last updated: Wednesday, 21-Oct-2020 12:12:03 EDT

Great Lakes cluster software catalog

        

Abaqus
==============================================================================
Description:  Abaqus FEA product suite for engineering problems.
Versions:     2017; 2018; 2019; 6.14-1
License:      Non-commercial research, Academic Institution License
              Agreement
Categories:   FEA, dynamic vibration, impact/crash, thermal coupling
==============================================================================


ABINIT
==============================================================================
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 basis.
Versions:     8.0.8
License:
Categories:   Electronic Structure, Ab Initio, Density Functional Theory
==============================================================================


AdapterRemoval
==============================================================================
Description:  This program searches for and removes remnant adapter
              sequences from your read data.
Versions:     2.3.1
License:      GNU GENERAL PUBLIC LICENSE
Categories:   Bioinformatics
==============================================================================


Allinea Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     19.0.4; 19.1.4; 20.0.2
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


Allinea Reports
==============================================================================
Description:  Parallel profiling tool.
Versions:     19.0.4; 19.1.4; 20.0.2
License:      Not available
Categories:   Programming, profiler, performance
==============================================================================


almaBTE
==============================================================================
Description:  almaBTE allows the user to calculate thermal transport
              properties of heterogeneous structures, using only ab-initio
              data, and solving the phonon Boltzmann Transport Equation
              (BTE).
Versions:     1.3.2
License:      http://www.almabte.eu/
Categories:   Electronic Structure, crystal structures, transport
==============================================================================


amber
==============================================================================
Description:  A package of molecular simulation programs which includes
              source code and demos.
Versions:     18
License:      Campus Agreement
Categories:   Computational Chemistry
==============================================================================


Anaconda2
==============================================================================
Description:  Python Data Science Distribution
Versions:     2019.03
License:
Categories:   Python, Programming, Scripting, numpy, scipy, matplotlib,
              ipython, jupyter
==============================================================================


Anaconda3
==============================================================================
Description:  Python Data Science Distribution
Versions:     2019.07; 2020.02; 5.2.0
License:
Categories:   Python, Programming, Scripting, numpy, scipy, matplotlib,
              ipython, jupyter
==============================================================================


Anvi'o
==============================================================================
Description:  Anvi'o is an analysis and visualization platform for 'omics
              data.
Versions:     5.4
License:      GPL3
Categories:   bioinformatics, genomics, visualization
==============================================================================


archivetar
==============================================================================
Description:  Parallel archive manipulation tool
Versions:     0.2.0; 0.3.0; 0.9.1
License:      https://github.com/brockpalen/archivetar/blob/master/LICENSE
Categories:   Utility
==============================================================================


Armadillo
==============================================================================
Description:  A high quality linear algebra library (matrix maths) for C++
              language, aiming towards a good balance between speed and ease
              of use
Versions:     9.600.6
License:      http://arma.sourceforge.net/faq.html#licenses
Categories:   Programming, C++, library
==============================================================================


ASE
==============================================================================
Description:  Atomic Simulation Environment (ASE) is a set of tools and
              Python modules for setting up, manipulating, running,
              visualizing and analyzing atomistic simulations.
Versions:     3.15.0
License:      https://wiki.fysik.dtu.dk/ase/development/licenseinfo.html
Categories:   Atomic Simulation
==============================================================================


Augustus
==============================================================================
Description:  AUGUSTUS is a program that predicts genes in eukaryotic
              genomic sequences.
Versions:     3.3
License:      GNU GPL
Categories:   Bioinformatics, Sequencing, gene prediction
==============================================================================


bamtools
==============================================================================
Description:  BamTools both a C++ API and a command-line toolkit for BAM
              files.
Versions:     2.5.1
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


bartender
==============================================================================
Description:  Bartender is a c++ tool that is designed to process random
              barcode data.
Versions:     1.1
License:      ???
Categories:   Bioinformatics gene genefinding genetics
==============================================================================


Bazel
==============================================================================
Description:  Bazel is an open-source build and test tool.
Versions:     0.29.1
License:      GPLv2 with linking exception
Categories:   programming
==============================================================================


bcftools
==============================================================================
Description:  BCFtools is a set of utilities that manipulate variant calls
              in the Variant Call Format (VCF) and its binary counterpart
              BCF
Versions:     1.7
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


bcl2fastq2
==============================================================================
Description:  demultiplexes sequencing data and converts base call (BCL)
              files into FASTQ files
Versions:     2.20.0.422
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


BEAST
==============================================================================
Description:  BEAST 2 is a cross-platform program for Bayesian
Versions:     2.6.2
License:      GNU LGPL 2.1
Categories:   Bioinformatics, Bayesian, MCMC
==============================================================================


BEDOPS
==============================================================================
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.
Versions:     2.4.35
License:      GNU GPL v2
Categories:   Bioinformatics, Genomics
==============================================================================


bedtools
==============================================================================
Description:  a swiss-army knife of tools for a wide-range of genomics
              analysis tasks.
Versions:     2.25.0; 2.29.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


BerkeleyGW
==============================================================================
Description:  BerkeleyGW 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.
Versions:     2.1
License:      http://www.berkeleygw.org/?q=node/6
Categories:   quasiparticle properties, materials
==============================================================================


BiodiversityR
==============================================================================
Description:  R libraries necessary for BiodiversityR
Versions:     3.6.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


bioperl
==============================================================================
Description:  BioPerl is Perl tools for Bioinformatics, genomics and Life
              Sciences.
Versions:     1.7.2
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


blasr
==============================================================================
Description:  Pacbio utilites for various sequence alignment tasks
Versions:     5.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


blat
==============================================================================
Description:  Standalone blat sequence search command line tool
Versions:     34x1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Boost
==============================================================================
Description:  Boost C++ library collection.
Versions:     1.70.0; 1.50.0; 1.73.0
License:      http://www.boost.org/users/license.html
Categories:   Programming, C++, library
==============================================================================


bowtie
==============================================================================
Description:  Bowtie is an ultrafast, memory-efficient short read aligner.
Versions:     1.2.2
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


bowtie2
==============================================================================
Description:  Bowtie 2 is an ultrafast and memory-efficient tool for
              aligning sequencing reads to long reference sequences.
Versions:     2.1.0; 2.3.4.3; 2.4.1
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Bucky
==============================================================================
Description:  program to combine molecular data from multiple loci
Versions:     1.4.4
License:      http://pages.stat.wisc.edu/~ane/bucky/index.html
Categories:   Bioinformatics, assemby
==============================================================================


bwa
==============================================================================
Description:  BWA is a software package for mapping low-divergent sequences
              against a large reference genome, such as the human genome.
Versions:     0.7.15
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


canu
==============================================================================
Description:  A single molecule sequence assembler for genomes large and
              small.
Versions:     1.8; 2.1
License:
Categories:   Bioinformatics, Sequencing
==============================================================================


