwriter-1.3.2, ica-1.0-2, IDPmisc-1.1.20, igraph-1.2.6, IHW-1.18.0, IlluminaHumanMethylation450kanno.ilmn12.hg19-0.6.0, IlluminaHumanMethylation450kmanifest-0.4.0, IlluminaHumanMethylationEPICanno.ilm10b2.hg19-0.6.0, IlluminaHumanMethylationEPICanno.ilm10b4.hg19-0.6.0, IlluminaHumanMethylationEPICmanifest-0.3.0, illuminaio-0.32.0, impute-1.64.0, interactiveDisplayBase-1.28.0, ipred-0.9-9, IRanges-2.24.1, irlba-2.3.3, isoband-0.2.3, isva-1.9, iterators-1.0.13, JADE-2.0-3, jpeg-0.1-8.1, jsonlite-1.7.2, KEGG.db-3.2.4, KEGGgraph-1.50.0, KEGGprofile-1.32.0, KEGGREST-1.30.1, kernlab-0.9-29, KernSmooth-2.23-18, knitr-1.30, ks-1.11.7, labeling-0.4.2, lambda.r-1.2.4, LaplacesDemon-16.1.4, later-1.1.0.1, lattice-0.20-41, latticeExtra-0.6-29, lava-1.6.8.1, lazyeval-0.2.2, LEA-3.2.0, leiden-0.3.6, lifecycle-0.2.0, limma-3.46.0, limSolve-1.5.6, listenv-0.8.0, lme4-1.1-26, lmerTest-3.1-3, lmtest-0.9-38, locfit-1.5-9.4, logistf-1.24, logspline-2.1.16, lpSolve-5.6.15, lpsymphony-1.18.0, lsa-0.73.2, lubridate-1.7.9.2, lumi-2.42.0, magrittr-2.0.1, MALDIquant-1.19.3, markdown-1.1, marray-1.68.0, maSigPro-1.62.0, MASS-7.3-53, MassSpecWavelet-1.56.0, mathjaxr-1.0-1, Matrix-1.2-18, MatrixGenerics-1.2.0, MatrixModels-0.4-1, matrixStats-0.57.0, mclust-5.4.7, MEDIPS-1.42.0, memoise-1.1.0, metagenomeSeq-1.32.0, metaMA-3.1.2, metap-1.4, MethylSeekR-1.30.0, methylumi-2.36.0, Mfuzz-2.50.0, mgcv-1.8-33, mhsmm-0.4.16, mice-3.12.0, mime-0.9, minfi-1.36.0, miniUI-0.1.1.1, minqa-1.2.4, missMethyl-1.24.0, mixOmics-6.14.0, mixtools-1.2.0, mlbench-2.1-1, MLInterfaces-1.70.0, mnormt-2.0.2, ModelMetrics-1.2.2.2, modeltools-0.2-23, MotifDb-1.32.0, motifStack-1.34.0, MsCoreUtils-1.2.0, MSnbase-2.16.0, multcomp-1.4-15, multicool-0.1-11, multtest-2.46.0, munsell-0.5.0, muscat-1.4.0, mutoss-0.1-12, mvtnorm-1.1-1, mzID-1.28.0, mzR-2.24.1, NADA-1.6-1.1, ncdf4-1.17, ncdfFlow-2.36.0, NCmisc-1.1.6, nleqslv-3.3.2, nlme-3.1-151, nloptr-1.2.2.2, nnet-7.3-14, NOISeq-2.34.0, nor1mix-1.3-0, numDeriv-2016.8-1.1, oligo-1.54.1, oligoClasses-1.52.0, openCyto-2.2.0, openssl-1.4.3, openxlsx-4.2.3, operator.tools-1.6.3, org.Hs.eg.db-3.12.0, org.Mm.eg.db-3.12.0, org.Rn.eg.db-3.12.0, OrganismDbi-1.32.0, parallelly-1.22.0, patchwork-1.1.0, pbapply-1.4-3, pbkrtest-0.4-8.6, pcaMethods-1.82.0, pcaPP-1.9-73, penalized-0.9-51, perm-1.0-0.0, permute-0.9-5, PFAM.db-3.12.0, pheatmap-1.0.12, phyloseq-1.34.0, pillar-1.4.7, pixmap-0.4-11, pkgbuild-1.2.0, pkgconfig-2.0.3, pkgload-1.1.0, plogr-0.2.0, plotly-4.9.2.1, plotrix-3.7-8, pls-2.7-3, plyr-1.8.6, png-0.1-7, polyclip-1.10-0, polyester-1.26.0, polynom-1.4-0, prabclus-2.3-2, praise-1.0.0, preprocessCore-1.52.0, preseqR-4.0.0, prettyunits-1.1.1, pROC-1.16.2, processx-3.4.5, prodlim-2019.11.13, proftools-0.99-3, progress-1.2.2, pRoloc-1.30.0, pRolocdata-1.28.0, pRolocGUI-2.0.0, promises-1.1.1, ProtGenerics-1.22.0, proxy-0.4-24, ps-1.5.0, PSCBS-0.65.0, PureCN-1.20.0, purrr-0.3.4, quadprog-1.5-8, quantreg-5.75, quantsmooth-1.56.0, qvalue