last updated: Thursday, 24-Jul-2025 01:00:06 EDT
Abaqus
==============================================================================
Description: Abaqus FEA product suite for engineering problems.
Versions: 2022
License: Non-commercial research, Academic Institution License
Agreement
Categories: FEA, dynamic vibration, impact/crash, thermal coupling
==============================================================================
Absoft Pro Fortran
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
Absoft Pro Fortran Compiler
Versions: 18.0.2
License: http://www.absoft.com/literature/Absoftlicense.pdf
Categories: fortran, compiler, f95/f90
==============================================================================
AFNI
==============================================================================
Description: AFNI suite of MRI neuroimaging tools.
Versions: 18.0.27; 22.2.07
License: https://afni.nimh.nih.gov/legal_info
Categories: fMRI, DTI, MRI, neuroimaging, neuroscience
==============================================================================
AMPL
==============================================================================
Description: AMPL algebraic modeling language.
Versions: 20220703
License: http://ampl.com/buy-ampl-terms-and-conditions/
Categories: Optimization, linear programming, algebraic modeling
==============================================================================
Anaconda3
==============================================================================
Description: Python Data Science Distribution
Versions: 2024.02; 2021.11; 2023.03
License: https://www.anaconda.com/eula-anaconda-individual-edition
Categories: Python, Programming, Scripting, numpy, scipy, matplotlib,
ipython, jupyter
==============================================================================
angsd
==============================================================================
Description: Angsd is a program for analysing NGS data.
Versions: 0.935
License: N/A
Categories: N/A
==============================================================================
ANSYS
==============================================================================
Description: ANSYS is a finite element simulation tool for multiphysics
simulations.
Versions: 21.2
License: Academic Research
Categories: CFD, FEM, finite element, multiphysics
==============================================================================
ANSYS EM
==============================================================================
Description: ANSYS EM: HFSS and Maxwell
Versions: 21.2
License: Academic Research
Categories: EM, CEM, HFSS, Maxwell
==============================================================================
ANTs
==============================================================================
Description: ANTs MRI image registration program
Versions: 2.4.1
License: ANTs is Apache License 2.0
Categories: image processing, image registration, fMRI, neuroimaging
==============================================================================
archivetar
==============================================================================
Description: Parallel archive manipulation tool
Versions: 0.15.6; 0.16.0; 0.17.0; 0.17.2; 0.18.0
License: https://github.com/brockpalen/archivetar/blob/master/LICENSE
Categories: Utility
==============================================================================
ARM Forge
==============================================================================
Description: Parallel debugging and profiling tools, DDT and MAP.
Versions: 21.1.3
License: Not available
Categories: Programming, profiler, debugger, performance
==============================================================================
autoconf
==============================================================================
Description: Autoconf -- system configuration part of autotools
Versions: 2.72
License: N/A
Categories: N/A
==============================================================================
automake
==============================================================================
Description: Automake -- make file builder part of autotools
Versions: 1.16.5
License: N/A
Categories: N/A
==============================================================================
aws-cli
==============================================================================
Description: AWS command line interface
Versions: False
License: https://aws.amazon.com/terms/
Categories: Amazon, AWS, utility
==============================================================================
bamtools
==============================================================================
Description: C++ API & command-line toolkit for working with BAM data.
Versions: 2.5.1; 2.5.2
License: N/A
Categories: N/A
==============================================================================
bcftools
==============================================================================
Description: BCFtools is a set of utilities that manipulate variant calls
in the Variant Call Format (VCF) and its binary counterpart
BCF. All commands work transparently with both VCFs and BCFs,
both uncompressed and BGZF-compressed.
Versions: 1.12
License: N/A
Categories: N/A
==============================================================================
bcl-convert
==============================================================================
Description: Converts the Binary Base Call (BCL) files produced by Illumina
sequencing systems to FASTQ files.
Versions: 4.2.4; 4.3.6
License: GPLv2
Categories: Bioinformatics
==============================================================================
bcl2fastq2
==============================================================================
Description: The bcl2fastq2 Conversion Software converts base call (BCL)
files from a sequencing run into FASTQ files.
Versions: 2.20.0.422
License: N/A
Categories: N/A
==============================================================================
bdftopcf
==============================================================================
Description: bdftopcf is a font compiler for the X server and font server.
Fonts in Portable Compiled Format can be read by any
architecture, although the file is structured to allow one
particular architecture to read them directly without
reformatting. This allows fast reading on the appropriate
machine, but the files are still portable (but read more
slowly) on other machines.
Versions: 1.1.1
License: N/A
Categories: N/A
==============================================================================
beast1
==============================================================================
Description: BEAST is a cross-platform program for Bayesian analysis of
molecular sequences using MCMC.
Versions: 1.10.4
License: N/A
Categories: N/A
==============================================================================
bedtools2
==============================================================================
Description: Collectively, the bedtools utilities are a swiss-army knife of
tools for a wide-range of genomics analysis tasks. The most
widely-used tools enable genome arithmetic: that is, set
theory on the genome.
Versions: 2.25.0; 2.30.0
License: N/A
Categories: N/A
==============================================================================
berkeley-db
==============================================================================
Description: Oracle Berkeley DB
Versions: 18.1.40
License: N/A
Categories: N/A
==============================================================================
bison
==============================================================================
Description: Bison is a general-purpose parser generator that converts an
annotated context-free grammar into a deterministic LR or
generalized LR (GLR) parser employing LALR(1) parser tables.
Versions: 3.8.2
License: N/A
Categories: N/A
==============================================================================
blast-plus
==============================================================================
Description: Basic Local Alignment Search Tool.
Versions: 2.12.0
License: N/A
Categories: N/A
==============================================================================
blat
==============================================================================
Description: BLAT (BLAST-like alignment tool) is a pairwise sequence
alignment algorithm.
Versions: 35
License: N/A
Categories: N/A
==============================================================================
Boost
==============================================================================
Description: Boost C++ library collection.
Versions: 1.78.0
License: http://www.boost.org/users/license.html
Categories: Programming, C++, library
==============================================================================
bowtie
==============================================================================
Description: Bowtie is an ultrafast, memory-efficient short read aligner
for short DNA sequences (reads) from next-gen sequencers.
Versions: 1.3.0
License: N/A
Categories: N/A
==============================================================================
bowtie2
==============================================================================
Description: Bowtie 2 is an ultrafast and memory-efficient tool for
aligning sequencing reads to long reference sequences
Versions: 2.4.1; 2.4.2
License: N/A
Categories: N/A
==============================================================================
BPCells
==============================================================================
Description: R libraries necessary for BPCells
Versions: 0.3.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
Bridger Assembler
==============================================================================
Description: Bridger is an efficient de novo trascriptome assembler for
RNA-Seq data.
Versions: 2014.12.01
License: GNU GENERAL PUBLIC LICENSE
Categories: Bioinformatics, Genomics, Healthcare, big data
==============================================================================
bwa
==============================================================================
Description: Burrow-Wheeler Aligner for pairwise alignment between DNA
sequences.
Versions: 0.7.15; 0.7.17
License: N/A
Categories: N/A
==============================================================================
bzip2
==============================================================================
Description: bzip2 is a freely available, patent free high-quality data
compressor. It typically compresses files to within 10% to 15%
of the best available techniques (the PPM family of
statistical compressors), whilst being around twice as fast at
compression and six times faster at decompression.