CAP3
==============================================================================
Description:  CAP3 Sequence Assembly Program
Versions:     20150210
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


CCDC
==============================================================================
Description:  Protein ligand docking software
Versions:     2019.3; 2020.0.1
License:      https://guides.lib.umich.edu/c.php?g=283163&p=6437098
Categories:   Protein, docking, ligand, molecule
==============================================================================


cd-hit
==============================================================================
Description:  CD-HIT is a very widely used program for clustering and
              comparing protein or nucleotide sequences.
Versions:     4.7
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellprofiler
==============================================================================
Description:  CellProfiler is free, open-source software for quantitative
              analysis of biological images.
Versions:     3.1.8; 3.1.9
License:      BSD 3-clause license
Categories:   Bioinformatics, biology, imaging, analysis
==============================================================================


cellranger
==============================================================================
Description:  Cell Ranger is a set of analysis pipelines that process
              Chromium single-cell RNA-seq output
Versions:     3.1.0; 4.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerARC
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              Multiome ATAC + Gene Expression sequencing data
Versions:     1.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerATAC
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              ATAC data
Versions:     1.2.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerDNA
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              data
Versions:     1.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Centrifuge
==============================================================================
Description:  Centrifuge is a very rapid and memory-efficient system for the
              classification of DNA sequences from microbial samples, with
              better sensitivity than and comparable accuracy to other
              leading systems.
Versions:     1.0.3
License:      GPL3
Categories:   bioinformatices sequencing indexing gene classifications reads
              genome
==============================================================================


CMake
==============================================================================
Description:  CMake cross-platform make system.
Versions:     3.13.2; 3.17.3
License:      https://cmake.org/licensing/
Categories:   Utility, programming, compiler
==============================================================================


COMSOL
==============================================================================
Description:  COMSOL is multiphysics simulation software.
Versions:     5.5
License:
              https:/www.comsol.com/documentation/5.5/COMSOL_SoftwareLicense
              Agreement.pdf
Categories:   Multiphysics, simulation
==============================================================================


concoct
==============================================================================
Description:  CONCOCT bins metagenomic contigs
Versions:     1.0.0
License:      FreeBSD
Categories:   bioinformatics, genomics
==============================================================================


CONVERGE
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
              CONVERGE is a CFD code with adaptive meshing.
Versions:     3.0.14; 3.0.8; 3.0.9
License:      Provided by licensed labs
Categories:   Fluid dynamics, CFD, adaptive mesh
==============================================================================


CUBIT
==============================================================================
Description:  CUBIT is a full-featured software toolkit for robust
              generation of two- and three-dimensional finite element
              meshes.
Versions:     13.2
License:      https://cubit.sandia.gov/public/licensing.html
Categories:   mesh
==============================================================================


cuda
==============================================================================
Description:  CUDA compilers and libraries.
Versions:     10.0.130; 10.1.105; 10.1.243; 11.0.2; 8.0.61; 9.1.85; 9.2.148
License:      http://docs.nvidia.com/cuda/eula/index.html
Categories:   CUDA, gpu, library, programming
==============================================================================


cudnn
==============================================================================
Description:  cuDNN libraries.
Versions:     10.0-v7.6; 10.1-v7.6.4; 10.1-v7.6; 11.0-v8.0.1; 9.2-v7.6.5
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, cuDNN, deep learning, neural
              network
==============================================================================


cufflinks
==============================================================================
Description:  Transcriptome assembly and differential expression analysis
              for RNA-Seq.
Versions:     2.2.1
License:      Cufflinks is provided under the OSI-approved Boost License
Categories:   Bioinformatics
==============================================================================


CUPTI
==============================================================================
Description:  CUDA Profiler Tools Interface
Versions:     10.1.105; 8.0.61; 9.2.148
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, Profiler
==============================================================================


cutadapt
==============================================================================
Description:  cutadapt removes adapter sequences from high-throughput
              sequencing data. This is usually necessary when the read
              length of the sequencing machine is longer than the molecule
              that is sequenced, for example when sequencing microRNAs.
Versions:     1.18
License:      Public Domain
Categories:   Bioinformatics, Sequencing
==============================================================================


dalton
==============================================================================
Description:  A powerful tool for a wide range of molecular properties at
              different levels of theory
Versions:     2018-3000mo400mc
License:
Categories:   Electronic Structure, Ab Initio, Density Functional Theory
==============================================================================


DosageConvertor
==============================================================================
Description:  DosageConvertor is a C++ tool to convert dosage files (in VCF
              format) from Minimac3/4 to other formats such as MaCH or
              PLINK.
Versions:     1.0.0
License:
Categories:   Containers, Bioinformatics, genetics
==============================================================================


Exonerate
==============================================================================
Description:  Exonerate is a generic tool for pairwise sequence comparison.
              It allows you to align sequences using a many alignment
              models, either exhaustive dynamic programming or a variety of
              heuristics.
Versions:     2.4.0
License:      GPLv3
Categories:   Bioinformatics, Sequencing, Alignment
==============================================================================


fastcn
==============================================================================
Description:  A pipeline for the fast estimation of copy-number based on
              read depth using the multi-mapper mrsFAST.
Versions:     1.0
License:      GPL
Categories:   Bioinformatics
==============================================================================


fastme
==============================================================================
Description:  A distance-based phylogeny inference program
Versions:     2.1.6.1
License:      GPL
Categories:   Bioinformatics
==============================================================================


fastqc
==============================================================================
Description:  A quality control tool for high throughput sequence data.
Versions:     0.11.5; 0.11.8
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


fasttree
==============================================================================
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.
Versions:     2.1.10
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


fastx-toolkit
==============================================================================
Description:  A collection of command line tools for Short-Reads FASTA/FASTQ
              files preprocessing
Versions:     0.0.14
License:      GNU Affero General Public License
Categories:   Bioinformatics, sequencing
==============================================================================


fdmnes
==============================================================================
Description:  FDMNES is an ab initio, free and open source, parallelled
              under MPI, code which calculates the XANES, RXS and XMCD
              spectra.
Versions:     2016.07.15; 2019.07.19
License:      free and open source
Categories:   Geometric and electronic structure, near-edge, ab initio
==============================================================================