-2.22.0, R.cache-0.14.0, R.devices-2.16.1, R.filesets-2.14.0, R.huge-0.9.0, R.methodsS3-1.8.1, R.oo-1.24.0, R.rsp-0.44.0, R.utils-2.10.1, R6-2.5.0, rainbow-3.6, randomcoloR-1.1.0.1, randomForest-4.6-14, RANN-2.6.1, rappdirs-0.3.1, rARPACK-0.11-0, RBGL-1.66.0, rbibutils-2.0, RColorBrewer-1.1-2, Rcpp-1.0.5, RcppAnnoy-0.0.18, RcppArmadillo-0.10.1.2.0, RcppEigen-0.3.3.7.0, RcppGSL-0.3.8, RcppHNSW-0.3.0, RcppParallel-5.0.2, RcppProgress-0.4.2, RcppZiggurat-0.1.6, RCurl-1.98-1.2, Rdpack-2.1, reader-1.0.6, readr-1.4.0, readxl-1.3.1, recipes-0.1.15, regioneR-1.22.0, rematch-1.0.1, rematch2-2.1.2, Repitools-1.36.0, ReportingTools-2.30.0, reshape-0.8.8, reshape2-1.4.4, ResidualMatrix-1.0.0, reticulate-1.18, Rfast-2.0.1, rGADEM-2.38.0, Rgraphviz-2.34.0, rhdf5-2.34.0, rhdf5filters-1.2.0, Rhdf5lib-1.12.0, Rhtslib-1.22.0, Ringo-1.54.0, rjson-0.2.20, rlang-0.4.9, RNASeqPower-1.30.0, rngtools-1.5, robustbase-0.93-6, ROC-1.66.0, ROCR-1.0-11, rpart-4.1-15, rprojroot-2.0.2, RProtoBufLib-2.2.0, rrcov-1.5-5, Rsamtools-2.6.0, Rsolnp-1.16, RSpectra-0.16-0, RSQLite-2.2.1, rstudioapi-0.13, Rsubread-2.4.2, rsvd-1.0.3, rtracklayer-1.50.0, Rtsne-0.15, RUnit-0.4.32, ruv-0.9.7.1, S4Vectors-0.28.1, sampling-2.8, samr-3.0, sandwich-3.0-0, SC3-1.18.0, scales-1.1.1, scater-1.18.3, scattermore-0.7, scran-1.18.2, scrime-1.3.5, sctransform-0.3.1, scuttle-1.0.3, segmented-1.3-1, SeqArray-1.30.0, seqLogo-1.56.0, SeqVarTools-1.28.1, Seurat-3.2.3, sfsmisc-1.1-7, shape-1.4.5, shiny-1.5.0, shinyBS-0.61, shinydashboard-0.7.1, shinydashboardPlus-0.7.5, shinyFiles-0.9.0, shinyhelper-0.3.2, shinyjs-2.0.0, shinypanel-0.1.2, shinyWidgets-0.5.4, ShortRead-1.48.0, siggenes-1.64.0, SingleCellExperiment-1.12.0, SingleR-1.4.0, sitmo-2.0.1, slam-0.1-48, SMVar-1.3.3, sn-1.6-2, snow-0.4-3, SnowballC-0.7.0, snowfall-1.84-6.1, SNPRelate-1.24.0, sourcetools-0.1.7, sp-1.4-4, SparseM-1.78, sparseMatrixStats-1.2.0, spatstat-1.64-1, spatstat.data-1.7-0, spatstat.utils-1.17-0, SPIA-2.42.0, splitstackshape-1.4.8, SQUAREM-2020.5, SSPA-2.30.0, stageR-1.12.0, statmod-1.4.35, stringi-1.5.3, stringr-1.4.0, SummarizedExperiment-1.20.0, survival-3.2-7, sva-3.38.0, sys-3.4, TeachingDemos-2.12, tensor-1.5, testthat-3.0.0, TFisher-0.2.0, TH.data-1.0-10, threejs-0.3.3, tibble-3.0.4, tidyr-1.1.2, tidyselect-1.1.0, tiff-0.1-6, timeDate-3043.102, tkWidgets-1.68.0, TMB-1.7.18, tmvnsim-1.0-2, truncnorm-1.0-8, tsne-0.1-3, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0, tximport-1.18.0, utf8-1.1.4, uwot-0.1.10, V8-3.4.0, variancePartition-1.20.0, VariantAnnotation-1.36.0, vctrs-0.3.5, vegan-2.5-7, venn-1.9, VennDiagram-1.6.20, VGAM-1.1-4, vipor-0.4.5, viridis-0.5.1, viridisLite-0.3.0, vsn-3.58.0, waldo-0.2.3, wateRmelon-1.34.0, waveslim-1.8.2, widgetTools-1.68.0, withr-2.3.0, Wrench-1.8.0, WriteXLS-6.1.0, xcms-3.12.0, xfun-0.19, xgboost-1.2.0.1, XML-3.99-0.5, xml2-1.3.2, xtable-1.8-4, XVector-0.30.0, yaml-2.2.1, zCompositions-1.3.4, zip-2.1.1, zlibbioc-1.36.0, zoo-1.8-8 Keyword:bio

