last updated: Friday, 24-May-2024 06:42:04 EDT

Great Lakes cluster software catalog

        

Abaqus
==============================================================================
Description:  Abaqus FEA product suite for engineering problems.
Versions:     2022; 2023; 2024
License:      Non-commercial research, Academic Institution License
              Agreement
Categories:   FEA, dynamic vibration, impact/crash, thermal coupling
==============================================================================


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
==============================================================================


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
==============================================================================


alphafold
==============================================================================
Description:  This package provides an implementation of the inference
              pipeline of AlphaFold v2
Versions:     2.3.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


amber
==============================================================================
Description:  A package of molecular simulation programs which includes
              source code and demos.
Versions:     22
License:      Campus Agreement
Categories:   Computational Chemistry
==============================================================================


AMPL
==============================================================================
Description:  AMPL algebraic modeling language.
Versions:     20220703
License:      http://ampl.com/buy-ampl-terms-and-conditions/
Categories:   Optimization, linear programming, algebraic modeling
==============================================================================


AMRfinder
==============================================================================
Description:  This software is designed to find acquired antimicrobial
              resistance genes and point mutations
Versions:     3.12.8
License:      'United States Government Work' under the terms of the United
              States Copyright Act
Categories:   Bioinformatics
==============================================================================


Anaconda3
==============================================================================
Description:  Python Data Science Distribution
Versions:     2024.02; 2023.03; 2021.11
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
==============================================================================


annotSV
==============================================================================
Description:  Annotation and Ranking of Human Structural Variations
Versions:     2.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


annovar
==============================================================================
Description:  ANNOVAR is an efficient software tool to functionally annotate
              genetic variants detected from diverse genomes
Versions:     9.2019
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


ANSYS
==============================================================================
Description:  ANSYS is a finite element simulation tool for multiphysics
              simulations.
Versions:     21.2; 22.2
License:      Academic Research
Categories:   CFD, FEM, finite element, multiphysics
==============================================================================


ANSYS EM
==============================================================================
Description:  ANSYS EM: HFSS and Maxwell
Versions:     21.2; 22.2
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
==============================================================================


Anvi'o
==============================================================================
Description:  Anvi'o is an analysis and visualization platform for 'omics
              data.
Versions:     7.1; 7
License:      GPL3
Categories:   bioinformatics, genomics, visualization
==============================================================================


arb
==============================================================================
Description:  The ARB software is a graphically oriented package comprising
              various tools for sequence database handling and data
              analysis.
Versions:     7.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


archivetar
==============================================================================
Description:  Parallel archive manipulation tool
Versions:     0.15.6; 0.16.0; 0.17.0
License:      https://github.com/brockpalen/archivetar/blob/master/LICENSE
Categories:   Utility
==============================================================================


ArchR
==============================================================================
Description:  R libraries necessary for ArchR
Versions:     1.0.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


ARM Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     21.1.3
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


armadillo
==============================================================================
Description:  rmadillo is a high quality linear algebra library (matrix
              maths) for the C++ language
Versions:     11.4.2; 12.6.7
License:      http://www.netlib.org/lapack/LICENSE.txt
Categories:   Libraries
==============================================================================


Asgard
==============================================================================
Description:  R libraries necessary for Asgard
Versions:     1.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


atactk
==============================================================================
Description:  A toolkit for working with ATAC-seq data.
Versions:     0.1.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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


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
==============================================================================


basespace
==============================================================================
Description:  BaseSpace Sequence Hub CLI
Versions:     1.5.3
License:      N/A
Categories:   Bioinformatics
==============================================================================


bbtools
==============================================================================
Description:  a suite of fast, multithreaded bioinformatics tools designed
              for analysis of DNA and RNA sequence data.
Versions:     38.96
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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; 1.12
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


bcl-convert
==============================================================================
Description:  Converts the Binary Base Call (BCL) files produced by Illumina
              sequencing systems to FASTQ files.
Versions:     4.2.4
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
==============================================================================


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
==============================================================================


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:     2.4.41
License:      GNU GPL v2
Categories:   Bioinformatics, Genomics
==============================================================================


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
==============================================================================


BioGeoBEARS
==============================================================================
Description:  R package that is designed to perform inference of
              biogeographic history on phylogenies, and also model testing
              and model choice of the many different possible models of how
              biogeography may evolve on a phylogeny(dispersal, vicariance,
              founder-event speciation, DEC, DIVA, BAYAREA, etc.)
Versions:     1.1.1
License:      N/A
Categories:   BioInformatics
==============================================================================


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


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
==============================================================================


blender
==============================================================================
Description:  Blender is the free and open source 3D creation suite
Versions:     4.0.2
License:      GNU General Public License
Categories:   visualization
==============================================================================