FDS
==============================================================================
Description:  Fire Dynamics Simulator (FDS) is a computational fluid
              dynamics (CFD) model of fire-driven fluid flow.
Versions:     6.6.0; 6.7.1; 6.7.4
License:      https://www.nist.gov/services-resources/software/fds-and-
              smokeview
Categories:   CFD, Navier-Stokes, fire
==============================================================================


FDTD Solutions
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
              Lumerical FDTD Solutions is a high performance 3D FDTD-method
              Maxwell solver for the design, analysis and optimization of
              nanophotonic devices, processes and materials.
Versions:     2020a
License:      commercial, https://www.lumerical.com/tcad-
              products/licensing/license_agreement.html
Categories:   FDTD, maxwell, design, solver, analysis, optimization, optics,
              photonics, 3D
==============================================================================


FFMPEG
==============================================================================
Description:  FFMPEG is a complete, cross-platform solution to record,
              convert and stream audio and video.
Versions:     3.0.2; 3.2.4
License:      https://ffmpeg.org/legal.html
Categories:   audio, video, codec, transcoder
==============================================================================


fftw
==============================================================================
Description:  Libraries for computation of discrete Fourier transform.
Versions:     3.3.8
License:      http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories:   Library, Development, Core
==============================================================================


FINE/Marine
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
              FINE/Marine is a licensed package for CFD simulation of mono-
              fluid and multi-fluid flows.
Versions:     9.1
License:      (Non-commercial) Academic Research
Categories:   finemarine, CFD, fluid, flow solver
==============================================================================


FreeSurfer
==============================================================================
Description:  FreeSurfer MRI processing and analysis software.
Versions:     6.0.0; 7.1.0
License:      http://freesurfer.net/fswiki/FreeSurferSoftwareLicense
Categories:   MRI, neuroimaging, neuroscience
==============================================================================


FSL
==============================================================================
Description:  FSL suite of MRI neuroimaging tools.
Versions:     6.0.1; 6.0.3
License:      http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories:   fMRI, DTI, neuroimaging, neuroscience
==============================================================================


funannotate
==============================================================================
Description:  Funannotate is a genome prediction, annotation, and comparison
              software package.
Versions:     1.7.3
License:      ???
Categories:   Bioinformatics gene genefinding genetics
==============================================================================


fusioncatcher
==============================================================================
Description:  FusionCatcher searches for novel/known somatic fusion genes,
Versions:     1.20
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


gatk
==============================================================================
Description:  Toolkit for variant discovery and genotyping
Versions:     3.7; 4.1.0.0
License:      Broad Institute Software License Agreement
Categories:   Bioinformatics
==============================================================================


Gaussian
==============================================================================
Description:  Gaussian is an electronic structure program.
Versions:     09-revD01; 16-revA03-avx2
License:      Academic, noncommercial research and instructional use only.
Categories:   electronic structure, molecular
==============================================================================


gcc
==============================================================================
Description:  GNU compiler suite
Versions:     4.8.5; 8.2.0; 9.2.0
License:      GPL
Categories:   Compiler, programming, development
==============================================================================


GDAL
==============================================================================
Description:  GDAL is a translator library for raster and vector geospatial
              data formats.
Versions:     3.0.1
License:      https://gdal.org/license.html
Categories:   GIS, geospatial, raster, vector, graphics
==============================================================================


genblast
==============================================================================
Description:  genBlast is a computational gene prediction program that is
              based on protein homology
Versions:     1.39
License:      ???
Categories:   Bioinformatics
==============================================================================


genscan
==============================================================================
Description:  GENSCAN is a general-purpose gene identification program
Versions:     1.0
License:      Academic at http://hollywood.mit.edu/gendist.html
Categories:   Bioinformatics, Sequencing
==============================================================================


GEOS
==============================================================================
Description:  OpenGIS Simple Features for SQL spatial predicate functions
              and spatial operators.
Versions:     3.7.2
License:      GNU LGPL v2.1
Categories:   GIS, Geometry, OSGeo
==============================================================================


ghostscript
==============================================================================
Description:  Ghostscript is an interpreter for the PostScript language and
              for PDF.
Versions:     9.27
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


git
==============================================================================
Description:  Git version control software
Versions:     2.20.1
License:      GPL version 2
Categories:   Utility, development, version control
==============================================================================


globus-cli
==============================================================================
Description:  The CLI provides an interface to Globus services from the
              shell, and is suited to both interactive and simple scripting
              use cases.
Versions:     1.11.0
License:
Categories:   Data movement
==============================================================================


GMT - Generic Mapping Tools
==============================================================================
Description:  an open source collection of 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.
Versions:     5.4.3
License:      LGPL
Categories:   GIS projection map plot geography
==============================================================================


Go
==============================================================================
Description:  Go is an open source programming language that makes it easy
              to build simple, reliable, and efficient software.
Versions:     1.12.5; 1.13
License:      https://golang.org/LICENSE?m=text
Categories:   Go, Programming
==============================================================================


graph-tool
==============================================================================
Description:  graph-tool is an efficient Python module for manipulation and
              statistical analysis of graphs (a.k.a. networks)
Versions:     2.29
License:      GNU GPLv3
Categories:   Networks, Graphs, Python
==============================================================================


gromacs
==============================================================================
Description:  GROMACS performs Newtonian simulatons of molecular dynamics.
Versions:     2019.3; 2020.2
License:
Categories:
==============================================================================


GSL
==============================================================================
Description:  GNU scientific libraries
Versions:     2.5
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


GT-Suite
==============================================================================
Description:  GT-SUITE is a multi-physics platform for constructing models
              of general systems.
Versions:     2017
License:      Non-commercial research, Academic Institution License
              Agreement
Categories:   multi-physics, CFD, acoustics, thermal, mechanical, dynamics,
              chemistry
==============================================================================