Versions: 1.0.8
License: N/A
Categories: N/A
==============================================================================
ca-certificates-mozilla
==============================================================================
Description: The Mozilla CA certificate store in PEM format
Versions: 2023-05-30
License: N/A
Categories: N/A
==============================================================================
Caiman
==============================================================================
Description: Caiman is a software package for analysis of calcium imaging
data.
Versions: 1.12.1
License: N/A
Categories: Neuroscience, data analysis, imaging
==============================================================================
canu
==============================================================================
Description: A single molecule sequence assembler for genomes large and
small.
Versions: 2.2
License: N/A
Categories: N/A
==============================================================================
cap3
==============================================================================
Description: CAP3 is DNA Sequence Assembly Program
Versions: 2015-02-11
License: N/A
Categories: N/A
==============================================================================
cellbender
==============================================================================
Description: CellBender is a software package for eliminating technical
artifacts from high-throughput single-cell RNA sequencing
(scRNA-seq) data.
Versions: 0.3.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
cellpose
==============================================================================
Description: cellpose is an anatomical segmentation algorithm written in
Python 3.
Versions: 3.0.10; 2.1.1
License: https://github.com/MouseLand/cellpose/blob/main/LICENSE
Categories: Biology, deep-learning, biomedical, cell segmentation, image
analysis
==============================================================================
cellranger
==============================================================================
Description: Cell Ranger is a set of analysis pipelines that process
Chromium single-cell RNA-seq output
Versions: 7.1.0; 7.2.0; 8.0.0; 8.0.1; 9.0.0; 9.0.1
License: GPLv2
Categories: Bioinformatics
==============================================================================
cellrangerARC
==============================================================================
Description: a set of analysis pipelines that process Chromium Single Cell
Multiome ATAC + Gene Expression sequencing data
Versions: 2.0.2
License: GPLv2
Categories: Bioinformatics
==============================================================================
cellrangerATAC
==============================================================================
Description: a set of analysis pipelines that process Chromium Single Cell
ATAC data
Versions: 2.1.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
clustal-omega
==============================================================================
Description: Clustal Omega: the last alignment program you'll ever need.
Versions: 1.2.4
License: N/A
Categories: N/A
==============================================================================
CMake
==============================================================================
Description: CMake cross-platform make system.
Versions: 3.22.2; 3.26.3; 4.0.3
License: https://cmake.org/licensing/
Categories: Utility, programming, compiler
==============================================================================
cmake
==============================================================================
Description: A cross-platform, open-source build system. CMake is a family
of tools designed to build, test and package software.
Versions: 3.30.5
License: N/A
Categories: N/A
==============================================================================
code-server
==============================================================================
Description: Run VS Code on any machine anywhere and access it in the
browser.
Versions: 4.100.2; 4.8.3; 4.91.0
License: MIT
Categories: file management, software development, scripting, IDE.
==============================================================================
connect-proxy
==============================================================================
Description: connect-proxy open connection over SOCKS4/5 proxies
Versions: 1.105
License: N/A
Categories: N/A
==============================================================================
cuda
==============================================================================
Description: CUDA compilers and libraries.
Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0;
12.1.1; 12.6.3; 12.8.1
License: http://docs.nvidia.com/cuda/eula/index.html
Categories: CUDA, gpu, library, programming
==============================================================================
cudnn
==============================================================================
Description: cuDNN libraries.
Versions: 10.2-v8.3.1; 11.2-v8.1.1; 11.3-v8.2.1; 11.5-v8.3.1;
11.6-v8.4.1; 11.7-v8.7.0; 11.8-v8.7.0; 12.1-v8.9.0;
12.6-v9.6.0; 12.8-v9.10.0
License: http://docs.nvidia.com/cuda/eula
Categories: CUDA, gpu, library, programming, cuDNN, deep learning, neural
network
==============================================================================
cufflinks
==============================================================================
Description: Cufflinks assembles transcripts, estimates their abundances,
and tests for differential expression and regulation in RNA-
Seq samples.
Versions: 2.2.1
License: N/A
Categories: N/A
==============================================================================
CUPTI
==============================================================================
Description: CUDA Profiler Tools Interface
Versions: 10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0;
12.1.1; 12.6.3; 12.8.1
License: http://docs.nvidia.com/cuda/eula
Categories: CUDA, gpu, library, programming, Profiler
==============================================================================
curl
==============================================================================
Description: cURL is an open source command line tool and library for
transferring data with URL syntax
Versions: 8.10.1
License: N/A
Categories: N/A
==============================================================================
delly2
==============================================================================
Description: Delly2 is an integrated structural variant prediction method
that can discover, genotype and visualize deletions, tandem
duplications, inversions and translocations at single-
nucleotide resolution in short-read massively parallel
sequencing data..
Versions: 0.9.1
License: N/A
Categories: N/A
==============================================================================
DESeq2
==============================================================================
Description: Estimate variance-mean dependence in count data from high-
throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution.
Versions: 1.46.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
diffutils
==============================================================================
Description: GNU Diffutils is a package of several programs related to
finding differences between files.
Versions: 3.10
License: N/A
Categories: N/A
==============================================================================
Eigen
==============================================================================
Description: Linear algebra template library
Versions: 3.4.0
License: https://eigen.tuxfamily.org/index.php
Categories: Linear algebra, numerical, development, library
==============================================================================
elfutils
==============================================================================
Description: elfutils is a collection of various binary tools such as eu-
objdump, eu-readelf, and other utilities that allow you to
inspect and manipulate ELF files. Refer to Table 5.Tools
Included in elfutils for Red Hat Developer for a complete list
of binary tools that are distributed with the Red Hat
Developer Toolset version of elfutils.
Versions: 0.191
License: N/A
Categories: N/A
==============================================================================
expat
==============================================================================
Description: Expat is an XML parser library written in C.
Versions: 2.6.4
License: N/A
Categories: N/A
==============================================================================
fastqc
==============================================================================
Description: A quality control tool for high throughput sequence data.
Versions: 0.11.5; 0.11.9; 0.12.1
License: N/A
Categories: N/A
==============================================================================
FEKO
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] Feko
is a computational electromagnetics software.
Versions: 2021.2; 2022.1
License: https://caen.engin.umich.edu/software/licensing/
Categories: computational electromagnetics
==============================================================================
FFMPEG
==============================================================================
Description: FFMPEG is a complete, cross-platform solution to record,
convert and stream audio and video.
Versions: 4.4.2; 5.1.2; 6.0.0
License: https://ffmpeg.org/legal.html
Categories: audio, video, codec, transcoder
==============================================================================
fftw
==============================================================================
Description: Libraries for computation of discrete Fourier transform.
Versions: 3.3.10
License: http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories: Library, Development, Core
==============================================================================
figtree
==============================================================================
Description: FigTree is designed as a graphical viewer of phylogenetic
trees and as a program for producing publication-ready
figures. As with most of my programs, it was written for my
own needs so may not be as polished and feature-complete as a
commercial program. In particular it is designed to display
summarized and annotated trees produced by BEAST.