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
==============================================================================


breseq
==============================================================================
Description:  breseq is a computational pipeline for the analysis of short-
              read re-sequencing data (e.g. Illumina, 454, IonTorrent,
              etc.). It uses reference-based alignment approaches to predict
              mutations in a sample relative to an already sequenced genome.
              breseq is intended for microbial genomes (<10 Mb) and re-
              sequenced samples that are only slightly diverged from the
              reference sequence (<1 mutation per 1000 bp).
Versions:     0.38.1
License:      GNU GPL v2 (license) and v3 (copying)
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
==============================================================================


busco
==============================================================================
Description:  BUSCO (Benchmarking Universal Single-Copy Orthologs)
Versions:     5.5.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


bwa
==============================================================================
Description:  Burrow-Wheeler Aligner for pairwise alignment between DNA
              sequences.
Versions:     0.7.15; 0.7.17
License:      N/A
Categories:   N/A
==============================================================================


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
==============================================================================


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
==============================================================================


CDO - Climate Data Operators
==============================================================================
Description:  Command line operators to manipulate and analyse Climate and
              NWP module Data
Versions:     2.0.6
License:      N/A
Categories:   cli, climate
==============================================================================


cellpose
==============================================================================
Description:  cellpose is an anatomical segmentation algorithm written in
              Python 3.
Versions:     2.1.1
License:      https://github.com/MouseLand/cellpose/blob/main/LICENSE
Categories:   Biology, deep-learning, biomedical, cell segmentation, image
              analysis
==============================================================================


cellprofiler
==============================================================================
Description:  CellProfiler is free, open-source software for quantitative
              analysis of biological images.
Versions:     3.1.9; 4.2.4
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:     6.1.2; 7.0.0; 7.0.1; 7.1.0; 7.2.0; 8.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerARC
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              Multiome ATAC + Gene Expression sequencing data
Versions:     2.0.1; 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
==============================================================================


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


centrifuge
==============================================================================
Description:  centrifuge
Versions:     1.0.4
License:      GNU GPL3
Categories:   Bioinformatics
==============================================================================


ChimeraX
==============================================================================
Description:  UCSF Chimera is a program for the interactive visualization
              and analysis of molecular structures
Versions:     1.7.1
License:      N/A
Categories:   Visualization, Bioinformatics, Molecular Structures, Modelling
==============================================================================


chromHMM
==============================================================================
Description:  ChromHMM is software for learning and characterizing chromatin
              states.
Versions:     1.24
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Circos
==============================================================================
Description:  Circos is a software package for visualizing data and
              information.
Versions:     0.69-8
License:      GNU GPL v3
Categories:   Bioinformatics, Visualization, Circular
==============================================================================


clang
==============================================================================
Description:  A front-end and tooling infrastructure for languages in the C
              language family
Versions:     14.0.6; 2022.1.2
License:      Apache License
Categories:   compilier c
==============================================================================


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
License:      https://cmake.org/licensing/
Categories:   Utility, programming, compiler
==============================================================================


code-server
==============================================================================
Description:  Run VS Code on any machine anywhere and access it in the
              browser.
Versions:     4.8.3
License:      MIT
Categories:   file management, software development, scripting, IDE.
==============================================================================


COMSOL
==============================================================================
Description:  COMSOL is multiphysics simulation software.
Versions:     6.0; 6.1
License:
              https:/www.comsol.com/documentation/6.0/COMSOL_SoftwareLicense
              Agreement.pdf
Categories:   Multiphysics, simulation
==============================================================================


CONVERGE
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: You must provide your own license
              to use this software] CONVERGE is a CFD code with adaptive
              meshing.
Versions:     3.1.8
License:      Provided by licensed labs
Categories:   Fluid dynamics, CFD, adaptive mesh
==============================================================================


Coq
==============================================================================
Description:  Coq is a formal proof management system.
Versions:     8.4pl5
License:      GNU Lesser General Public License (LGPL) version 2.1
Categories:   proof, Gallina
==============================================================================


CPLEX
==============================================================================
Description:  CPLEX is a high-performance optimizer for linear programming
Versions:     12.6.2; 12.9; 20.1.0
License:      https://developer.ibm.com/academic/
Categories:   optimizer, linear programming
==============================================================================


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:     10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0;
              12.1.1; 12.3.0
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;
              12.3-v8.9.6
License:      https://docs.nvidia.com/deeplearning/cudnn/sla
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; 12.3.0
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
==============================================================================


Cytoscape
==============================================================================
Description:  Complex Visualization Software
Versions:     3.10.2
License:      GNU Lesser General Public License
              https://www.gnu.org/licenses/lgpl-3.0.html
Categories:   visualization
==============================================================================


dalton
==============================================================================
Description:  A powerful tool for a wide range of molecular properties at
              different levels of theory
Versions:     2020.1-3000mo400mc; 2020.1-gcc; 2020.1-intel-mpi; 2020.1-intel
License:      N/A
Categories:   Electronic Structure, Ab Initio, Density Functional Theory
==============================================================================