racon bio 1.4.3, 20170719

Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/isovic/racon/ URL: https://github.com/isovic/racon/ Keyword:bio

randfold bio 2.0.1

Description: Minimum free energy of folding randomization test software Homepage: http://bioinformatics.psb.ugent.be/software/details/Randfold 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/

raremetal - 4.15.1

Description: A tool for rare variants meta-analysis Homepage: https://github.com/statgen/Raremetal URL: https://github.com/statgen/Raremetal

raxml bio 8.2.12, 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

raxml-ng - 0.9.0, 1.0.1

Description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Homepage: https://github.com/amkozlov/raxml-ng URL: https://github.com/amkozlov/raxml-ng

raxml-pthreads - 8.2.12

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

ray bio 3.0.1, 3.0.0

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

rcorrector - 1.0.4

Description: Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. Homepage: https://github.com/mourisl/Rcorrector URL: https://github.com/mourisl/Rcorrector

rdkit chem 2019.03.4, 2018.03.3, 2020.09.1b1

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 (default), python/3.6.3, python/3.7.4 Keyword:chem

re2c - 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/

reapr bio 1.0.18

Description: REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. Homepage: https://www.sanger.ac.uk/science/tools/reapr Extensions: File::Spec::Link-0.5, Getopt::Long-2.5, List::Util-1.50 Keyword:bio

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, 3.1.1, 3.0

Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://bitbucket.org/scheres/relion-3.0_beta.git URL: https://bitbucket.org/scheres/relion-3.0_beta.git Keyword:chem

remora tools 1.8.3, 1.8.2

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

repasthpc bio 2.3.0, 2.0, 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/ URL: https://repast.github.io/ Keyword:bio

repeatmasker bio 4.1.0, 4-0-9-p2, 4.1.1, 4-0-7

Description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Homepage: http://www.repeatmasker.org/ URL: http://www.repeatmasker.org/ Keyword:bio

repeatmodeler bio 1.0.11, 2.0.1

Description: RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Homepage: http://repeatmasker.org/RepeatModeler/ URL: http://repeatmasker.org/RepeatModeler/ 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