Versions: 1.4.4
License: N/A
Categories: N/A
==============================================================================
findutils
==============================================================================
Description: The GNU Find Utilities are the basic directory searching
utilities of the GNU operating system.
Versions: 4.9.0
License: N/A
Categories: N/A
==============================================================================
flex
==============================================================================
Description: Flex is a tool for generating scanners.
Versions: 2.6.3
License: N/A
Categories: N/A
==============================================================================
font-util
==============================================================================
Description: X.Org font package creation/installation utilities and fonts.
Versions: 1.4.1
License: N/A
Categories: N/A
==============================================================================
fontsproto
==============================================================================
Description: X Fonts Extension.
Versions: 2.1.3
License: N/A
Categories: N/A
==============================================================================
FreeSurfer
==============================================================================
Description: FreeSurfer MRI processing and analysis software.
Versions: 7.2.0
License:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLi
cense
Categories: MRI, neuroimaging, neuroscience
==============================================================================
freetype
==============================================================================
Description: FreeType is a freely available software library to render
fonts. It is written in C, designed to be small, efficient,
highly customizable, and portable while capable of producing
high-quality output (glyph images) of most vector and bitmap
font formats.
Versions: 2.13.2
License: N/A
Categories: N/A
==============================================================================
fribidi
==============================================================================
Description: GNU FriBidi: The Free Implementation of the Unicode
Bidirectional Algorithm.
Versions: 1.0.12
License: N/A
Categories: N/A
==============================================================================
FSL
==============================================================================
Description: FSL suite of MRI neuroimaging tools.
Versions: 6.0.5.2
License: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories: fMRI, DTI, neuroimaging, neuroscience
==============================================================================
gatk
==============================================================================
Description: Toolkit for variant discovery and genotyping
Versions: 3.7; 4.1.0.0; 4.2.2.0
License: Broad Institute Software License Agreement
Categories: Bioinformatics
==============================================================================
Gaussian
==============================================================================
Description: Gaussian is an electronic structure program.
Versions: 09-revD01; 16-revA03-avx2; 16-revC01-avx2
License: Academic, noncommercial research and instructional use only.
Categories: electronic structure, molecular
==============================================================================
gcc
==============================================================================
Description: GNU compiler suite
Versions: 10.3.0; 11.2.0; 13.2.0
License: GPL
Categories: Compiler, programming, development
==============================================================================
gcc-runtime
==============================================================================
Description: Package for GCC compiler runtime libraries
Versions: 13.2.0
License: N/A
Categories: N/A
==============================================================================
GDAL
==============================================================================
Description: GDAL is a translator library for raster and vector geospatial
data formats.
Versions: 3.5.1; 3.8.3
License: https://gdal.org/license.html
Categories: GIS, geospatial, raster, vector, graphics
==============================================================================
gdbm
==============================================================================
Description: GNU dbm (or GDBM, for short) is a library of database
functions that use extensible hashing and work similar to the
standard UNIX dbm. These routines are provided to a programmer
needing to create and manipulate a hashed database.
Versions: 1.23
License: N/A
Categories: N/A
==============================================================================
GEOS
==============================================================================
Description: OpenGIS Simple Features for SQL spatial predicate functions
and spatial operators.
Versions: 3.10.2; 3.12.1
License: GNU LGPL v2.1
Categories: GIS, Geometry, OSGeo
==============================================================================
gettext
==============================================================================
Description: GNU internationalization (i18n) and localization (l10n)
library.
Versions: 0.22.5
License: N/A
Categories: N/A
==============================================================================
git
==============================================================================
Description: Git version control software
Versions: 2.39.1
License: GPL version 2
Categories: Utility, development, version control
==============================================================================
git-annex
==============================================================================
Description: Manage large files with git, without storing the file contents
in git
Versions: 10.20220928
License: AGPL version 3.0
Categories: Utility, development, version control, file management
==============================================================================
glibc
==============================================================================
Description: The GNU C Library provides many of the low-level components
used directly by programs written in the C or C++ languages.
Versions: 2.28
License: N/A
Categories: N/A
==============================================================================
glmGamPoi
==============================================================================
Description: R libraries necessary for glmGamPoi
Versions: 3.20
License: GPLv2
Categories: Bioinformatics
==============================================================================
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: 3.4.0
License: N/A
Categories: Data movement
==============================================================================
glpk
==============================================================================
Description: The GLPK (GNU Linear Programming Kit) package is intended for
solving large-scale linear programming (LP), mixed integer
programming (MIP), and other related problems. It is a set of
routines written in ANSI C and organized in the form of a
callable library.
Versions: 5.0
License: N/A
Categories: N/A
==============================================================================
gmake
==============================================================================
Description: GNU Make is a tool which controls the generation of
executables and other non-source files of a program from the
program's source files.
Versions: 4.4.1
License: N/A
Categories: N/A
==============================================================================
gmp
==============================================================================
Description: GMP is a free library for arbitrary precision arithmetic,
operating on signed integers, rational numbers, and floating-
point numbers.
Versions: 6.3.0
License: N/A
Categories: N/A
==============================================================================
Go
==============================================================================
Description: The Go programming language is an open source project to make
programmers more productive.
Versions: 1.18
License: https://go.dev/LICENSE?m=text
Categories: Go, Programming, golang
==============================================================================
gperf
==============================================================================
Description: GNU gperf is a perfect hash function generator. For a given
list of strings, it produces a hash function and hash table,
in form of C or C++ code, for looking up a value depending on
the input string. The hash function is perfect, which means
that the hash table has no collisions, and the hash table
lookup needs a single string comparison only.
Versions: 3.1
License: N/A
Categories: N/A
==============================================================================
graphite2
==============================================================================
Description: Graphite is a system that can be used to create 'smart fonts'
capable of displaying writing systems with various complex
behaviors. A smart font contains not only letter shapes but
also additional instructions indicating how to combine and
position the letters in complex ways.
Versions: 1.3.14
License: N/A
Categories: N/A
==============================================================================
GSL
==============================================================================
Description: GNU scientific libraries
Versions: 2.7
License: GPL
Categories: Programming, library, mathematics
==============================================================================
gst-libav
==============================================================================
Description: GStreamer plugin for the libav* library.
Versions: 1.16.1
License: https://github.com/GStreamer/gst-libav?tab=LGPL-2.1-1-ov-
file#readme
Categories: multimedia
==============================================================================
Gurobi
==============================================================================
Description: Gurobi optimization problem solver.
Versions: 10.0.2; 11.0.3; 12.0.1; 9.5.1
License: http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories: Optimization, linear programming
==============================================================================
HDF5
==============================================================================
Description: HDF5 data libraries and utilities.
Versions: 1.10.8; 1.8.22
License: https://www.hdfgroup.org/products/licenses.html
Categories: Utility, programming, library
==============================================================================
HELIOS
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
HELIOS Generalized Geometry Lattice Analysis package. Includes
Casmo and Simulate from teh Studsvik suite.
Versions: 1.12; 1.12-sing; 1.13
License: N/A
Categories: Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR
lattices
==============================================================================
hisat2
==============================================================================
Description: HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (whole-genome, transcriptome,
and exome sequencing data) against the general human
population (as well as against a single reference genome).