DeepLabCut
==============================================================================
Description:  DeepLabCut™ is an efficient method for 2D and 3D markerless
              pose estimation
Versions:     2.1.10.4; 2.2.3; 2.3.9
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Delft3DFM
==============================================================================
Description:  Delft3DFM is a hydrodynamic numerical model for simulating
              fluid flow and sediment transport in rivers, estuaries, and
              coastal regions.
Versions:     142431; 2021.03
License:      https://oss.deltares.nl/web/delft3dfm/source-code-license
Categories:   hydrodynamic modeling, sediment transport modeling, river
              modeling, coastal modeling
==============================================================================


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
==============================================================================


DIAMOND
==============================================================================
Description:  Accelerated BLAST compatible local sequence aligner
Versions:     2.1.8.162
License:      GPL-3.0 License
Categories:   Bioinformatics
==============================================================================


dorado
==============================================================================
Description:  Dorado is a high-performance, easy-to-use, open source
              basecaller for Oxford Nanopore reads.
Versions:     0.3.0; 0.3.1; 0.3.4; 0.4.1; 0.4.3; 0.5.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


dorado_server
==============================================================================
Description:  Dorado is a high-performance, easy-to-use, open source
              basecaller for Oxford Nanopore reads.
Versions:     7.3.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


dRep
==============================================================================
Description:  a python program which performs rapid pair-wise comparison of
              genome sets
Versions:     3.4.5
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Eigen
==============================================================================
Description:  Linear algebra template library
Versions:     3.4.0
License:      https://eigen.tuxfamily.org/index.php
Categories:   Linear algebra, numerical, development, library
==============================================================================


elastix
==============================================================================
Description:  elastix: a toolbox for rigid and nonrigid registration of
              images.
Versions:     5.0.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


EnTAP
==============================================================================
Description:  EnTAP is an eukaryotic non-model annotation pipeline.
Versions:     1.0.1
License:      GPL-3.0 License
Categories:   Bioinformatics
==============================================================================


epacts
==============================================================================
Description:  EPACTS - Efficient and Parallelizable Association Container
              Toolbox
Versions:     3.4.2
License:      GNU GPL3
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


fastANI
==============================================================================
Description:  FastANI is developed for fast alignment-free computation of
              whole-genome Average Nucleotide Identity (ANI)
Versions:     1.34
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


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
==============================================================================


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; 2021.05.03; 2022.06.15
License:      free and open source
Categories:   Geometric and electronic structure, near-edge, ab initio
==============================================================================


FDTD Solutions
==============================================================================
Description:  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:     2022R1.4
License:      Academic Research
Categories:   FDTD, maxwell, design, solver, analysis, optimization, optics,
              photonics, 3D
==============================================================================


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
==============================================================================


fiji
==============================================================================
Description:  fiji is just ImageJ
Versions:     1.5.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


FreeSurfer
==============================================================================
Description:  FreeSurfer MRI processing and analysis software.
Versions:     6.0.0; 7.2.0; 7.4.1
License:
              https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLi
              cense
Categories:   MRI, neuroimaging, neuroscience
==============================================================================


FSL
==============================================================================
Description:  FSL suite of MRI neuroimaging tools.
Versions:     6.0.1; 6.0.5.2
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:     1.8.4
License:      ???
Categories:   Bioinformatics gene genefinding genetics
==============================================================================


gatk
==============================================================================
Description:  Toolkit for variant discovery and genotyping
Versions:     3.7; 4.3.0.0; 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; 8.2.0
License:      GPL
Categories:   Compiler, programming, development
==============================================================================


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
==============================================================================


GDC Data Transfer Tool
==============================================================================
Description:  The GDC Data Transfer Tool is a utility for transferring data
              to and from the Genomic Data Commons (GDC), facilitating the
              efficient exchange of genomic and clinical data.
Versions:     1.6.1
License:      N/A
Categories:   genomic data, data transfer, bioinformatics
==============================================================================


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
==============================================================================


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
==============================================================================


GitHub CLI
==============================================================================
Description:  A command-line interface to GitHub.
Versions:     2.49.2
License:      https://github.com/cli/cli/blob/trunk/LICENSE
Categories:   GitHub, command-line, utility
==============================================================================


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:     3.19.0; 3.4.0
License:      N/A
Categories:   Data movement
==============================================================================


GLPK
==============================================================================
Description:  The GNU Linear Programming Kit, GLPK, is a library of ANSI C
              routines for solving large scale linear programming problems
              using the revised simplex method.
Versions:     5.0
License:      https://www.gnu.org/licenses/licenses.html#GPL
Categories:   Library, Development, Mathematics, Solver
==============================================================================


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:  The Go programming language is an open source project to make
              programmers more productive.
Versions:     1.18; 1.22.2
License:      https://go.dev/LICENSE?m=text
Categories:   Go, Programming, golang
==============================================================================


groff
==============================================================================
Description:  GNU roff
Versions:     1.22.4
License:      GNU
Categories:   Bioinformatics
==============================================================================


gromacs
==============================================================================
Description:  GROMACS performs Newtonian simulatons of molecular dynamics.
Versions:     2021.7; 2022.2
License:      N/A
Categories:   N/A
==============================================================================