rgaugury - 2.1.3

Description: This project aims to develop a sophisticated informatics tools for large scale of resistance gene analogs identification, including major groups of RGAs, such as NBS encoding genes, receptor like proteins and receptor like protein kinases. It is thus named as RGA augury or RGAugury standalone pipeline. Homepage: https://bitbucket.org/yaanlpc/rgaugury/src/master/ URL: https://bitbucket.org/yaanlpc/rgaugury/src/master/ Extensions: Config::IniFiles-3.000002, Data::Dumper-2.173, GD-2.71, GD::Arrow-0.01, GD::SVG-0.33, GD::Text-0.86, Log::Log4perl-1.49, SVG-2.84

rlooper - 1.0

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

rmats - 4.0.2, 4.1.1

Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. Homepage: http://rnaseq-mats.sourceforge.net/ URL: http://rnaseq-mats.sourceforge.net/

rmblast bio 2.10.0, 2.6.0, 2.9.0

Description: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. Homepage: http://www.repeatmasker.org/RMBlast.html URL: http://www.repeatmasker.org/RMBlast.html Keyword:bio

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

roary bio 3.12.0

Description: Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Homepage: https://sanger-pathogens.github.io/Roary/ URL: https://sanger-pathogens.github.io/Roary/ Keyword:bio

root tools 6.08.02, 6.14.04, 5.34.36, 6.20.04

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: https://root.cern.ch/drupal/ URL: https://root.cern.ch/drupal/ Keyword:tools

rosetta chem 3.12, 3.9, 3.10, 2019.21.60746, 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. This is a weekly release. Homepage: https://www.rosettacommons.org URL: https://www.rosettacommons.org Keyword:chem

rsem bio 1.3.0, 1.3.1

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

rstudio-server tools 1.2.1335, 1.1.447, 1.3.1093, 1.1.206

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/ URL: 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 URL: https://itk.org Keyword:bio

ruby tools 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: addressable-2.4.0, arr-pm-0.0.10, backports-3.11.4, bundler-2.0.1, cabin-0.9.0, childprocess-1.0.1, clamp-1.3.0, connection_pool-2.2.2, diff-lcs-1.3, ethon-0.12.0, faraday-0.15.4, faraday_middleware-0.13.1, ffi-1.10.0, gh-0.15.1, highline-2.0.1, json-2.1.0, launchy-2.4.3, multi_json-1.13.1, multipart-post-2.0.0, mustermann-1.0.3, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-3.0.3, pusher-client-0.6.2, rack-2.0.6, rack-protection-2.0.5, rack-test-1.1.0, rspec-3.8.0, rspec-core-3.8.0, rspec-expectations-3.8.2, rspec-mocks-3.8.0, rspec-support-3.8.0, sinatra-2.0.5, tilt-2.0.9, typhoeus-1.3.1, 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 1.47.0, 1.28.0, 1.41.0

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

sabre bio 1.00

Description: A barcode demultiplexing and trimming tool for FastQ files Homepage: https://github.com/najoshi/sabre URL: https://github.com/najoshi/sabre Keyword:bio

sagemath tools 8.1

Description: SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Homepage: http://www.sagemath.org/ Keyword:tools

salmon bio 1.3.0, 0.11.3, 0.12.0, 0.14.2-1, 0.8.2, 0.14.0, 0.9.1, 1.1.0

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 URL: 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

samstat - 1.5.1

Description: Displaying sequence statistics for next generation sequencing Homepage: http://samstat.sourceforge.net/ URL: http://samstat.sourceforge.net/

samtools bio 1.3.1, 1.5, 0.1.20, 1.10, 0.1.17, 1.9, 0.1.18, 1.8

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: http://www.htslib.org/ URL: http://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 2.0.2, 1.8.0, 2.1.0

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 2017b, 2019a, 2019b, 2018b

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/ Keyword:math

scotch math 6.0.4, 6.0.9, 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: https://gforge.inria.fr/projects/scotch/ URL: https://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

sdl tools 1.2.15

Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/ Keyword:tools

sdl2 tools 2.0.10, 2.0.7

Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/ URL: http://www.libsdl.org/ Keyword:tools

sdsl-lite - 2.1.1

Description: The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close to the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operation performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical. Homepage: https://github.com/simongog/sdsl-lite

sedifoam phys 0.1

Description: SediFoam is a hybrid CFD-DEM solver for particle-laden flows based on two open-source codes: OpenFOAM, an object-oriented CFD platform by OpenCFD, and LAMMPS, a highly efficient molecular dynamics solver by Sandia National Laboratories. The solver has ben rigorously and extensively validated [Gupta2015b]. A capability demonstration of the present solver in the context of sediment transport is published in Sun and Xiao [Sun2016]. Other application include sand dune migration [Sun2016b], cohesive particle setteling [Sun2017cohesive], sediment transport of irregular partilces [Sun2017irregular], particle plume in stratified flows [Wang2016]. Homepage: https://github.com/xiaoh/sediFoam Keyword:phys