GTDB-Tk
==============================================================================
Description:  GTDB-Tk is a software toolkit for assigning objective
              taxonomic classifications to bacterial and archaeal genomes
              based on the Genome Database Taxonomy GTDB. It is designed to
              work with recent advances that allow hundreds or thousands of
              metagenome-assembled genomes (MAGs) to be obtained directly
              from environmental samples. It can also be applied to isolate
              and single-cell genomes.
Versions:     0.3.3
License:      GNU GPLv3
Categories:   Genome Database Taxonomy, Taxonomic Classification
==============================================================================


gubbins
==============================================================================
Description:  Genealogies Unbiased By recomBinations In Nucleotide Sequences
Versions:     2.3.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


guppy
==============================================================================
Description:  Local accelerated basecalling for Nanopore data
Versions:     4.0.15
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Gurobi
==============================================================================
Description:  Gurobi optimization problem solver.
Versions:     8.1.1; 9.0.2
License:      http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:   Optimization, linear programming
==============================================================================


HDF5
==============================================================================
Description:  HDF5 data libraries and utilities.
Versions:     1.10.5; 1.8.21
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


heap
==============================================================================
Description:  Heap, enables robustly sensitive and accurate calling of SNPs
Versions:     0.8.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


HISAT2
==============================================================================
Description:  HISAT2 is a fast and sensitive alignment program for mapping
              next-generation sequencing reads (both DNA and RNA) to a
              population of human genomes (as well as against a single
              reference genome).
Versions:     2.1.0
License:      http://www.gnu.org/licenses/gpl-3.0.html
Categories:   Biostatistics, Python, Application
==============================================================================


HMMER
==============================================================================
Description:  HMMER: biosequence analysis using profile hidden Markov models
Versions:     3.1b2
License:      GNU GPL v3
Categories:   Bioinformatics, Sequencing, Markov
==============================================================================


homer
==============================================================================
Description:  HOMER is a suite of tools for Motif Discovery and ChIP-Seq
              analysis.
Versions:     4.10; 4.8
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


htslib
==============================================================================
Description:  C library for high-throughput sequencing data formats
Versions:     1.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


IDL
==============================================================================
Description:  IDL analysis and visualization software.
Versions:     8.5; 8.7.2
License:      http://www.harrisgeospatial.com/company/legal/eula.aspx
Categories:   Visualization
==============================================================================


igv
==============================================================================
Description:  The Integrative Genomics Viewer (IGV): a high-performance
              visualization tool for interactive exploration of large,
              integrated genomic datasets.
Versions:     2.7.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Image libraries
==============================================================================
Description:  Image libraries
Versions:     190711.1; 160610; 170303; 190711
License:      more than one
Categories:   libraries, programming, jpeg, gif, png, jbigkit, tiff,
              libwebp, lcms2, jasper
==============================================================================


impi
==============================================================================
Description:  Intel MPI runtime
Versions:     2018.4.274; 4.1.3; 2018.3.222
License:      GPL
Categories:   MPI, MPICH, programming
==============================================================================


indri
==============================================================================
Description:  Indri is a search engine that provides state-of-the-art text
              search and a rich structured query language for text
              collections
Versions:     5.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Intel
==============================================================================
Description:  Intel compiler suite.
Versions:     14.0.4; 18.0.5; 19.1
License:      None provided
Categories:   Library, Development, Core
==============================================================================


ITK
==============================================================================
Description:  ITK is an open-source system for medical image processing.
Versions:     5.1.0
License:      https://software.intel.com/en-us/license/intel-simplified-
              software-license
Categories:   Library, development, image processing, MRI, NIfTI
==============================================================================


iVar
==============================================================================
Description:  iVar is a computational package that contains functions for
              viral amplicon-based sequencing
Versions:     1.2.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


JAGS
==============================================================================
Description:  JAGS is Just Another Gibbs Sampler. It is a program for
              analysis of
Versions:     4.3.0
License:      GNU GPL v2
Categories:   Bayesian, Markov, MCMC
==============================================================================


jed
==============================================================================
Description:  The JED Programmer's Editor
Versions:     0.99-19
License:      GNU General Public License
Categories:   Editors
==============================================================================


jellyfish
==============================================================================
Description:  Jellyfish is a tool for fast, memory-efficient counting of
              k-mers in DNA.
Versions:     2.2.8
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Julia
==============================================================================
Description:  Julia is a high-level, high-performance dynamic language for
              technical computing. The main homepage for Julia can be found
              at julialang.org.
Versions:     1.1.1; 1.4.0
License:      MIT Licenses
Categories:   Programming
==============================================================================


kallisto
==============================================================================
Description:  kallisto is a program for quantifying abundances of
              transcripts from bulk and single-cell RNA-Seq data, or more
              generally of target sequences using high-throughput sequencing
              reads.
Versions:     0.46.0
License:      BSD Simplified 2-Clause
Categories:   Bioinformatics
==============================================================================


Knitro
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
              Knitro is an optimization software library for finding
              solutions of both continuous optimization models as well as
              discrete optimization models with integer or binary variables.
              Knitro is primarily designed for finding local optimal
              solutions of large scale continuous nonlinear problems.
Versions:     10.1.0-z
License:      https://www.artelys.com/en/optimization-tools/knitro
Categories:   optimization, nonlinear solver
==============================================================================


LAMMPS
==============================================================================
Description:  LAMMPS is a classical molecular dynamics code that models an
              ensemble of particles.
Versions:     31Mar17; 7Aug19
License:      http://lammps.sandia.gov/doc/Section_intro.html#open-source-
              distribution
Categories:   molecular dynamics
==============================================================================


LAPACK
==============================================================================
Description:  LAPACK is written in Fortran 90 and provides routines for
              solving systems of simultaneous linear equations, least-
              squares solutions of linear systems of equations, eigenvalue
              problems, and singular value problems.
Versions:     3.8.0
License:      http://www.netlib.org/lapack/LICENSE.txt
Categories:   Libraries
==============================================================================


Launcher
==============================================================================
Description:  A framework for running large collections of serial or multi-
              threaded applications
Versions:     3.5; 3.7
License:      GPLv2
Categories:   Core
==============================================================================


longranger
==============================================================================
Description:  Long Ranger is a set of analysis pipelines that processes
              Chromium sequencing output to align reads and call and phase
              SNPs, indels, and structural variants.
Versions:     2.2.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


macs2
==============================================================================
Description:  Model-based Analysis of ChIP-Seq (MACS), for identifying
              transcript factor binding sites.
Versions:     2.1.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


mafft
==============================================================================
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.
Versions:     7.310
License:      http://mafft.cbrc.jp/alignment/software/license66.txt
Categories:   Bioinformatics, Alignment
==============================================================================


magma
==============================================================================
Description:  Magma is a software package for computations in algebra,
              number theory, algebraic geometry and algebraic combinatorics.
Versions:     2.25-2
License:      Restricted; contact ITS Software Services.
Categories:   Algebra, number theory, algebraic geometry and combinatorics.
==============================================================================