GSL
==============================================================================
Description:  GNU scientific libraries
Versions:     2.7; 2.7.1
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
==============================================================================


gubbins
==============================================================================
Description:  Genealogies Unbiased By recomBinations In Nucleotide Sequences
Versions:     2.3.1; 3.3.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


guppy
==============================================================================
Description:  Local accelerated basecalling for Nanopore data
Versions:     6.1.2; 6.2.1; 6.3.4; 6.3.8; 6.4.2; 6.4.6; 6.5.7
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Gurobi
==============================================================================
Description:  Gurobi optimization problem solver.
Versions:     10.0.2; 9.5.1
License:      http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:   Optimization, linear programming
==============================================================================


Harvest
==============================================================================
Description:  Harvest is a suite of core-genome alignment and visualization
              tools
Versions:     1.1.2
License:      GNU GPL v2
Categories:   Bioinformatics, Genomics
==============================================================================


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
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
==============================================================================


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


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
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:     1.12; 1.13; 1.9
License:      N/A
Categories:   N/A
==============================================================================


humann
==============================================================================
Description:  HMP Unified Metabolic Analysis Network
Versions:     3.6
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) 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
License:      more than one
Categories:   libraries, programming, jpeg, gif, png, jbigkit, tiff,
              libwebp, lcms2, jasper, ImageMagick
==============================================================================


ImageMagick
==============================================================================
Description:  ImageMagick is used to create, edit, compose, or convert
              digital images.
Versions:     7.1.0-25
License:      https://imagemagick.org/script/license.php
Categories:   libraries, programming, jpeg, gif, png, jbigkit, tiff,
              libwebp, lcms2
==============================================================================


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; 2018.4.274
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
==============================================================================


Intel
==============================================================================
Description:  Intel compiler suite.
Versions:     18.0.5; 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:  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
==============================================================================


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
==============================================================================


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 Bayesian hierarchical models.
Versions:     4.3.0
License:      GNU GPL v2
Categories:   Bayesian, Markov, MCMC
==============================================================================


JasPer
==============================================================================
Description:  JasPer is a library for the coding and manipulation of images
              in the JPEG-2000 format.
Versions:     2.0.33
License:      https://github.com/jasper-
              software/jasper/blob/master/LICENSE.txt
Categories:   JPEG-2000
==============================================================================


jcuda
==============================================================================
Description:  Java bindings for the CUDA runtime and driver API
Versions:     10.1.0
License:      GPLv2
Categories:   Core
==============================================================================


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


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; 1.8.2; 1.9.2
License:      MIT Licenses
Categories:   Programming
==============================================================================


Kaiju
==============================================================================
Description:  Fast taxonomic classification of metagenomic sequencing reads
              using a protein reference database
Versions:     1.9.0
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


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 arc-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/solvers/knitro/
Categories:   optimization, nonlinear solver
==============================================================================


LAMMPS
==============================================================================
Description:  LAMMPS is a classical molecular dynamics code that models an
              ensemble of particles.
Versions:     02Aug2023; 23Jun2022; 27May21; 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:     3.10.1
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
==============================================================================


LDhat
==============================================================================
Description:  LDhat is a package written in the C and C++ languages for the
              analysis of recombination rates from population genetic data.
Versions:     2.2a
License:      Unlicensed code
Categories:   Bioinformatics, Alignment
==============================================================================


LDhelmet
==============================================================================
Description:  LDhelmet is a software program for statistical inference of
              fine-scale crossover recombination rates from population
              genetic data.
Versions:     1.10
License:      GPL-3: https://github.com/popgenmethods/LDhelmet
Categories:   Bioinformatics, Inference
==============================================================================


Leptonica
==============================================================================
Description:  Image processing and image analysis library
Versions:     1.82.0
License:      http://www.leptonica.org/about-the-license.html
Categories:   image processing, image analysis, OCR
==============================================================================


LIGGGHTS
==============================================================================
Description:  LIGGGHTS is an Open Source Discrete Element Method Particle
              Simulation Software.
Versions:     3b38a7d-2020-10-08
License:      GPL
Categories:   molecular dynamics, particulate materials
==============================================================================


Linaro Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     23.0.3
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


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
==============================================================================


LS-DYNA
==============================================================================
Description:  LS-DYNA finite element analysis software.
Versions:     R10.2.0; R11.1.0; R12.0.0; R13.1.0; R15.0.2; R9.3.1
License:      None provided
Categories:   Finite element, multiphysics, simulation
==============================================================================


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; 2.28-7
License:      Restricted; contact ITS Software Services.
Categories:   Algebra, number theory, algebraic geometry and combinatorics.
==============================================================================


makedepf90
==============================================================================
Description:  Create Makefile dependency list for Fortran source files.
Versions:     2.8.9
License:      GNU General Public License v2.0
Categories:   development utility, Fortran
==============================================================================


mash
==============================================================================
Description:  Fast genome and metagenome distance estimation using MinHash
Versions:     2.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


mashtree
==============================================================================
Description:  Create a tree using Mash distances.
Versions:     1.4.6
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Mathematica
==============================================================================
Description:  Mathematical and technical computing package.
Versions:     12.3.1; 13.2.1
License:      http://www.wolfram.com/legal/agreements/wolfram-
              mathematica.html
Categories:   Mathematics, symbolic algebra
==============================================================================