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

segemehl - 0.3.4

Description: segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/

selscan bio 1.2.0

Description: selscan -- a program to calculate EHH-based scans for positive selection in genomes selscan currently implements EHH, iHS, XP-EHH, nSL, and iHH12 and requires phased data. It should be run separately for each chromosome and population (or population pair for XP-EHH). selscan is 'dumb' with respect ancestral/derived coding and simply expects haplotype data to be coded 0/1. Unstandardized iHS scores are thus reported as ln(iHH1/iHH0) based on the coding you have provided. Homepage: https://github.com/szpiech/selscan Keyword:bio

seqan bio 2.4.0

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/ Keyword:bio

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/

seqmule bio 1.2.6

Description: SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study. Homepage: http://seqmule.openbioinformatics.org/en/latest/ Keyword:bio

seqtk bio 1.2, 1.2-r101c, 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

sextractor phys 2.19.5

Description: SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. Homepage: ://www.astromatic.net/software/sextractor Keyword:phys

sga bio 0.10.15

Description: SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. For running examples see src/examples and the sga wiki https://github.com/jts/sga/wiki For questions or support contact jared.simpson --at-- oicr.on.ca Homepage: https://github.com/jts/sga/wiki 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/ URL: 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

shrimp - 2.2.3

Description: SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation. Homepage: http://compbio.cs.toronto.edu/shrimp/

sickle bio 1.33

Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle URL: https://github.com/najoshi/sickle Keyword:bio

siesta chem 4.0, 4.1-b4, 4.1-b2, 4.1-b3, 4.0.1, 4.1-MaX-3.0

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. This version was built with Lua support. Homepage: http://departments.icmab.es/leem/siesta URL: http://departments.icmab.es/leem/siesta Keyword:chem

sift4g bio 2.0.0

Description: SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. Homepage: http://sift.bii.a-star.edu.sg/ Keyword:bio

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

simu - 0.9.4

Description: SIMU simulats a GWAS based on real genotype data. This tool is a extension of gcta --simu-qt and gcta --simu-cc functionality. Homepage: https://github.com/precimed/simu URL: https://github.com/precimed/simu

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 - 3.10.2, 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

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/

slim - 3.3.2, 3.4.0

Description: SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. Homepage: https://messerlab.org/slim/ URL: https://messerlab.org/slim/

snap bio 2013-11-29, 2017-05-17

Description: SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. Homepage: http://korflab.ucdavis.edu/software.html URL: http://korflab.ucdavis.edu/software.html Keyword:bio

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 4.2.0, 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/ URL: http://bioinfo.lifl.fr/RNA/sortmerna/ Keyword:bio

spades bio 3.10.1, 3.11.1, 3.13.1, 3.13.0

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

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

speedseq bio 0.1.2

Description: A flexible framework for rapid genome analysis and interpretation Homepage: https://github.com/hall-lab/speedseq URL: https://github.com/hall-lab/speedseq Keyword:bio

spglib chem 1.9.9, 1.16.0

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

spherls phys 1.0.0

Description: SPHERLS simulates the interaction of radial pulsation and convection in stars. Homepage: https://github.com/cgeroux/SPHERLS/ Keyword:phys

sprng math 5.0

Description: Scalable Parallel Pseudo Random Number Generators Library Homepage: http://www.sprng.org/ URL: http://www.sprng.org/ Keyword:math

squid bio 1.9g

Description: Author: Sean Eddy A C library that is bundled with much of the above software. C function library for sequence analysis. SQUID is my own personal library of C functions and utility programs for sequence analysis. I don't really suggest that you use it in your programs, as I change it at will. However, it does contains some small utility programs that some people have found useful in scripts that drive large HMMER tasks. Homepage: http://eddylab.org/software.html Keyword:bio

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 2.0Beta10a, 1.46, 2.3e, 1.45, 2.3b, 2.0b, 1.44, 2.53, 1.35, 2.3d