Versions: 2.2.0
License: N/A
Categories: N/A
==============================================================================
homer
==============================================================================
Description: Software for motif discovery and next generation sequencing
analysis
Versions: 4.11.1
License: N/A
Categories: N/A
==============================================================================
HPC compilers
==============================================================================
Description: Compiler suite.
Versions: 22.3; 24.7
License: https://docs.nvidia.com/hpc-sdk/eula/hpc-sdk-ea-eula.pdf
Categories: Compiler, development, debugger, profiler
==============================================================================
htslib
==============================================================================
Description: C library for high-throughput sequencing data formats.
Versions: 1.13; 1.9
License: N/A
Categories: N/A
==============================================================================
igv
==============================================================================
Description: The Integrative Genomics Viewer (IGV) is a high-performance
visualization tool for interactive exploration of large,
integrated genomic datasets. It supports a wide variety of
data types, including array-based and next-generation sequence
data, and genomic annotations.
Versions: 2.8.9
License: N/A
Categories: N/A
==============================================================================
ilastik
==============================================================================
Description: Interactive learning and segmentation toolkit.
Versions: 1.4.0
License: https://www.ilastik.org/license.html
Categories: Machine learning, image classification, image analysis.
==============================================================================
Image libraries
==============================================================================
Description: Image libraries
Versions: 220318.1; 220318
License: more than one
Categories: libraries, programming, jpeg, gif, png, jbigkit, tiff,
libwebp, lcms2, jasper, ImageMagick
==============================================================================
imagemagick
==============================================================================
Description: ImageMagick is a software suite to create, edit, compose, or
convert bitmap images.
Versions: 7.1.0-33
License: N/A
Categories: N/A
==============================================================================
impi
==============================================================================
Description: Intel MPI runtime
Versions: 2021.5.1
License: GPL
Categories: MPI, MPICH, programming
==============================================================================
impute2
==============================================================================
Description: IMPUTE2 is a genotype imputation and haplotype phasing program
based on ideas from Howie et al. 2009.
Versions: 2.3.2
License: N/A
Categories: N/A
==============================================================================
inputproto
==============================================================================
Description: X Input Extension.
Versions: 2.3.2
License: N/A
Categories: N/A
==============================================================================
Intel
==============================================================================
Description: Intel compiler suite.
Versions: 2022.1.2
License: None provided
Categories: Library, Development, Core
==============================================================================
Intel VTune Profiler
==============================================================================
Description: Intel VTune Profiler is a performance analysis tool for
analyzing code execution and identifying performance
bottlenecks in applications developed for Intel architectures.
Versions: 2022.1.0
License: None Provided
Categories: performance analysis, profiling, software optimization
==============================================================================
ITK
==============================================================================
Description: ITK is an open-source system for medical image processing.
Versions: 5.2.1; 5.3.0
License: https://software.intel.com/en-us/license/intel-simplified-
software-license
Categories: Library, development, image processing, MRI, NIfTI
==============================================================================
itk
==============================================================================
Description: The Insight Toolkit (ITK) is an open-source, cross-platform
toolkit for N-dimensional scientific image processing,
segmentation, and registration.
Versions: 5.2.1
License: N/A
Categories: N/A
==============================================================================
JAGS
==============================================================================
Description: JAGS is Just Another Gibbs Sampler. It is a program for
analysis of Bayesian hierarchical models.
Versions: 4.3.0
License: GNU GPL v2
Categories: Bayesian, Markov, MCMC
==============================================================================
joe
==============================================================================
Description: JOE editor.
Versions: 4.6
License: https://joe-editor.sourceforge.io/
Categories: Editor, development, utility
==============================================================================
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: 1.10.2; 1.7.2
License: MIT Licenses
Categories: Programming
==============================================================================
kbproto
==============================================================================
Description: X Keyboard Extension.
Versions: 1.0.7
License: N/A
Categories: N/A
==============================================================================
krb5
==============================================================================
Description: Network authentication protocol
Versions: 1.21.3
License: N/A
Categories: N/A
==============================================================================
Lahey Fortran
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
Lahey Fortran - f95/f90 fortran compiler
Versions: 8.1b
License: http://www.lahey.com/docs/lfpro73help/f95gslicense.htm
Categories: fortran, compiler, f95/f90
==============================================================================
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: 3.10.1
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: 3.7
License: GPLv2
Categories: Core
==============================================================================
LFTP
==============================================================================
Description: File transfer program
Versions: 4.9.2
License: GNU General Public License
Categories: file transfer, transfer
==============================================================================
libbsd
==============================================================================
Description: This library provides useful functions commonly found on BSD
systems, and lacking on others like GNU systems, thus making
it easier to port projects with strong BSD origins, without
needing to embed the same code over and over again on each
project.
Versions: 0.12.2
License: N/A
Categories: N/A
==============================================================================
libffi
==============================================================================
Description: The libffi library provides a portable, high level programming
interface to various calling conventions. This allows a
programmer to call any function specified by a call interface
description at run time.
Versions: 3.4.6
License: N/A
Categories: N/A
==============================================================================
libfontenc
==============================================================================
Description: libfontenc - font encoding library.
Versions: 1.1.8
License: N/A
Categories: N/A
==============================================================================
libgd
==============================================================================
Description: GD graphics library
Versions: 2.3.3
License: https://github.com/libgd/libgd?tab=License-1-ov-file#readme
Categories: multimedia
==============================================================================
libice
==============================================================================
Description: libICE - Inter-Client Exchange Library.
Versions: 1.1.1
License: N/A
Categories: N/A
==============================================================================
libiconv
==============================================================================
Description: GNU libiconv provides an implementation of the iconv()
function and the iconv program for character set conversion.
Versions: 1.17
License: N/A
Categories: N/A
==============================================================================
libidn2
==============================================================================
Description: Libidn2 is a free software implementation of IDNA2008,
Punycode and TR46. Its purpose is to encode and decode
internationalized domain names.
Versions: 2.3.7
License: N/A
Categories: N/A
==============================================================================
libjpeg-turbo
==============================================================================
Description: libjpeg-turbo is a fork of the original IJG libjpeg which uses
SIMD to accelerate baseline JPEG compression and
decompression.
Versions: 3.0.3
License: N/A
Categories: N/A
==============================================================================
libmd
==============================================================================
Description: This library provides message digest functions found on BSD
systems either on their libc (NetBSD, OpenBSD) or libmd
(FreeBSD, DragonflyBSD, macOS, Solaris) libraries and lacking
on others like GNU systems.
Versions: 1.0.4
License: N/A
Categories: N/A
==============================================================================
libpng
==============================================================================
Description: libpng is a library for working with PNG image files.
Versions: 1.5.30; 1.6.39
License: N/A
Categories: Graphics, Imaging
==============================================================================
libpthread-stubs
==============================================================================
Description: The libpthread-stubs package provides weak aliases for pthread
functions not provided in libc or otherwise available by
default.
Versions: 0.5
License: N/A
Categories: N/A
==============================================================================
libsigsegv
==============================================================================
Description: GNU libsigsegv is a library for handling page faults in user
mode.
Versions: 2.14
License: N/A
Categories: N/A
==============================================================================
libsm
==============================================================================
Description: libSM - X Session Management Library.