Matlab
==============================================================================
Description:  Matlab programming environment.
Versions:     R2021b; R2022b; R2023b
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
==============================================================================


MCNP
==============================================================================
Description:  MCNP general-purpose Monte Carlo N-Particle code.
Versions:     6.2
License:      None provided
Categories:   simulation, monte carlo, nuclear, radiation transport
==============================================================================


medaka
==============================================================================
Description:  tool to create consensus sequences and variant calls from
              nanopore sequencing data
Versions:     1.7.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


megahit
==============================================================================
Description:  MEGAHIT is an ultra-fast and memory-efficient NGS assemble
Versions:     1.2.9
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


melt
==============================================================================
Description:  Mobile Element Locator Tool (MELT) discovers, annotates, and
              genotypes non-reference Mobile Element Insertions (MEIs) in
              Illumina DNA paired-end whole genome sequencing
Versions:     2.2.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


meme
==============================================================================
Description:  meme suite: Motif-based sequence analysis tools
Versions:     5.5.5
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


metaphlan3
==============================================================================
Description:  MetaPhlAn is a tool for profiling the composition of microbial
              communities from metagenomic shotgun sequencing data
Versions:     3.0; 4.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


METIS
==============================================================================
Description:  METIS - Serial Graph Partitioning and Fill-reducing Matrix
              Ordering
Versions:     5.1.0; 5.2.1
License:      http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download
Categories:   matrix, matrices, partitioning, ordering
==============================================================================


mGEMS
==============================================================================
Description:  Bacterial sequencing data binning on strain-level based on
              probabilistic taxonomic classification.
Versions:     1.2.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


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
==============================================================================


mlst
==============================================================================
Description:  Scan contig files against traditional PubMLST typing schemes
Versions:     2.23.0
License:      GNU GPL v3
Categories:   Bioinformatics
==============================================================================


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


mothur
==============================================================================
Description:  The goal of mothur is to have a single resource to analyze
              molecular data that is used by microbial ecologists.
Versions:     1.48.0; 1.46.1
License:      GNU GPL v2
Categories:   Bioinformatics, Genomics
==============================================================================


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
==============================================================================


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; 3.2.7a
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:     3.0.3-dfd3360; 3.0.4
License:      Mozilla Public License, http://mozilla.org/MPL/2.0/
Categories:   fMRI, diffusion-weighted MRI, tractography, neuroimaging
==============================================================================


mSWEEP
==============================================================================
Description:  Fast and accurate bacterial community composition estimation
Versions:     1.6.1; 1.6.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


mummer
==============================================================================
Description:  MUMmer
Versions:     4.0.0rc1
License:      Artistic License 2.0
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


N/A
==============================================================================
Description:  N/A
Versions:     3.7.0; 2.9.2
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
==============================================================================


NCO
==============================================================================
Description:  The NCO toolkit manipulates and analyzes data stored in
              netCDF-accessible formats, including DAP, HDF4, and HDF5.
Versions:     4.7.2; 5.0.6
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
==============================================================================


NECAT
==============================================================================
Description:  NECAT is an error correction and de-novo assembly tool for
              Nanopore long noisy reads.
Versions:     0.0.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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:     4.6.2; 4.8.1
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
==============================================================================


neuron
==============================================================================
Description:  Simulation environment for building and using computational
              models of neurons and networks of neurons.
Versions:     8.2.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


new_fugue
==============================================================================
Description:  a program that calculates linkage disequilibrium measures from
              genotype files.
Versions:     2010-05-25
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


OCaml
==============================================================================
Description:  OCaml is a general-purpose, industrial-strength programming
              language with an emphasis on expressiveness and safety.
Versions:     4.02.0; 4.14.0
License:      GNU Lesser General Public License (LGPL) version 2.1
Categories:   type safety, programming
==============================================================================


OCaml Package Manager
==============================================================================
Description:  source-based package manager for OCaml.
Versions:     2.1.3
License:      GNU Lesser General Public License (LGPL) version 2.1
Categories:   package manager, programming
==============================================================================


octave
==============================================================================
Description:  GNU Octave is a high-level language, primarily intended for
              numerical computations.
Versions:     7.3.0
License:      N/A
Categories:   N/A
==============================================================================


oligoarrayaux
==============================================================================
Description:  OligoArrayAux is a subset of the UNAFold package for use with
              OligoArray.
Versions:     3.8
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
License:      https://opensource.org/licenses/BSD-3-Clause
Categories:   Programming, C++, library
==============================================================================