Mathematica
==============================================================================
Description:  Mathematical and technical computing package.
Versions:     12.0.0; 12.1.0
License:      http://www.wolfram.com/legal/agreements/wolfram-
              mathematica.html
Categories:   Mathematics, symbolic algebra
==============================================================================


Matlab
==============================================================================
Description:  Matlab programming environment.
Versions:     R2018b; R2019b; R2020a
License:
Categories:   Mathematics, programming, simulation
==============================================================================


MCL
==============================================================================
Description:  The MCL algorithm is short for the Markov Cluster Algorithm, a
              fast and scalable unsupervised cluster algorithm for graphs
              (also known as networks) based on simulation of (stochastic)
              flow in graphs.
Versions:     1:14-137
License:      GNU GPL v3
Categories:   Clustering, Graphs
==============================================================================


Meep
==============================================================================
Description:  Meep (or MEEP) is a free finite-difference time-domain (FDTD)
              simulation software package.
Versions:     1.14.0
License:      GPL
Categories:
==============================================================================


MEGAHIT
==============================================================================
Description:  MEGAHIT is an ultra-fast and memory-efficient NGS assembler.
              It is optimized for metagenomes, but also works well on
              generic single genome assembly (small or mammalian size) and
              single-cell assembly.
Versions:     1.2.8
License:      GNU GPL v3
Categories:   Bioinformatics, Genomics, Assembly
==============================================================================


mesa
==============================================================================
Description:  A 3D graphics library
Versions:     19.0.8
License:
Categories:   3D Graphics, OpenGL
==============================================================================


minimap2
==============================================================================
Description:  Minimap2 is a versatile sequence alignment program that aligns
              DNA or mRNA sequences against a large reference database.
Versions:     2.17
License:
Categories:   Containers, Bioinformatics, genetics
==============================================================================


MKL
==============================================================================
Description:  Intel optimized BLAS/LAPACK libraries, also including FFT and
              other mathematical and statistical routines.
Versions:     11.1.2; 2018.0.4; 2020.0.0
License:      https://software.intel.com/en-us/license/intel-simplified-
              software-license
Categories:   Library, Development, Core, BLAS, LAPACK
==============================================================================


monocle 3
==============================================================================
Description:  A toolkit for analyzing single-cell gene expression
              experiments
Versions:     3.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


mothur
==============================================================================
Description:  Mothur fill the needs of the microbial ecology community.
Versions:     1.42.1; 1.42.3; 1.43.0
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


MPI for Python (mpi4py)
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     3.0.2
License:      https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst
Categories:   Programming, python, MPI, mpi4py
==============================================================================


mpibzip2
==============================================================================
Description:  MPI Parallel bzip2 compataible compressor/decompressor
Versions:     0.6
License:
Categories:   Utility
==============================================================================


MPIFileUtils
==============================================================================
Description:  Parallel file manipulation utilities.
Versions:     0.10.2-arcts
License:      https://github.com/brockpalen/mpifileutils/blob/master/LICENSE
Categories:   Utility
==============================================================================


MrBayes
==============================================================================
Description:  MrBayes is a program for Bayesian inference and model choice
              across a wide range of phylogenetic and evolutionary models.
              MrBayes uses Markov chain Monte Carlo (MCMC) methods to
              estimate the posterior distribution of model parameters.
Versions:     3.2.6
License:      GNU GPL v3 or later
Categories:   Bioinformatics, phylogenetics, Bayesian, MCMC
==============================================================================


MRtrix
==============================================================================
Description:  MRtrix provides a set of tools to perform various advanced
              diffusion MRI analyses.
Versions:     3.0_RC3
License:      Mozill Public License, http://mozilla.org/MPL/2.0/
Categories:   fMRI, diffusion-weighted MRI, tractography, neuroimaging
==============================================================================


mummer
==============================================================================
Description:  a system for aligning large DNA sequences to one another.
Versions:     4.0.0beta2
License:      open source with citation: https://mummer4.github.io/
Categories:   Bioinformatics, allignment
==============================================================================


MUSCLE
==============================================================================
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.
Versions:     3.8.31
License:      Public Domain
              (http://www.drive5.com/muscle/manual/license.html)
Categories:   Bioinformatics, Alignment
==============================================================================


ncbi-blast
==============================================================================
Description:  Basic Local Alignment Search Tool (BLAST) is the most widely
              used sequence similarity tool.
Versions:     2.9.0
License:      United States Government Work under the terms of the United
              States Copyright Act
Categories:   Bioinformatics
==============================================================================


NCL
==============================================================================
Description:  NCAR command language for visualization.
Versions:     6.6.2
License:      http://www2.ucar.edu/terms-of-use
Categories:   Visualization, NetCDF, HDF5
==============================================================================


NCO
==============================================================================
Description:  The NCO toolkit manipulates and analyzes data stored in
              netCDF-accessible formats, including DAP, HDF4, and HDF5.
Versions:     4.7.2
License:      GNU GPL v1.3 or later
Categories:   Utilities, netCDF
==============================================================================


ncview
==============================================================================
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. It runs on
              UNIX platforms under X11, R4 or higher.
Versions:     2.1.8
License:      GNU GPL V3
Categories:   netCDF, visual browser, utility
==============================================================================


NetCDF
==============================================================================
Description:  Libraries for creating and manipulating NetCDF files.
Versions:     4.6.2
License:      https://www.ucar.edu/terms-of-use
Categories:   Library, Development, Core
==============================================================================


NetCDF Fortran
==============================================================================
Description:  Libraries for creating and manipulating NetCDF files using
              Fortran.
Versions:     4.4.5
License:      https://www.ucar.edu/terms-of-use
Categories:   Library, Development, Core
==============================================================================


NEURON
==============================================================================
Description:  NEURON is a simulation environment for modeling individual
              neurons and networks of neurons.
Versions:     7.5; 7.8.0
License:      GNU GPL
Categories:   Neuron, Simulation
==============================================================================


NLopt
==============================================================================
Description:  NLopt is library for nonlinear optimization
Versions:     2.6.2
License:      LGPL
Categories:   Programming, development
==============================================================================