Versions: 1.2.4
License: N/A
Categories: N/A
==============================================================================
libtiff
==============================================================================
Description: LibTIFF - Tag Image File Format (TIFF) Library and Utilities.
Versions: 4.7.0
License: N/A
Categories: N/A
==============================================================================
libtirpc
==============================================================================
Description: Libtirpc is a port of Suns Transport-Independent RPC library
to Linux.
Versions: 1.3.3
License: N/A
Categories: N/A
==============================================================================
libtool
==============================================================================
Description: libtool -- library building part of autotools.
Versions: 2.4.7
License: N/A
Categories: N/A
==============================================================================
libunistring
==============================================================================
Description: This library provides functions for manipulating Unicode
strings and for manipulating C strings according to the
Unicode standard.
Versions: 1.2
License: N/A
Categories: N/A
==============================================================================
libxau
==============================================================================
Description: The libXau package contains a library implementing the X11
Authorization Protocol. This is useful for restricting client
access to the display.
Versions: 1.0.11
License: N/A
Categories: N/A
==============================================================================
libxcrypt
==============================================================================
Description: libxcrypt is a modern library for one-way hashing of
passwords.
Versions: 4.4.35
License: N/A
Categories: N/A
==============================================================================
libxdmcp
==============================================================================
Description: libXdmcp - X Display Manager Control Protocol library.
Versions: 1.1.5
License: N/A
Categories: N/A
==============================================================================
libxfont
==============================================================================
Description: libXfont provides the core of the legacy X11 font system,
handling the index files (fonts.dir, fonts.alias,
fonts.scale), the various font file formats, and rasterizing
them. It is used by the X servers, the X Font Server (xfs),
and some font utilities (bdftopcf for instance), but should
not be used by normal X11 clients. X11 clients access fonts
via either the new API's in libXft, or the legacy API's in
libX11.
Versions: 1.5.4
License: N/A
Categories: N/A
==============================================================================
libxml2
==============================================================================
Description: Libxml2 is the XML C parser and toolkit developed for the
Gnome project (but usable outside of the Gnome platform), it
is free software available under the MIT License.
Versions: 2.13.4
License: N/A
Categories: N/A
==============================================================================
LibYAML
==============================================================================
Description: A C library for parsing and emitting YAML (YAML Ain't Markup
Language)
Versions: 0.2.5
License: MIT License
Categories: Development/Libraries
==============================================================================
Linaro Forge
==============================================================================
Description: Parallel debugging and profiling tools, DDT and MAP.
Versions: 23.0.3
License: Not available
Categories: Programming, profiler, debugger, performance
==============================================================================
m4
==============================================================================
Description: GNU M4 is an implementation of the traditional Unix macro
processor.
Versions: 1.4.19
License: N/A
Categories: N/A
==============================================================================
mamba
==============================================================================
Description: Python Data Science Distribution
Versions: 3.10; 3.11; 3.12
License: https://github.com/mamba-org/mamba?tab=BSD-3-Clause-1-ov-
file#readme
Categories: Python, Programming, Scripting, numpy, scipy, matplotlib,
ipython, jupyter, mamba
==============================================================================
Matlab
==============================================================================
Description: Matlab programming environment.
Versions: R2019b; R2021b; R2022b; R2023b; R2024b
License: N/A
Categories: Mathematics, programming, simulation
==============================================================================
Matplotlib
==============================================================================
Description: Visualization with Python.
Versions: 3.5.3
License: https://github.com/matplotlib/matplotlib/tree/main/LICENSE
Categories: Programming, python, visualization, graph, image
==============================================================================
minimap2
==============================================================================
Description: Minimap2 is a versatile sequence alignment program that aligns
DNA or mRNA sequences against a large reference database.
Mappy provides a convenient interface to minimap2.
Versions: 2.14
License: N/A
Categories: N/A
==============================================================================
mkfontdir
==============================================================================
Description: mkfontdir creates the fonts.dir files needed by the legacy X
server core font system. The current implementation is a
simple wrapper script around the mkfontscale program, which
must be built and installed first.
Versions: 1.0.7
License: N/A
Categories: N/A
==============================================================================
mkfontscale
==============================================================================
Description: mkfontscale creates the fonts.scale and fonts.dir index files
used by the legacy X11 font system.
Versions: 1.2.3
License: N/A
Categories: N/A
==============================================================================
MKL
==============================================================================
Description: Intel optimized BLAS/LAPACK libraries, also including FFT and
other mathematical and statistical routines.
Versions: 2018.0.4
License: https://software.intel.com/en-us/license/intel-simplified-
software-license
Categories: Library, Development, Core, BLAS, LAPACK
==============================================================================
mothur
==============================================================================
Description: This project seeks to develop a single piece of open-source,
expandable software to fill the bioinformatics needs of the
microbial ecology community.
Versions: 1.46.1
License: N/A
Categories: N/A
==============================================================================
MPI for Python (mpi4py)
==============================================================================
Description: Numerical libraries for use within Python.
Versions: 3.1.3
License: https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst
Categories: Programming, python, MPI, mpi4py
==============================================================================
MPIFileUtils
==============================================================================
Description: Parallel file manipulation utilities.
Versions: 0.10.2-arcts
License: https://github.com/brockpalen/mpifileutils/blob/master/LICENSE
Categories: Utility
==============================================================================
MPlayer
==============================================================================
Description: MPlayer is a free and open-source media player software that
supports a wide variety of audio and video formats. It runs on
multiple platforms including Linux, Windows, and macOS.
Versions: 1.5
License: GNU General Public License version 2
Categories: media player, multimedia
==============================================================================
MRtrix
==============================================================================
Description: MRtrix provides a set of tools to perform various advanced
diffusion MRI analyses.
Versions: 3.0.3-dfd3360; 3.0.4
License: Mozilla Public License, http://mozilla.org/MPL/2.0/
Categories: fMRI, diffusion-weighted MRI, tractography, neuroimaging
==============================================================================
N/A
==============================================================================
Description: N/A
Versions: 5.0.7; 3.0.1; 1.18.0; 2025.05.0
License: N/A
Categories: N/A
==============================================================================
nagf95
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact arcts-support@umich.edu]
NAGWARE - f95/f90 fortran compiler
Versions: 6.1-6120; 6.2-6214
License: file:///sw/pkgs/coe/c/nagf95/6.1-6120/lic_agr.txt
Categories: fortran, compiler
==============================================================================
nasm
==============================================================================
Description: NASM (Netwide Assembler) is an 80x86 assembler designed for
portability and modularity. It includes a disassembler as
well.
Versions: 2.16.03
License: N/A
Categories: N/A
==============================================================================
Natural Bond Orbital (NBO)
==============================================================================
Description: Computational chemistry program for the analysis of many-
electron molecular wavefunctions.
Versions: 7.0
License: (c) Copyright 1996-2018 Board of Regents of the University of
Wisconsin System on behalf of the Theoretical Chemistry
Institute. All rights reserved.
Categories: Computational Chemistry, Quantum Chemistry, simulation.
==============================================================================
ncftp
==============================================================================
Description: NcFTP Client is a set of application programs implementing the
File Transfer Protocol.