OpenFOAM
==============================================================================
Description:  OpenFOAM is a free, open source CFD software.
Versions:     v2112; v2212
License:      http://www.openfoam.com/documentation/licencing.php
Categories:   omputational fluid dynamics, CFD, heat transfer
==============================================================================


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
==============================================================================


OpenMPI
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     4.1.3; 4.1.4; 4.1.6; 3.1.6
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


OpenRefine
==============================================================================
Description:  OpenRefine (previously Google Refine) is a powerful free, open
              source 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:     3.7.0
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
==============================================================================


OpenSees
==============================================================================
Description:  software framework for simulating the dynamic response of
              structural and geotechnical systems
Versions:     3.6.0
License:
              https://opensees.github.io/OpenSeesDocumentation/developer/lic
              ense.html
Categories:   structural, geotechnical, engineering simulation
==============================================================================


OpenSim
==============================================================================
Description:  OpenSim is a powerful and open source tool for modeling and
              simulation of movement.
Versions:     4.4.1
License:      http://www.apache.org/licenses/LICENSE-2.0
Categories:   musculoskeletal, modeling, simulation
==============================================================================


openslide
==============================================================================
Description:  OpenSlide reads whole slide image files.
Versions:     3.4.1
License:      N/A
Categories:   N/A
==============================================================================


orca
==============================================================================
Description:  An ab initio, DFT, and semi-empirical SCF-MO package
Versions:     4.2.1; 5.0.3
License:      Academic
Categories:   Chemistry, ab initio
==============================================================================


orthofinder
==============================================================================
Description:  Accurate inference of orthologous gene groups made easy.
Versions:     2.3.3
License:      GPL
Categories:   Bioinformatics
==============================================================================


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:     5.11.1
License:      http://www.paraview.org/license/
Categories:   Visualization, data analysis,
==============================================================================


perl-modules
==============================================================================
Description:  Perl addin modules for use with Perl version 5.26.3.
Versions:     1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


PGI compilers
==============================================================================
Description:  Compiler suite.
Versions:     20.4
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; 3.0.0
License:      MIT License, Apache License V2.0
Categories:   Bioinformatics
==============================================================================


plink
==============================================================================
Description:  PLINK a whole genome association analysis toolset.
Versions:     1.9; 2.0; 2.3a; 2.3a3; 2.3dev; 2.4a4
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
==============================================================================


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:     9.0.0; 9.3.1
License:      MIT
Categories:   GIS, Library
==============================================================================


prokka
==============================================================================
Description:  Prokka: rapid prokaryotic genome annotation
Versions:     1.14.5
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


Pycharm
==============================================================================
Description:  The Python IDE for Professional Developers
Versions:     2022.2.2
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


PyMsBayes
==============================================================================
Description:  A multi-processing Python wrapper and API for approximate-
              Bayesian phylgeographical inference
Versions:     0.3.7
License:      GNU GPL v3
Categories:   Python, Bayesian, Phylogeographical, msReject
==============================================================================


Python
==============================================================================
Description:  Python is a general purpose programming language
Versions:     3.10.4; 3.11.5; 3.12.1; 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
==============================================================================


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


Quantum ESPRESSO
==============================================================================
Description:  Quantum ESPRESSO is an integrated suite of codes for
              electronic-structure calculations and materials modeling at
              the nanoscale.
Versions:     7.1-gpu; 7.1; 7.2
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:     4.2.0; 4.3.1; 4.3.2; 4.4.0
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science
==============================================================================


r-seurat
==============================================================================
Description:  Tools for Single Cell Genomics
Versions:     4.1.1
License:      N/A
Categories:   N/A
==============================================================================


racon
==============================================================================
Description:  Consensus module for raw de novo DNA assembly of long
              uncorrected reads.
Versions:     1.4.20
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


ragtag
==============================================================================
Description:  RagTag is a collection of software tools for scaffolding and
              improving modern genome assemblies.
Versions:     2.1.0
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


Rchipenrich
==============================================================================
Description:  R libraries necessary for Chipenrich
Versions:     3.16
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


rclone
==============================================================================
Description:  rclone is a command line program to sync files and directories
              to and from many cloud storage providers
Versions:     1.57.0; 1.64.0
License:      MIT License
Categories:   File transfer, Utilities
==============================================================================


Rgeospatial
==============================================================================
Description:  A collection of R geospatial libraries
Versions:     2022-08-18; 2023-04-25; 2023-07-01; 2024-01-15; 2024-05-11
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, geospatial,
              geography, spatial, map
==============================================================================


Rgiotto
==============================================================================
Description:  R libraries necessary for Giotto
Versions:     1.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


Rmonocle3
==============================================================================
Description:  R libraries necessary for Monocle3
Versions:     1.3.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Rnumbat
==============================================================================
Description:  An R installation for haplotype-aware CNV calling
Versions:     1.2.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Ropenblas
==============================================================================
Description:  R OpenBLAS provides an optimized library for faster linear
              algebra computations.
Versions:     4.2.0; 4.3.1; 4.4.0
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:     1.3.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