NumPy
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     1.17.0
License:      http://www.numpy.org/license.html
Categories:   Programming, numerical library, BLAS, LAPACK, python
==============================================================================


nwchem
==============================================================================
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.
Versions:     6.8.1
License:
Categories:
==============================================================================


openblas
==============================================================================
Description:  BLAS provides standard interfaces for linear algebra,
              including BLAS1 (vector-vector operations), BLAS2 (matrix-
              vector operations), and BLAS3 (matrix-matrix operations).
Versions:     0.3.5; 0.3.9
License:      https://opensource.org/licenses/BSD-3-Clause
Categories:   Programming, C++, library
==============================================================================


OpenCV
==============================================================================
Description:  OpenCV (Open Source Computer Vision Library) is an open source
              computer vision and machine learning software library.
Versions:     3.1.0; 3.2.0
License:      http://opencv.org/
Categories:   computer vision, machine learning
==============================================================================


OpenCV Python Module
==============================================================================
Description:  This module sets up PYTHONPATH for python-anaconda to use
              OpenCV.
Versions:     2; 3
License:      N/A
Categories:   Python
==============================================================================


OpenFOAM
==============================================================================
Description:  OpenFOAM is a free, open source CFD software.
Versions:     4.1; extend-4.1; v1712; v1906; extend-4.0; v6-20190620
License:      http://www.openfoam.com/documentation/licencing.php
Categories:   CFD
==============================================================================


OpenJDK
==============================================================================
Description:  OpenJDK is a free and open-source implementation of the Java
              Platform.
Versions:     11.0.2; 12.0.2
License:      GPLv2 with linking exception
Categories:   Java, programming
==============================================================================


OpenMPI
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     1.10.7; 3.1.4; 3.1.6; 4.0.2; 4.0.4; 4.0.3
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


OpenRefine
==============================================================================
Description:  OpenRefine (previously Google Refine) is a powerful tool for
              working with messy data: cleaning it; transforming it from one
              format into another; and extending it with web services and
              external data.
Versions:     3.3
License:      BSD 3-Clause New or Revised License (see
              https://github.com/OpenRefine/OpenRefine/blob/master/LICENSE.t
              xt)
Categories:   Data cleaning, big data, data conversion
==============================================================================


openslide
==============================================================================
Description:  OpenSlide is a C library that provides a simple interface to
              read whole-slide images
Versions:     3.4.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


orca
==============================================================================
Description:  An ab initio, DFT, and semi-empirical SCF-MO package
Versions:     4.0.0; 4.2.1
License:      Academic
Categories:   Chemistry, ab initio
==============================================================================


orthofinder
==============================================================================
Description:  A robust statistical framework for reconstructing genomes from
              metagenomic data
Versions:     2e72973705c6; 2.3.3
License:      GPL and
              https://bitbucket.org/berkeleylab/metabat/src/master/Legal.txt
Categories:   Bioinformatics
==============================================================================


p4VASP
==============================================================================
Description:  This software is Open Source. p4VASP is a visualization suite
              for the Vienna Ab-initio Simulation Package (VASP).
Versions:     0.3.30
License:      http://www.p4vasp.at
Categories:   Electronic Structure, crystal symmetries, vizualization
==============================================================================


Parallel HDF5 (PHDF5)
==============================================================================
Description:  Parallel HDF5 data libraries and utilities.
Versions:     1.10.5
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


Paraview
==============================================================================
Description:  Paraview data analysis and visualization application.
Versions:     5.7.0
License:      http://www.paraview.org/paraview-license/
Categories:   Visualization, data analysis
==============================================================================


perl
==============================================================================
Description:  Perl is a general-purpose programming language
Versions:     5.22.1
License:      GPLv2
Categories:   Core
==============================================================================


perl-modules/1.0
==============================================================================
Description:  Perl addin modules for use with Perl version 5.16.3.
Versions:     1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


PGI compilers
==============================================================================
Description:  Compiler suite.
Versions:     19.1; 20.1
License:      http://www.pgroup.com/doc/LICENSE.txt
Categories:   Compiler, development, debugger, profiler
==============================================================================


PGPLOT Graphics Subroutine Library
==============================================================================
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.
Versions:     5.2
License:      PGPLOT is not public-domain software. However, it is freely
              available for non-commercial use. The source code and
              documentation are copyrighted by California Institute of
              Technology, and may not be redistributed or placed on public
              Web servers without permission. The software is provided is''
              with no warranty.
Categories:   Graphics, Plotting Software
==============================================================================


picard-tools
==============================================================================
Description:  A set of tools for working with high-throughput sequencing
              data
Versions:     2.8.1
License:      MIT License, Apache License V2.0
Categories:   Bioinformatics
==============================================================================


plink
==============================================================================
Description:  PLINK a whole genome association analysis toolset.
Versions:     1.9; 2.0
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


POVRAY
==============================================================================
Description:  High-quality raytracer for 3D graphics.
Versions:     3.7
License:
Categories:
==============================================================================


prank
==============================================================================
Description:  PRANK is a probabilistic multiple alignment program for DNA,
              codon and amino-acid sequences.
Versions:     170427
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Prodigal
==============================================================================
Description:  Prodigal (Prokaryotic Dynamic Programming Genefinding
              Algorithm) is a microbial (bacterial and archaeal) gene
              finding program.
Versions:     2.6.3
License:      GPL3
Categories:   Bioinformatics gene genefinding genetics
==============================================================================


PROJ
==============================================================================
Description:  PROJ is a generic coordinate transformation software.
Versions:     6.1.1
License:      MIT
Categories:   GIS, Library
==============================================================================


Python
==============================================================================
Description:  Python is a general purpose programming language
Versions:     3.7.4
License:      https://docs.python.org/3/license.html
Categories:   Programming, language
==============================================================================


qiime
==============================================================================
Description:  QIIME. (canonically pronounced chime) stands for Quantitative
              Insights Into Microbial Ecology.
Versions:     1.8.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


QoRTs
==============================================================================
Description:  package for management of RNS-Seq datasets
Versions:     .pkgInfo2; 1.3.6
License:      Public Domain
Categories:   bioinformatics, genomics
==============================================================================


qpopt
==============================================================================
Description:  Software package for solving dense linear and quadratic
              programs. If the quadratic objective function is convex
              (definite or semi definite), the solution obtained is a global
              optimum. For non-convex problems, the solution may be a local
              optimum or a dead-point (or unbounded).
Versions:     1.0-10
License:      http://www.sbsi-sol-optimize.com/asp/sol_qpopt.htm (Stanford
              University license)
Categories:   General-purpose dense linear programming, Convex or non-convex
              quadratic programming
==============================================================================