Versions: 3.2.6
License: N/A
Categories: N/A
==============================================================================
ncurses
==============================================================================
Description: The ncurses (new curses) library is a free software emulation
of curses in System V Release 4.0, and more. It uses terminfo
format, supports pads and color and multiple highlights and
forms characters and function-key mapping, and has all the
other SYSV-curses enhancements over BSD curses.
Versions: 6.5
License: N/A
Categories: N/A
==============================================================================
NERS-CLASS-SW
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
Software for NERS classses: mcc2-3, rebus, dif3d, twodant.
Versions: 1.0
License: N/A
Categories: Nuclear
==============================================================================
NetCDF
==============================================================================
Description: Libraries for creating and manipulating NetCDF files.
Versions: 4.8.1; 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: 4.5.3
License: https://www.ucar.edu/terms-of-use
Categories: Library, Development, Core
==============================================================================
NetCDF-CXX
==============================================================================
Description: C++ API to the NetCDF-C libraries.
Versions: 4.3.1
License: https://www.ucar.edu/terms-of-use
Categories: Library, Development, Core
==============================================================================
nextflow
==============================================================================
Description: Data-driven computational pipelines.
Versions: 24.10.0
License: N/A
Categories: N/A
==============================================================================
nghttp2
==============================================================================
Description: nghttp2 is an implementation of HTTP/2 and its header
compression algorithm HPACK in C.
Versions: 1.63.0
License: N/A
Categories: N/A
==============================================================================
nsight-compute
==============================================================================
Description: NVIDIA Nsight Compute - interactive profiler for CUDA kernels.
Versions: 2025.2
License: https://docs.nvidia.com/nsight-compute/License.html
Categories: CUDA, gpu, profiling, performance
==============================================================================
NumPy
==============================================================================
Description: Numerical libraries for use within Python.
Versions: 1.22.3
License: https://github.com/numpy/numpy
Categories: Programming, numerical library, BLAS, LAPACK, python
==============================================================================
Ollama
==============================================================================
Description: Lightweight platform for deploying and fine-tuning large
language models (LLMs)
Versions: ollama
License: See official documentation
Categories: AI/ML
==============================================================================
openblas
==============================================================================
Description: BLAS provides standard interfaces for linear algebra,
including vector-vector operations, matrix-vector operations,
and matrix-matrix operations.
Versions: 0.3.19; 0.3.23; 0.3.28
License: https://opensource.org/licenses/BSD-3-Clause
Categories: Programming, C++, library
==============================================================================
OpenJDK
==============================================================================
Description: OpenJDK is a free and open-source implementation of the Java
Platform.
Versions: 18.0.1.1
License: GPLv2 with linking exception
Categories: Java, programming
==============================================================================
openjdk
==============================================================================
Description: The free and opensource java implementation
Versions: 17.0.11_9
License: N/A
Categories: N/A
==============================================================================
OpenMPI
==============================================================================
Description: OpenMPI implementation of the MPI protocol
Versions: 4.1.3; 4.1.4; 4.1.6; 5.0.3; 5.0.6; 4.1.7
License: https://www.open-mpi.org/community/license.php
Categories: Utility, Development, Core
==============================================================================
openslide
==============================================================================
Description: OpenSlide reads whole slide image files.
Versions: 3.4.1
License: N/A
Categories: N/A
==============================================================================
openssl
==============================================================================
Description: OpenSSL is an open source project that provides a robust,
commercial-grade, and full-featured toolkit for the Transport
Layer Security (TLS) and Secure Sockets Layer (SSL) protocols.
It is also a general-purpose cryptography library.
Versions: 3.4.0
License: N/A
Categories: N/A
==============================================================================
Pandas
==============================================================================
Description: Data analysis and manipulation.
Versions: 1.4.2
License: https://github.com/pandas-dev/pandas
Categories: Programming, statistics, data analysis, data management,
python
==============================================================================
Pandoc
==============================================================================
Description: A universal document converter.
Versions: 2.17.1.1
License: http://www.gnu.org/copyleft/gpl.html
Categories: Utility, document converter, markup
==============================================================================
Parabricks
==============================================================================
Description: Parabricks is a software suite for performing secondary
analysis of next generation sequencing (NGS) of DNA and RNA
data
Versions: 4.0.1-1
License: Apache License 2.0 https://docs.nvidia.com/clara/parabricks/4.
0.1/documentation/thirdpartysoftwarenotices.html
Categories: Genomics, Healthcare, big data, pipelines
==============================================================================
Parallel HDF5 (PHDF5)
==============================================================================
Description: Parallel HDF5 data libraries and utilities.
Versions: 1.12.1
License: https://www.hdfgroup.org/products/licenses.html
Categories: Utility, programming, library
==============================================================================
Paraview
==============================================================================
Description: Paraview data analysis and visualization application.
Versions: 5.12.0; 5.12.1
License: http://www.paraview.org/paraview-license/
Categories: Visualization, data analysis
==============================================================================
pcre2
==============================================================================
Description: The PCRE2 package contains Perl Compatible Regular Expression
libraries. These are useful for implementing regular
expression pattern matching using the same syntax and
semantics as Perl 5.
Versions: 10.44
License: N/A
Categories: N/A
==============================================================================
perl
==============================================================================
Description: Perl 5 is a highly capable, feature-rich programming language
with over 27 years of development.
Versions: 5.40.0
License: N/A
Categories: N/A
==============================================================================
pigz
==============================================================================
Description: A parallel implementation of gzip for modern multi-processor,
multi-core machines.
Versions: 2.8
License: N/A
Categories: N/A
==============================================================================
pkgconf
==============================================================================
Description: pkgconf is a program which helps to configure compiler and
linker flags for development frameworks. It is similar to pkg-
config from freedesktop.org, providing additional
functionality while also maintaining compatibility.
Versions: 2.2.0
License: N/A
Categories: N/A
==============================================================================
plink
==============================================================================
Description: PLINK a whole genome association analysis toolset.
Versions: 1.9; 2.0; 2.3a; 2.3a3; 2.3dev
License: GPLv3
Categories: Bioinformatics
==============================================================================
Poetry
==============================================================================
Description: Python packaging and dependency management.
Versions: 1.6.1
License: https://github.com/python-poetry/poetry
Categories: Programming, dependency management, python
==============================================================================
presto
==============================================================================
Description: R libraries necessary for presto
Versions: 1.0.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
PROJ
==============================================================================
Description: PROJ is a generic coordinate transformation software.
Versions: 9.0.0; 9.3.1
License: MIT
Categories: GIS, Library
==============================================================================
py-macs2
==============================================================================
Description: MACS2 Model-based Analysis of ChIP-Seq
Versions: 2.2.4
License: N/A
Categories: N/A
==============================================================================
py-weblogo
==============================================================================
Description: WebLogo is a web based application designed to make the
generation of sequence logos as easy and painless as possible.
Versions: 3.7.12
License: N/A
Categories: N/A
==============================================================================
PyArrow
==============================================================================
Description: In-memory analytics for use within Python.
Versions: 8.0.0
License: https://github.com/apache/arrow/blob/master/LICENSE.txt
Categories: Programming, python
==============================================================================
Python
==============================================================================
Description: Python is a general purpose programming language
Versions: 3.10.4; 3.11.5; 3.13.2; 3.9.12
License: https://docs.python.org/3/license.html
Categories: Programming, language
==============================================================================
PyTorch
==============================================================================
Description: Python tensor library for deep learning.