RSeurat
==============================================================================
Description:  R libraries necessary for Seurat
Versions:     4.3.0; 5.0.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
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; 4.3.2; 4.4.0
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, tidyverse
==============================================================================


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:     9.6
License:      GPL
Categories:   Mathematics software
==============================================================================


saige
==============================================================================
Description:  SAIGE is an R package with Scalable and Accurate
              Implementation of Generalized mixed model
Versions:     0.44.6.4; 1.1.6.2
License:      BSD Simplified 2-Clause
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
License:      Not available
Categories:   Statistics, econometrics
==============================================================================


schrodinger
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact drugdiscovery@umich.edu]
              Schrodinger Suite
Versions:     2022-2; 2022-3; 2024-1
License:      Paid license for Academic use
Categories:   chemistry, molecular dynamics
==============================================================================


SciPy
==============================================================================
Description:  Scientific libraries for use within Python.
Versions:     1.8.0
License:      https://github.com/scipy/scipy
Categories:   Programming, python, solver
==============================================================================


SeisSol
==============================================================================
Description:  SeisSol is a seismic solver.
Versions:     201807_Kaikoura-623-g6f221c5
License:      https://github.com/SeisSol/SeisSol/blob/master/LICENSE
Categories:   Core
==============================================================================


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
==============================================================================


seqtk
==============================================================================
Description:  Seqtk is a fast and lightweight tool for processing sequences
              in the FASTA or FASTQ format
Versions:     1.3
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


shovill
==============================================================================
Description:  Assemble bacterial isolate genomes from Illumina paired-end
              reads
Versions:     1.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Singularity
==============================================================================
Description:  Program for running containerized applications
Versions:     3.10.4; 3.11.1
License:      https://github.com/sylabs/singularity/blob/master/LICENSE.md
Categories:   Container, docker, reproducible research
==============================================================================


sklvq
==============================================================================
Description:  scikit-learning vector quantization
Versions:     0.1.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


slim
==============================================================================
Description:  SLiM: An Evolutionary Simulation Framework
Versions:     4.0.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


SnakeMake
==============================================================================
Description:  The Snakemake workflow management system is a tool to create
              reproducible and scalable data analyses.
Versions:     7.34.2
License:      MIT License
Categories:   python, workflow automation, workflow, management
==============================================================================


snippy
==============================================================================
Description:  Rapid haploid variant calling and core genome alignment
Versions:     4.6.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


SOAPdenovo-Trans
==============================================================================
Description:  SOAPdenovo-Trans is a de novo transcriptome assembler designed
              specifically for RNA-Seq data.
Versions:     1.0.5
License:      GNU GENERAL PUBLIC LICENSE v3.0
Categories:   Bioinformatics, Genomics, Healthcare, big data
==============================================================================


sortmerna
==============================================================================
Description:  a tool for filtering, mapping and OTU-picking NGS reads
Versions:     2.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


spaceranger
==============================================================================
Description:  a set of analysis pipelines that process Visium spatial RNA-
              seq output and brightfield microscope images
Versions:     1.3.0; 2.0.0; 2.0.1; 2.1.1; 3.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Spack Package Manager
==============================================================================
Description:  A flexible package manager supporting multiple versions,
              configurations, platforms, and compilers.
Versions:     0.21
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
==============================================================================


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


spark
==============================================================================
Description:  Apache Spark is a unified analytics engine for large-scale
              data processing
Versions:     3.2.1; 3.5.1
License:      Apache, https://www.apache.org/licenses/LICENSE-2.0
Categories:   Statistics, big data, data science
==============================================================================


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
License:      N/A
Categories:   N/A
==============================================================================


Stacks
==============================================================================
Description:  Stacks is a software pipeline for building loci from short-
              read sequences, such as those generated on the Illumina
              platform
Versions:     2.65
License:      N/A
Categories:   Bioinformatics, Assembly
==============================================================================


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
License:      Academic Research
Categories:   CFD
==============================================================================


Stata/MP
==============================================================================
Description:  Statistical analysis software.
Versions:     17; 18
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


Stata/SE
==============================================================================
Description:  Statistical analysis software.
Versions:     17; 18
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
==============================================================================


Subread
==============================================================================
Description:  Subread package: high-performance read alignment,
              quantification and mutation discovery
Versions:     2.0.3
License:      GPLv3
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
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
==============================================================================


table2asn
==============================================================================
Description:  table2asn is a command-line program that creates sequence
              records for submission to GenBank
Versions:     1.26.678
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


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
==============================================================================


terastitcher
==============================================================================
Description:  A tool for fast automatic 3D-stitching of teravoxel-sized
              microscopy images
Versions:     1.10.18; 1.11.10
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Tesseract
==============================================================================
Description:  Optical character recognition, document conversion, text
              processing
Versions:     5.2.0
License:      https://github.com/tesseract-ocr/tesseract/blob/main/LICENSE
Categories:   image processing, image analysis, OCR, optical character
              recognition, document conversion, text processing
==============================================================================


themisto
==============================================================================
Description:  Themisto is a succinct colored de Bruijn graph supporting
              pseudo-alignment
Versions:     1.0; 2.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


tmux
==============================================================================
Description:  Terminal multiplexer
Versions:     3.3a
License:      https://opensource.org/licenses/ISC
Categories:   Terminal, multiplex
==============================================================================