Quantum ESPRESSO
==============================================================================
Description:  Quantum ESPRESSO is an integrated suite of codes for
              electronic-structure calculations and materials modeling at
              the nanoscale.
Versions:     6.4.1; 6.5
License:      http://www2.mmm.ucar.edu/wrf/users/public.html
Categories:   electronic structure, materials modeling, ab initio quantum
              chemistry
==============================================================================


R
==============================================================================
Description:  R environment for statistical computing and graphics
Versions:     3.6.1; 3.4.1; 4.0.2; 2.3.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science
==============================================================================


RAxML
==============================================================================
Description:  RAxML (Randomized Axelerated Maximum Likelihood) is a program
              for sequential and parallel Maximum Likelihood based inference
              of large phylogenetic trees. It can also be used for post-
              analyses of sets of phylogenetic trees, analyses of alignments
              and, evolutionary placement of short reads.
Versions:     8.2.11
License:      GNU GPL v3
Categories:   Bioinformatics, Phylogentics
==============================================================================


rclone
==============================================================================
Description:  rclone is a command line program to sync files and directories
              to and from many cloud storage providers
Versions:     1.49.1
License:      MIT License
Categories:   File transfer, Utilities
==============================================================================


Rgeospatial
==============================================================================
Description:  A collection of R geospatial libraries
Versions:     2019-09-29
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, geospatial,
              geography, spatial, map
==============================================================================


roary
==============================================================================
Description:  Roary is a high speed stand alone pan genome pipeline
Versions:     3.12.0
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Ropenblas
==============================================================================
Description:  R OpenBLAS provides an optimized library for faster linear
              algebra computations.
Versions:     3.6.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, linear algebra, big data, data science
==============================================================================


Rosetta
==============================================================================
Description:  algorithms for computational modeling and analysis of protein
              structures
Versions:     3.13
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


RSEM
==============================================================================
Description:  RSEM is a software package for estimating gene and isoform
              expression levels from RNA-Seq data.
Versions:     1.3.1; 1.3.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


RSeurat
==============================================================================
Description:  R libraries necessary for Seurat
Versions:     3.6.1; 4.0.0; 3.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


RStudio Server
==============================================================================
Description:  RStudio Desktop is a graphichal user interface for R.
Versions:     1.2.1335; 1.3.959
License:      AGPL v3
Categories:   Statistics, graphics, big data, data science, IDE
==============================================================================


Rtidyverse
==============================================================================
Description:  R Tidyverse environment for statistical computing and graphics
Versions:     3.6.1; 4.0.2
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, tidyverse
==============================================================================


S-Lang
==============================================================================
Description:  An Interpreted powerful extension languange
Versions:     2.3.2
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


sage
==============================================================================
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. Mission: Creating a viable free open
              source alternative to Magma, Maple, Mathematica and Matlab.
Versions:     9.1
License:      GPL
Categories:   Mathematics software
==============================================================================


saige
==============================================================================
Description:  SAIGE is an R package with Scalable and Accurate
              Implementation of Generalized mixed model
Versions:     0.39
License:      BSD Simplified 2-Clause
Categories:   Bioinformatics
==============================================================================


salmon
==============================================================================
Description:  Salmon is a tool for wicked-fast transcript quantification
              from RNA-seq data.
Versions:     0.11.3; 0.7.2
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


samtools
==============================================================================
Description:  SAM (Sequence Alignment/Map) format is a generic format for
              storing large nucleotide sequence alignments.
Versions:     0.1.19; 1.5; 1.9
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


SAS
==============================================================================
Description:  SAS statistical system software.
Versions:     9.4-TS1M5
License:      Not available
Categories:   Statitics, econometrics
==============================================================================


SciPy
==============================================================================
Description:  Scientific libraries for use within Python.
Versions:     1.3.1
License:      http://www.scipy.org/scipylib/license.html
Categories:   Programming, python, solver
==============================================================================


SeqKit
==============================================================================
Description:  SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q
              file manipulation in Golang
Versions:     0.10.2
License:      MIT
Categories:   Bioinformatics
==============================================================================


shapeit
==============================================================================
Description:  SHAPEIT is a fast and accurate method for estimation of
              haplotypes (aka phasing) from genotype or sequencing data.
Versions:     2.r094; 4.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


sickle
==============================================================================
Description:  A windowed adaptive trimming tool for FASTQ files using
              quality
Versions:     1.33
License:      MIT software license
Categories:   bioinformatics trimming fastq
==============================================================================


Singularity
==============================================================================
Description:  Program for running containerized applications
Versions:     3.5.2
License:      https://github.com/sylabs/singularity/blob/master/LICENSE.md
Categories:   Container, docker, reproducible research
==============================================================================


SMALT
==============================================================================
Description:  SMALT aligns DNA sequencing reads with a reference genome
Versions:     0.7.6
License:      GPLv3
Categories:   Bioinformatics, Sequencing
==============================================================================


snptest
==============================================================================
Description:  SNPTEST is a program for the analysis of single SNP
              association in genome-wide studies
Versions:     2.5.4
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


spaceranger
==============================================================================
Description:  a set of analysis pipelines that process Visium spatial RNA-
              seq output and brightfield microscope images
Versions:     1.0.0; 1.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


spades
==============================================================================
Description:  SPAdes – St. Petersburg genome assembler – is an assembly
              toolkit containing various assembly pipelines
Versions:     3.14.0; 3.11.1
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


spanki
==============================================================================
Description:  TPMCalculator quantifies mRNA abundance directly from the
              alignments by parsing BAM files.
Versions:     0.0.3; 0.5.0
License:
Categories:   Bioinformatics
==============================================================================


spark
==============================================================================
Description:  Apache Spark is a unified analytics engine for large-scale
              data processing
Versions:     2.4.5; 3.0.0
License:      Apache, https://www.apache.org/licenses/LICENSE-2.0
Categories:   Statistics, big data, data science
==============================================================================


sratoolkit
==============================================================================
Description:  The SRA Toolkit and SDK from NCBI is a collection of tools and
              libraries for using data in the INSDC Sequence Read Archives.
Versions:     2.10.4; 2.7.0; 2.8.2-1; 2.9.6
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Stacks
==============================================================================
Description:  Stacks is a software pipeline for building loci from short-
              read sequences, such as those generated on the Illumina
              platform.
Versions:     2.41
License:      GNU GPL v3
Categories:   Phylogenetics, Genomics, Pipeline
==============================================================================