Versions: 1.12.1; 2.0.1
License: https://pytorch.org/
Categories: Programming, python, machine learning, tensor, GPU
==============================================================================
Qt5
==============================================================================
Description: Development Tools Qt is designed for developing applications
and user interfaces
Versions: 5.12.11
License: GNU Lesser General Public License v. 3 (“LGPL”)
Categories: Development
==============================================================================
R
==============================================================================
Description: R environment for statistical computing and graphics
Versions: 4.2.0; 4.3.1; 4.4.0; 4.4.3
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science
==============================================================================
r-seurat
==============================================================================
Description: Tools for Single Cell Genomics.
Versions: 5.1.0; 4.1.1
License: N/A
Categories: N/A
==============================================================================
raxml
==============================================================================
Description: RAxML (Randomized Axelerated Maximum Likelihood) is a program
for sequential and parallel Maximum Likelihood based inference
of large phylogenetic trees.
Versions: 8.2.11; 8.2.12
License: N/A
Categories: N/A
==============================================================================
rclone
==============================================================================
Description: rclone is a command line program to sync files and directories
to and from many cloud storage providers
Versions: 1.57.0
License: MIT License
Categories: File transfer, Utilities
==============================================================================
readline
==============================================================================
Description: The GNU Readline library provides a set of functions for use
by applications that allow users to edit command lines as they
are typed in. Both Emacs and vi editing modes are available.
The Readline library includes additional functions to maintain
a list of previously-entered command lines, to recall and
perhaps reedit those lines, and perform csh-like history
expansion on previous commands.
Versions: 8.2
License: N/A
Categories: N/A
==============================================================================
renderproto
==============================================================================
Description: X Rendering Extension.
Versions: 0.11.1
License: N/A
Categories: N/A
==============================================================================
Rgeospatial
==============================================================================
Description: A collection of R geospatial libraries
Versions: 2022-08-18; 2023-04-25; 2023-07-01; 2024-05-11; 2025-04-21
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science, geospatial,
geography, spatial, map
==============================================================================
rmats
==============================================================================
Description: MATS is a computational tool to detect differential
alternative splicing events from RNA-Seq data.
Versions: 4.0.2
License: N/A
Categories: N/A
==============================================================================
Ropenblas
==============================================================================
Description: R OpenBLAS provides an optimized library for faster linear
algebra computations.
Versions: 4.2.0; 4.3.1; 4.4.0; 4.4.3
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, linear algebra, big data, data science
==============================================================================
RStudio Server
==============================================================================
Description: RStudio Desktop is a graphichal user interface for R.
Versions: 2022.07.1; 2022.07.2; 2023.06.1; 2023.09.1; 2024.04.1
License: AGPL v3
Categories: Statistics, graphics, big data, data science, IDE
==============================================================================
Rtidyverse
==============================================================================
Description: R Tidyverse environment for statistical computing and graphics
Versions: 4.2.0; 4.3.1; 4.4.0; 4.4.3
License: GPL, https://www.r-project.org/Licenses/
Categories: Statistics, graphics, big data, data science, tidyverse
==============================================================================
ruby
==============================================================================
Description: A dynamic, open source programming language with a focus on
simplicity and productivity
Versions: 3.3.7
License: GPLv3
Categories: Bioinformatics
==============================================================================
Rust
==============================================================================
Description: general purpose programming language
Versions: 1.81.0
License: MIT, Apache 2.0
Categories: development, programming, languages
==============================================================================
Rutils-BFX
==============================================================================
Description: R libraries necessary for the BFX core
Versions: 1.0
License: GPLv2
Categories: Bioinformatics
==============================================================================
salmon
==============================================================================
Description: Salmon is a tool for quantifying the expression of transcripts
using RNA-seq data.
Versions: 1.9.0
License: N/A
Categories: N/A
==============================================================================
samtools
==============================================================================
Description: SAM Tools provide various utilities for manipulating
alignments in the SAM format, including sorting, merging,
indexing and generating alignments in a per-position format
Versions: 1.13; 1.9
License: N/A
Categories: N/A
==============================================================================
SAS
==============================================================================
Description: SAS statistical system software.
Versions: 9.4-TS1M7; 9.4-TS1M8
License: Not available
Categories: Statistics, econometrics
==============================================================================
scCATCH
==============================================================================
Description: R libraries necessary for scCATCH
Versions: 3.2.2
License: GPLv2
Categories: Bioinformatics
==============================================================================
SciPy
==============================================================================
Description: Scientific libraries for use within Python.
Versions: 1.8.0
License: https://github.com/scipy/scipy
Categories: Programming, python, solver
==============================================================================
scrnsaverproto
==============================================================================
Description: MIT Screen Saver Extension.
Versions: 1.2.2
License: N/A
Categories: N/A
==============================================================================
seqkit
==============================================================================
Description: A cross-platform and ultrafast toolkit for FASTA/Q file
manipulation in Golang.
Versions: 2.3.0
License: N/A
Categories: N/A
==============================================================================
ShellCheck
==============================================================================
Description: ShellCheck, a static analysis tool for shell scripts
Versions: 0.9.0
License: GPLv3
https://github.com/koalaman/shellcheck/blob/master/LICENSE
Categories: Shell, Bash, Linter, static-analysis, developer-tools
==============================================================================
Singularity
==============================================================================
Description: Program for running containerized applications
Versions: 4.1.3; 4.3.1
License: https://github.com/sylabs/singularity/blob/master/LICENSE.md
Categories: Container, docker, reproducible research
==============================================================================
spaceranger
==============================================================================
Description: a set of analysis pipelines that process Visium spatial RNA-
seq output and brightfield microscope images
Versions: 2.0.1; 2.1.1; 3.0.0; 3.0.1; 3.1.1; 3.1.2; 3.1.3; 4.0.1
License: GPLv2
Categories: Bioinformatics
==============================================================================
Spack Package Manager
==============================================================================
Description: A flexible package manager supporting multiple versions,
configurations, platforms, and compilers.
Versions: 0.21; 0.23
License: Apache-2.0
Categories: Software Installation, compiling, package manager
==============================================================================
spades
==============================================================================
Description: SPAdes - St. Petersburg genome assembler - is intended for
both standard isolates and single-cell MDA bacteria
assemblies.
Versions: 3.15.5
License: N/A
Categories: N/A
==============================================================================
sqlite
==============================================================================
Description: SQLite is a C-language library that implements a small, fast,
self-contained, high-reliability, full-featured, SQL database
engine.
Versions: 3.46.0
License: N/A
Categories: N/A
==============================================================================
sratoolkit
==============================================================================
Description: The NCBI SRA Toolkit enables reading ('dumping') of sequencing
files from the SRA database and writing ('loading') files into
the .sra format.
Versions: 2.10.9; 2.9.6
License: N/A
Categories: N/A
==============================================================================
star
==============================================================================
Description: STAR is an ultrafast universal RNA-seq aligner.
Versions: 2.7.11a; 2.7.6a
License: N/A
Categories: N/A
==============================================================================
Star-CCM+
==============================================================================
Description: Star-CCM+ is a CFD application that supports parallel
processing.