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
==============================================================================


TractSeg
==============================================================================
Description:  Tool for fast and accurate white matter bundle segmentation
              from Diffusion MRI.
Versions:     2.8
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


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
==============================================================================


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:     2.12.0; 2.15.1
License:
              https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/
              master/LICENSE
Categories:   Bioinformatics, Assembly, Transcriptome
==============================================================================


UCSC-utilities
==============================================================================
Description:  UCSC Genome Browser Utilites.
Versions:     4.0.0
License:      http://genome.ucsc.edu/license/
Categories:   Bioinformatics
==============================================================================


UCX
==============================================================================
Description:  Unified Communication X (UCX)
Versions:     1.14.1
License:      https://github.com/openucx/ucx?tab=License-1-ov-file#readme
Categories:   Communication
==============================================================================


unrar
==============================================================================
Description:  unrar is a utility from RARLAB for extracting RAR archives.
Versions:     6.12
License:      UnRAR is freeware. See $UNRAR_HOME/license.txt
Categories:   utility, archive
==============================================================================


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


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 arcts-support@umich.edu]
              VASP, The Vienna Ab initio simulation package, a plane wave
              electronic structure code.
Versions:     5.4.4.18Apr17.p1; 5.4.4.18Apr17.p1.sol; 6.4.2; 6.4.2.sol
License:      https://www.vasp.at/index.php/faqs
Categories:   electronic structure code, molecular dynamics
==============================================================================


vcflib
==============================================================================
Description:  vcflib is both a C++ library and cmdline tools for parsing and
              manipulating VCF files.
Versions:     1.0.1+dfsg-3
License:      MIT
Categories:   bioinformatics, genomics, VCF
==============================================================================


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:   N/A
==============================================================================


verkko
==============================================================================
Description:  Verkko is implemented as a Snakemake workflow, launched by a
              wrapper script to parse options and create a config.yml file.
Versions:     1.4.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


VESTA
==============================================================================
Description:  VESTA is a 3D visualization program for structural models,
              volumetric data such as electron/nuclear densities, and
              crystal morphologies.
Versions:     3.5.8
License:      https://jp-minerals.org/vesta/en/doc/VESTAli1.html
Categories:   Chemistry
==============================================================================


VisIt
==============================================================================
Description:  VisIt data analysis and visualization application.
Versions:     3.3.1
License:      N/A
Categories:   Visualization, data analysis
==============================================================================


VLC
==============================================================================
Description:  VLC media player
Versions:     3.0.9
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Wannier90
==============================================================================
Description:  Maximally-localised Wannier functions (MLWFs) and Wannier90
Versions:     1.2
License:      http://www.wannier.org
Categories:   MLWFs, electronic structure code
==============================================================================


whisper
==============================================================================
Description:  Whisper is a general-purpose speech recognition model.
Versions:     v20230314
License:      MIT License
              https://github.com/openai/whisper/blob/main/LICENSE
Categories:   Bioinformatics, Sequencing
==============================================================================


WIEN2k
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu]
              WIEN2k allows performing electronic structure calculations of
              solids using density functional theory (DFT), based on the
              full-potential (linearized) augmented plane-wave ((L)APW) +
              local orbitals (lo) method
Versions:     23.2-mpi; 23.2-omp; 23.2
License:      http://www.wien2k.at/order/index.html
Categories:   Licenced
==============================================================================


wigToBigWig
==============================================================================
Description:  Convert ascii format wig file to binary big wig format
Versions:     4.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Wine32
==============================================================================
Description:  Wine is a compatibility layer that allows Windows applications
              to run on Linux and macOS.
Versions:     3.0.3
License:      https://www.winehq.org/about
Categories:   compatibility layer
==============================================================================


winnowmap
==============================================================================
Description:  Winnowmap is a long-read mapping algorithm optimized for
              mapping ONT and PacBio reads
Versions:     2.03
License:      GNU GPL v3
Categories:   Bioinformatics
==============================================================================


xcb-devel
==============================================================================
Description:  xcb development libraries and headers
Versions:     0.4.1
License:      MIT License
Categories:   Libraries, Headers
==============================================================================


XCrySDen
==============================================================================
Description:  XCrySDen is a crystalline and molecular structure
              visualisation program aiming at display of isosurfaces and
              contours, which can be superimposed on crystalline structures
              and interactively rotated and manipulated.
Versions:     1.6
License:      GPLv2
Categories:   Chemistry
==============================================================================


Yasm
==============================================================================
Description:  Yasm assembler.
Versions:     2.15.05; 1.3.0
License:      https://www.nasm.us/
Categories:   assembler, programming
==============================================================================