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

star bio 2.6.0a, 2.7.3a, 2.5.3a, 2.6.1a, 2.7.1a, 2.6.1c, 2.7.4a, 2.7.0a, 2.7.5a, 2.5.2b, 2.6.0c

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR URL: https://github.com/alexdobin/STAR Keyword:bio

star-fusion - 1.10.0

Description: STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. Homepage: https://github.com/STAR-Fusion/STAR-Fusion URL: https://github.com/STAR-Fusion/STAR-Fusion Extensions: AutoLoader-5.74, Carp::Assert-0.21, common::sense-3.74, constant-1.33, Cwd-3.75, Data::Dumper-2.173, Data::Dumper-2.173, DB_File-1.852, Encode-3.01, ExtUtils::CBuilder-0.280231, ExtUtils::CppGuess-0.19, ExtUtils::MakeMaker-7.36, ExtUtils::ParseXS-3.35, IO::File-1.39, IO::Select-1.39, IO::Socket-1.39, IPC::Cmd-1.02, JSON::XS-4.02, List::Util-1.50, Locale::Maketext::Simple-0.21, MIME::Base64-3.15, Module::CoreList-5.20190620, Module::Load-0.34, Module::Load::Conditional-0.68, Module::Metadata-1.000036, Net::Domain-3.11, Params::Check-0.38, parent-0.237, Perl::OSType-1.010, PerlIO::gzip-0.20, Pod::Escapes-1.07, Pod::Man-4.12, Pod::Simple-3.39, Scalar::Util-1.50, Set::IntervalTree-0.12, Socket-2.029, Storable-3.15, Test-1.26, Test::More-1.302164, Text::ParseWords-3.30, Text::Wrap-2013.0523, Time::Local-1.28, Types::Serialiser-1.0, URI::Escape-1.76, XSLoader-0.24

starccm phys 13.06.012-R8, 12.06.011-R8, 11.06.011-R8, 14.06.013-R8, 12.04.011-R8, 15.04.010-R8, 13.04.010-R8, 14.02.012-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 12.06.011, 14.02.012, 13.04.010, 11.06.011, 14.06.013, 14.04.013, 13.06.012, 15.04.010, 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

strelka - 2.9.10

Description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Homepage: https://github.com/Illumina/strelka URL: https://github.com/Illumina/strelka

stride - 2020

Description: Secondary structure assignment from known atomic coordinates of proteins Homepage: http://webclu.bio.wzw.tum.de/stride URL: http://webclu.bio.wzw.tum.de/stride

stringtie bio 2.1.3, 1.3.3b, 1.3.4d, 2.0, 2.1.0

Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/stringtie/ URL: http://ccb.jhu.edu/software/stringtie/ Keyword:bio

structure bio 2.3.4

Description: The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Homepage: http://web.stanford.edu/group/pritchardlab/software/ URL: http://web.stanford.edu/group/pritchardlab/software/ Keyword:bio

su2 math 6.0.1, 7.0.5, 7.0.8, 5.0.0, 6.2.0, 6.1.0, 7.0.0

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 URL: http://su2.stanford.edu Keyword:math

subread bio 1.5.2, 1.6.4, 2.0.1, 2.0.0

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

suitesparse math 4.5.4, 5.7.1, 5.4.0

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

sumo - 1.1.0

Description: Simulation of Urban MObility, or SUMO for short, is an open source, microscopic, multi-modal traffic simulation. It allows to simulate how a given traffic demand which consists of single vehicles moves through a given road network. The simulation allows to address a large set of traffic management topics. It is purely microscopic: each vehicle is modelled explicitly, has an own route, and moves individually through the network. Simulations are deterministic by default but there are various options for introducing randomness. Homepage: http://sumo.sourceforge.net/userdoc/Sumo_at_a_Glance.html

sundials - 5.3.0, 2.7.0, 4.1.0

Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computation.llnl.gov/projects/sundials URL: https://computation.llnl.gov/projects/sundials

superlu math 5.2.1, 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/ URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math

superlu_dist - 6.1.1

Description: SuperLU_DIST contains a set of subroutines to solve a sparse linear system A*X=B. It uses Gaussian elimination with static pivoting (GESP). Homepage:

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

svaba - 1.1.0

Description: Structural variation and indel detection by local assembly Homepage: https://github.com/walaj/svaba URL: https://github.com/walaj/svaba

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

sympack - 1.1

Description: symPACK is a sparse symmetric matrix direct linear solver. Homepage: https://github.com/symPACK/symPACK

tabix bio 0.2.6

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

tau tools 2.27.1

Description: The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Homepage: http://tau.uoregon.edu Keyword:tools

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, 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

thrift - 0.13.0

Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.6.3, python/3.7.4, python/3.8.0

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 URL: 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, 2.1.2

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

torch ai 20170530, 20171030, 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

towhee chem 8.1.0

Description: Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases. Homepage: http://towhee.sourceforge.net/ Keyword:chem

tpp - 5.2.0

Description: The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. On cedar we can also provide TPP web interface (tpp_gui) per group upon user request Homepage: http://ww.peptideatlas.org/ URL: http://ww.peptideatlas.org/

trans-abyss bio 1.5.5, 2.0.1

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

transdecoder bio 5.5.0, 3.0.1

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

treemix - 1.13

Description: TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. Homepage: http://bitbucket.org/nygcresearch/treemix URL: http://bitbucket.org/nygcresearch/treemix

trf bio 4.09.1

Description: A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter. The output consists of two files: a repeat table file and an alignment file. The repeat table, viewable in a web browser, contains information about each repeat, including its location, size, number of copies and nucleotide content. Clicking on the location indices for one of the table entries opens a second browser page that shows an alignment of the copies against a consensus pattern. The program is very fast, analyzing sequences on the order of .5Mb in just a few seconds. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected. Homepage: https://tandem.bu.edu/trf/trf.html URL: https://tandem.bu.edu/trf/trf.html Keyword:bio

trilinos tools 13.0.1, 12.10.1, 12.12.1

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: https://trilinos.org URL: https://trilinos.org Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 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, 2.8.4, 2.9.0, 2.8.5, 2.5.0, 2.6.5

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/ URL: http://trinityrnaseq.github.io/ Keyword:bio

trinotate bio 3.0.2, 3.2.2, 3.2.1, 3.2.0

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/ URL: https://trinotate.github.io/ Extensions: CGI-4.51, Text::NSP-1.31 Keyword:bio

trnascan-se bio 2.0.7, 2.0.0

Description: tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. Homepage: http://lowelab.ucsc.edu/ URL: http://lowelab.ucsc.edu/ Keyword:bio

tsnecuda - 2.1

Description: tsne-cuda is an optimized CUDA version of t-Stochastic Neighborhood Embedding (t-SNE) - a highly successful method for dimensionality reduction and visualization of high dimensional datasets. Homepage: https://github.com/CannyLab/tsne-cuda URL: https://github.com/CannyLab/tsne-cuda

ucx - 1.5.2, 1.6.0, 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 3.14.0, 3.16.1, 3.13.0

Description: Valgrind: Debugging and profiling tools Homepage: https://valgrind.org URL: https://valgrind.org 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

vasp chem 5.4.4, 4.6, 5.4.1, 6.1.0, 6.1.2

Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version Transition State Tools for VASP (http://theory.cm.utexas.edu/vtsttools/) as well as VASPsol (https://github.com/henniggroup/VASPsol) has been implemented to the original vasp . Homepage: http://www.vasp.at Keyword:chem

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/

vcflib - 1.0.1

Description: The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the defacto standard reporting format for a wide array of genomic variant detectors. vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both: - an API for parsing and operating on records of genomic variation as it can be described by the VCF format, - and a collection of command-line utilities for executing complex manipulations on VCF files. The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. Homepage: https://github.com/vcflib/vcflib#vcflib URL: https://github.com/vcflib/vcflib#vcflib

vcftools bio 0.1.16, 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 URL: https://vcftools.github.io Keyword:bio

velvet bio 1.2.10

Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ 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

viennarna bio 2.4.9, 2.4.11, 2.4.10

Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/ Keyword:bio

vinalc - 1.3.0

Description: A very popular PC-based molecular docking program, AutoDock Vina, was modified and parallelized, using an MPI and multithreading hybrid scheme, and potentially can be used in the future on exascale machines, without sacrificing accuracy. The resulting program scales up to more than 15K CPUs with a very low overhead cost. Homepage: https://plsuser.llnl.gov/bbs/vinalc/index.html URL: https://plsuser.llnl.gov/bbs/vinalc/index.html