STAR
==============================================================================
Description:  Spliced Transcripts Alignment to a Reference
Versions:     2.5.2a; 2.7.5a
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


stargazer
==============================================================================
Description:  Stargazer is a bioinformatics tool for calling star alleles
              (haplotypes) in PGx genes
Versions:     1.0.8
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Stata/MP
==============================================================================
Description:  Statistical analysis software.
Versions:     15; 16
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


Stata/SE
==============================================================================
Description:  Statistical analysis software.
Versions:     15; 16
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


subread
==============================================================================
Description:  a tool kit for processing next-gen sequencing data
Versions:     1.6.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


swig
==============================================================================
Description:  SWIG is an interface compiler.
Versions:     3.0.12
License:      http://www.swig.org/legal.html
Categories:   Programming, compiler
==============================================================================


szip
==============================================================================
Description:  Szip is a compression library used with HDF5.
Versions:     2.1.1; 1.6.2
License:      https://www.hdfgroup.org/doc_resource/SZIP/
Categories:   Utility, compression
==============================================================================


tabix
==============================================================================
Description:  A useful tool that indexes large .vcf files
Versions:     1.7-2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


TBB
==============================================================================
Description:  Intel Thread Building Blocks.
Versions:     2020.0
License:      https://software.intel.com/en-us/articles/end-user-license-
              agreement
Categories:   Library, development, core, thread
==============================================================================


TensorFlow
==============================================================================
Description:  Machine learning platform for use within Python.
Versions:     1.15.0; 2.1.0
License:      Apache License 2.0
Categories:   Programming, machine learning library, python
==============================================================================


tophat
==============================================================================
Description:  TopHat is a program that aligns RNA-Seq reads to a genome in
              order to identify exon-exon splice junctions.
Versions:     2.1.1
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


transdecoder
==============================================================================
Description:  TransDecoder identifies candidate coding regions within
              transcriptsequences, such as those generated by de novo RNA-
              Seq transcript assemblyusing Trinity, or constructed based on
              RNA-Seq alignments to the genomeusing Tophat and Cufflinks.
Versions:     5.0.1
License:      BSD 3-clause
Categories:   bioinformatics sequencing coding transcript
==============================================================================


Transrate
==============================================================================
Description:  Transrate is software for de-novo transcriptome assembly
              quality analysis.
Versions:     1.0.3
License:      MIT License
Categories:   Bioinformatics, Assembly
==============================================================================


trimgalore
==============================================================================
Description:  a wrapper script to automate quality and adapter trimming
Versions:     0.6.5
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


trimmomatic
==============================================================================
Description:  Trimmomatic: A flexible read trimming tool for Illumina NGS
              data
Versions:     0.36
License:      GNU GPL v3
Categories:   Bioinformatics, Sequencing
==============================================================================


Trinity
==============================================================================
Description:  Trinity assembles transcript sequences from Illumina RNA-Seq
              data.
Versions:     2.10.0; 2.8.6
License:
              https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/
              master/LICENSE
Categories:   Bioinformatics, Assembly, Transcriptome
==============================================================================


UCSC-utilities
==============================================================================
Description:  UCSC Genome Browser Utilites.
Versions:     2019.09.10
License:      http://genome.ucsc.edu/license/
Categories:   Bioinformatics
==============================================================================


use.own
==============================================================================
Description:  Module to add personal module directory to module path.
Versions:     1.0
License:      None
Categories:   utility
==============================================================================


valgrind
==============================================================================
Description:  Valgrind is an instrumentation framework for building dynamic
              analysis tools.
Versions:     3.13.0; 3.15.0
License:      GNU GPL v2
Categories:   Utilities, Instrumentation
==============================================================================


VASP
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
              VASP, The Vienna Ab initio simulation package, a plane wave
              electronic structure code.
Versions:     5.4.4.18Apr17.p1
License:      https://www.vasp.at/index.php/faqs
Categories:   electronic structure code, molecular dynamics
==============================================================================


vcftools
==============================================================================
Description:  VCFtools is a program package designed for working with VCF
              files, such as those generated by the 1000 Genomes Project.
              The aim of VCFtools is to provide easily accessible methods
              for working with complex genetic variation data in the form of
              VCF files.
Versions:     0.1.15
License:      GPLv3
Categories:
==============================================================================


velvet
==============================================================================
Description:  Velvet is a de novo genomic assembler specially designed for
              short read sequencing technologies such as Solexa or 454.
Versions:     1.2.09
License:      GNU GPL v2
Categories:   Bioinformatics, Assembly
==============================================================================


veryfasttree
==============================================================================
Description:  VeryFastTree is a highly-tuned implementation of the
              FastTree-2 tool
Versions:     3.0.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


VisIt
==============================================================================
Description:  VisIt data analysis and visualization application.
Versions:     3.1.2
License:
Categories:   Visualization, data analysis
==============================================================================


vsearch
==============================================================================
Description:  We have implemented a tool called VSEARCH which supports de
              novo and reference based chimera detection, clustering, full-
              length and prefix dereplication, reverse complementation,
              masking, all-vs-all pairwise global alignment, exact and
              global alignment searching, shuffling, subsampling and
              sorting. It also supports FASTQ file analysis, filtering and
              conversion.
Versions:     2.7.1
License:      GNU GPL v3 or under the BSD 2-clause license
Categories:   Bioinformatics, metagenomics
==============================================================================


weblogo
==============================================================================
Description:  WebLogo is a web based application designed to make the
              generation of sequence logos as easy and painless as possible.
Versions:     2.8.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


WRF-Hydro
==============================================================================
Description:  The WRF-Hydro modeling system provides a means to couple
              hydrological model components to atmospheric models and other
              Earth System modeling architectures
Versions:     5.0.3
License:      https://ral.ucar.edu/projects/wrf_hydro/terms-of-use
Categories:   Weather Forecasting, atmospheric modeling, meteorology
==============================================================================


xmakemol
==============================================================================
Description:  xmakemol is a molecular/crystal structure visualization
              program.
Versions:     5.16h
License:
Categories:   Electronic Structure, crystal symmetries, vizualization
==============================================================================


Yasm
==============================================================================
Description:  Yasm assembler.
Versions:     1.3.0
License:      https://github.com/yasm/yasm/blob/master/BSD.txt
Categories:   assembler, programming
==============================================================================