Versions: 17.04.007-R8; 17.04.007; 19.02.013-R8; 19.02.013
License: Academic Research
Categories: CFD
==============================================================================
Stata/MP
==============================================================================
Description: Statistical analysis software.
Versions: 17; 18; 19
License: http://www.stata.com/order/end-user-license-agreement/
Categories: Statistics, econometrics
==============================================================================
Stata/SE
==============================================================================
Description: Statistical analysis software.
Versions: 17; 18; 19
License: http://www.stata.com/order/end-user-license-agreement/
Categories: Statistics, econometrics
==============================================================================
stringtie
==============================================================================
Description: Transcript assembly and quantification for RNA-Seq
Versions: 2.2.1; 2.1.7
License: GPLv2
Categories: Bioinformatics
==============================================================================
szip
==============================================================================
Description: Szip is a compression library used with HDF5.
Versions: 2.1.1
License: https://www.hdfgroup.org/doc_resource/SZIP/
Categories: Utility, compression
==============================================================================
tar
==============================================================================
Description: GNU Tar provides the ability to create tar archives, as well
as various other kinds of manipulation.
Versions: 1.34
License: N/A
Categories: N/A
==============================================================================
TBB
==============================================================================
Description: Intel Thread Building Blocks.
Versions: 2022.1.2
License: https://software.intel.com/en-us/articles/end-user-license-
agreement
Categories: Library, development, core, thread
==============================================================================
tcl
==============================================================================
Description: Tcl (Tool Command Language) is a very powerful but easy to
learn dynamic programming language, suitable for a very wide
range of uses, including web and desktop applications,
networking, administration, testing and many more. Open source
and business-friendly, Tcl is a mature yet evolving language
that is truly cross platform, easily deployed and highly
extensible.
Versions: 8.6.12
License: N/A
Categories: N/A
==============================================================================
Tecplot 360 & Tecplot Chorus
==============================================================================
Description: Plotting and visualization software that gives full control
over 2-D and 3-D plot parameters.
Versions: 2022r1
License: N/A
Categories: plotting, visualization
==============================================================================
TensorFlow
==============================================================================
Description: Machine learning platform for use within Python.
Versions: 2.7.0
License: Apache License 2.0
Categories: Programming, machine learning library, python
==============================================================================
TensorRT
==============================================================================
Description: An SDK for high-performance deep learning inference.
Versions: 11.8-v8.6.1
License: Apache License 2.0
Categories: Programming, Machine Learning, Tensorflow, Inference
==============================================================================
texinfo
==============================================================================
Description: Texinfo is the official documentation format of the GNU
project.
Versions: 7.1
License: N/A
Categories: N/A
==============================================================================
tmux
==============================================================================
Description: Terminal multiplexer
Versions: 3.3a
License: https://opensource.org/licenses/ISC
Categories: Terminal, multiplex
==============================================================================
trimgalore
==============================================================================
Description: Trim Galore! is a wrapper around Cutadapt and FastQC to
consistently apply adapter and quality trimming to FastQ
files, with extra functionality for RRBS data.
Versions: 0.6.7
License: N/A
Categories: N/A
==============================================================================
Trinity
==============================================================================
Description: Trinity assembles transcript sequences from Illumina RNA-Seq
data.
Versions: 2.15.1
License:
https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/
master/LICENSE
Categories: Bioinformatics, Assembly, Transcriptome
==============================================================================
UCX
==============================================================================
Description: Unified Communication X (UCX)
Versions: 1.14.1
License: https://github.com/openucx/ucx?tab=License-1-ov-file#readme
Categories: Communication
==============================================================================
use.own
==============================================================================
Description: Module to add personal module directory to module path.
Versions: False
License: None
Categories: utility
==============================================================================
util-linux-uuid
==============================================================================
Description: Util-linux is a suite of essential utilities for any Linux
system.
Versions: 2.40.2
License: N/A
Categories: N/A
==============================================================================
util-macros
==============================================================================
Description: This is a set of autoconf macros used by the configure.ac
scripts in other Xorg modular packages, and is needed to
generate new versions of their configure scripts with
autoconf.
Versions: 1.20.1
License: N/A
Categories: N/A
==============================================================================
valgrind
==============================================================================
Description: An instrumentation framework for building dynamic analysis.
Versions: 3.20.0
License: N/A
Categories: N/A
==============================================================================
VASP
==============================================================================
Description: [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu]
VASP, The Vienna Ab initio simulation package, a plane wave
electronic structure code.
Versions: 5.4.1.05Feb16.p2.b; 5.4.4.18Apr17; 5.4.4.18Apr17.p1;
5.4.4.18Apr17.vaspsol.170729; old-4.6.36Feb09;
old-5.2.12.11Nov2011; old-5.3.2.13Sep2012;
old-5.3.3.18Dec2012; old-5.3.5.31Mar2014;
old-5.3.5.31Mar2014wannier90v12
License: https://www.vasp.at/index.php/faqs
Categories: electronic structure code, molecular dynamics
==============================================================================
vtk
==============================================================================
Description: data visualization
Versions: 9.3.1
License: BSD
Categories: Graphics
==============================================================================
which
==============================================================================
Description: GNU which - is a utility that is used to find which executable
(or alias or shell function) is executed when entered on the
shell prompt.
Versions: 2.21
License: N/A
Categories: N/A
==============================================================================
xcb-devel
==============================================================================
Description: xcb development libraries and headers
Versions: 0.4.1
License: MIT License
Categories: Libraries, Headers
==============================================================================
xextproto
==============================================================================
Description: X Protocol Extensions.
Versions: 7.3.0
License: N/A
Categories: N/A
==============================================================================
xproto
==============================================================================
Description: X Window System Core Protocol.
Versions: 7.0.31
License: N/A
Categories: N/A
==============================================================================
xtrans
==============================================================================
Description: xtrans is a library of code that is shared among various X
packages to handle network protocol transport in a modular
fashion, allowing a single place to add new transport types.
It is used by the X server, libX11, libICE, the X font server,
and related components.
Versions: 1.5.2
License: N/A
Categories: N/A
==============================================================================
xz
==============================================================================
Description: XZ Utils is free general-purpose data compression software
with high compression ratio. XZ Utils were written for POSIX-
like systems, but also work on some not-so-POSIX systems. XZ
Utils are the successor to LZMA Utils.
Versions: 5.4.6
License: N/A
Categories: N/A
==============================================================================
Yasm
==============================================================================
Description: Yasm assembler.
Versions: 1.3.0; 2.15.05
License: https://github.com/yasm/yasm/blob/master/BSD.txt
Categories: assembler, programming
==============================================================================
zip
==============================================================================
Description: Zip is a compression and file packaging/archive utility.
Versions: 3.0
License: N/A
Categories: N/A
==============================================================================
zlib-ng
==============================================================================
Description: zlib replacement with optimizations for next generation
systems.
Versions: 2.2.1
License: N/A
Categories: N/A
==============================================================================
zstd
==============================================================================
Description: Zstandard, or zstd as short version, is a fast lossless
compression algorithm, targeting real-time compression
scenarios at zlib-level and better compression ratios.
Versions: 1.5.6
License: N/A
Categories: N/A
==============================================================================