virsorter - 1.0.6

Description: VirSorter: mining viral signal from microbial genomic data. Homepage: https://github.com/simroux/VirSorter URL: https://github.com/simroux/VirSorter Extensions: List::MoreUtils-0.428, Parallel::ForkManager-1.06

visit vis 2.13.0, 2.12.3, 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 1.9.4a43, 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: https://www.ks.uiuc.edu/Research/vmd URL: https://www.ks.uiuc.edu/Research/vmd Keyword:vis

vmtk - 1.4.0

Description: vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. Homepage: http://www.vmtk.org URL: http://www.vmtk.org

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 2.15.2, 2.5.0, 2.13.3, 2.9.1, 2.13.4, 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, 8.2.0, 8.1.1, 9.0.1

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 URL: http://www.vtk.org Compatible modules: python/3.5.4, python/3.6.3, python/3.7.4 Keyword:vis

vtk-mpi vis 9.0.1, 6.3.0

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 URL: http://www.vtk.org Compatible modules: python/3.8, python/3.7, python/3.6 Keyword:vis

vtune tools 2018.3, 2019.3, 2020.1

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

wannier90 - 1.2, 3.0.0, 3.1.0

Description: The Maximally-Localised Generalised Wannier Functions calculates the counterpart of localized molecular orbitals for crystalline systems from the wavefuction. Homepage: http://www.wannier.org/ URL: http://www.wannier.org/

wannier90-abinit - 2.0.1.1

Description: A tool for obtaining maximally-localised Wannier functions Homepage: http://www.wannier.org URL: http://www.wannier.org

wgrib2 geo 3.0.0, 2.0.7

Description: A program to decode/manipulate GRIB-2 files. Homepage: http://www.cpc.noaa.gov/products/wesley/wgrib2/ URL: http://www.cpc.noaa.gov/products/wesley/wgrib2/ Keyword:geo

wham math 2.0.9.1

Description: fast, memory efficient implementation of the Weighted Histogram Analysis Method (WHAM). Homepage: http://membrane.urmc.rochester.edu/content/wham Keyword:math

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 3.9.1, 3.8.0, 3.8.1, 4.1, 4.2

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. The WPS Geographical Input Data are included in the geog directory. Homepage: http://www.wrf-model.org Keyword:geo

wrf geo 4.2.1, 3.9.1.1, 4.1.2, 3.8.1, 3.8.0, 4.1.3

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

wtdbg2 - 2.5

Description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output Homepage: https://github.com/ruanjue/wtdbg2 URL: https://github.com/ruanjue/wtdbg2

wxwidgets tools 3.1.1

Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature. Homepage: http://www.wxwidgets.org/ Keyword:tools

xcrysden vis 1.6.2, 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

xdrfile tools 1.1.4

Description: library for reading and writing xtc, edr and trr files Homepage: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library URL: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library Keyword:tools

xerces-c++ tools 3.1.1, 3.2.2

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/ URL: http://xerces.apache.org/xerces-c/ Keyword:tools

xgboost math 0.7

Description: XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. Homepage: https://github.com/dmlc/xgboost Keyword:math

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

xmm-sas phys 16.1.0

Description: The Science Analysis System (SAS) is a collection of tasks, scripts and libraries, specifically designed to reduce and analyze data collected by the XMM-Newton observatory. Homepage: https://www.cosmos.esa.int/web/xmm-newton/sas Extensions: Switch-2.17, XML::LibXML-2.0132 Keyword:phys

xtb - 6.3.3, 6.3.0
yaehmop chem 3.0.3

Description: "Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) was developed by Greg Landrum whilest a graduate student in the research group of Professor Roald Hoffmann at Cornell University. YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions. Homepage: http://yaehmop.sourceforge.net/ Keyword:chem

yambo - 4.5.0

Description: Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. Homepage: http://www.yambo-code.org URL: http://www.yambo-code.org

yaxt tools 0.9.0, 0.5.1, 0.6.0

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

Message Passing Interface

GNU Compiler Collection, an open source compiler collection

Intel Math Kernel Library, a software library of optimized math routines

General Purpose cluster: Béluga, Cedar, or Graham

HyperText Transfer Protocol